diff --git a/tools/openms/AccurateMassSearch.xml b/tools/openms/AccurateMassSearch.xml
index 293a31b3e..f2413333c 100644
--- a/tools/openms/AccurateMassSearch.xml
+++ b/tools/openms/AccurateMassSearch.xml
@@ -137,12 +137,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <param name="mass_error_value" argument="-algorithm:mass_error_value" type="float" optional="false" value="5.0" label="Tolerance allowed for accurate mass search" help=""/>
-      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="false" display="radio" label="Unit of mass error (ppm or Da)" help="">
+      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="false" label="Unit of mass error (ppm or Da)" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_error_unit"/>
       </param>
-      <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="false" display="radio" label="Positive or negative ionization mode" help="If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
+      <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="false" label="Positive or negative ionization mode" help="If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
         <option value="positive" selected="true">positive</option>
         <option value="negative">negative</option>
         <option value="auto">auto</option>
@@ -151,7 +151,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="isotopic_similarity" argument="-algorithm:isotopic_similarity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" help=""/>
       <param name="use_feature_adducts" argument="-algorithm:use_feature_adducts" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to filter AMS candidates mismatching available feature adduct annotation" help=""/>
       <param name="keep_unidentified_masses" argument="-algorithm:keep_unidentified_masses" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Keep features that did not yield any DB hit" help=""/>
-      <param name="id_format" argument="-algorithm:id_format" type="select" optional="false" display="radio" label="Use legacy (ProteinID/PeptideID based storage of metabolomics data) with mzTab-v1.0.0 as output format or novel Identification Data (ID) with mzTab-v2.0.0-M as output format (ID and its MzTab-M output is currently only support for featureXML files)" help="">
+      <param name="id_format" argument="-algorithm:id_format" type="select" optional="false" label="Use legacy (ProteinID/PeptideID based storage of metabolomics data) with mzTab-v1.0.0 as output format or novel Identification Data (ID) with mzTab-v2.0.0-M as output format (ID and its MzTab-M output is currently only support for featureXML files)" help="">
         <option value="legacy" selected="true">legacy</option>
         <option value="ID">ID</option>
         <expand macro="list_string_san" name="id_format"/>
diff --git a/tools/openms/AssayGeneratorMetabo.xml b/tools/openms/AssayGeneratorMetabo.xml
index b341d911b..2d09e35bb 100644
--- a/tools/openms/AssayGeneratorMetabo.xml
+++ b/tools/openms/AssayGeneratorMetabo.xml
@@ -89,7 +89,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
       <option value="traML">traml</option>
       <option value="pqp">pqp</option>
     </param>
-    <param argument="-fragment_annotation" type="select" optional="false" display="radio" label="Fragment annotation method" help="">
+    <param argument="-fragment_annotation" type="select" optional="false" label="Fragment annotation method" help="">
       <option value="none">none</option>
       <option value="sirius" selected="true">sirius</option>
       <expand macro="list_string_san" name="fragment_annotation"/>
@@ -99,14 +99,14 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
     <param argument="-total_occurrence_filter" type="float" optional="false" min="0.0" max="1.0" value="0.1" label="Filter compound based on total occurrence in analysed samples" help=""/>
     <param argument="-fragment_annotation_score_threshold" type="float" optional="false" min="0.0" max="1.0" value="0.8" label="Filters annotations based on the explained intensity of the peaks in a spectrum" help=""/>
     <param argument="-decoy_generation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decoys will be generated using the fragmentation tree re-rooting approach" help="This option does only work in combination with the fragment annotation via Sirius"/>
-    <param argument="-decoy_generation_method" type="select" optional="false" display="radio" label="Uses different methods for decoy generation" help="Basis for the method is the fragmentation-tree re-rooting approach ('original'). This approach can be extended by using 'resolve_overlap', which will resolve overlapping fragments of the highest intensity fragments chosen, by adding -CH2 mass to the overlapping fragments. 'Add_shift' will add a -CH2 mass shift to the target fragments and use them as additional decoys if fragmentation-tree re-rooting failed. 'Both' combines the extended methods (resolve_overlap, add_shift)">
+    <param argument="-decoy_generation_method" type="select" optional="false" label="Uses different methods for decoy generation" help="Basis for the method is the fragmentation-tree re-rooting approach ('original'). This approach can be extended by using 'resolve_overlap', which will resolve overlapping fragments of the highest intensity fragments chosen, by adding -CH2 mass to the overlapping fragments. 'Add_shift' will add a -CH2 mass shift to the target fragments and use them as additional decoys if fragmentation-tree re-rooting failed. 'Both' combines the extended methods (resolve_overlap, add_shift)">
       <option value="original" selected="true">original</option>
       <option value="resolve_overlap">resolve_overlap</option>
       <option value="add_shift">add_shift</option>
       <option value="both">both</option>
       <expand macro="list_string_san" name="decoy_generation_method"/>
     </param>
-    <param argument="-method" type="select" optional="false" display="radio" label="Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used)" help="">
+    <param argument="-method" type="select" optional="false" label="Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used)" help="">
       <option value="highest_intensity" selected="true">highest_intensity</option>
       <option value="consensus_spectrum">consensus_spectrum</option>
       <expand macro="list_string_san" name="method"/>
@@ -123,7 +123,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
     <section name="deisotoping" title="deisotoping" help="" expanded="false">
       <param name="use_deisotoper" argument="-deisotoping:use_deisotoper" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Deisotoper (if no fragment annotation is used)" help=""/>
       <param name="fragment_tolerance" argument="-deisotoping:fragment_tolerance" type="float" optional="false" value="1.0" label="Tolerance used to match isotopic peaks" help=""/>
-      <param name="fragment_unit" argument="-deisotoping:fragment_unit" type="select" optional="false" display="radio" label="Unit of the fragment tolerance" help="">
+      <param name="fragment_unit" argument="-deisotoping:fragment_unit" type="select" optional="false" label="Unit of the fragment tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="fragment_unit"/>
@@ -138,7 +138,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
     <section name="preprocessing" title="" help="" expanded="false">
       <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="false" min="1" value="1" label="Number of mass traces each feature has to have to be included" help="To use this parameter, setting the feature_only flag is necessary"/>
       <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="false" value="10.0" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
-      <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" optional="false" display="radio" label="Unit of the precursor_mz_tolerance" help="">
+      <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" optional="false" label="Unit of the precursor_mz_tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/>
@@ -163,7 +163,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
       <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="false" min="0" value="100" label="Time out in seconds per fragmentation tree computations" help="0 for an infinite amount of time"/>
       <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="false" min="0" value="100" label="Maximal computation time in seconds for a single compound" help="0 for an infinite amount of time"/>
       <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable recalibration of input spectra" help=""/>
-      <param name="profile" argument="-sirius:profile" type="select" optional="false" display="radio" label="Name of the configuration profile" help="">
+      <param name="profile" argument="-sirius:profile" type="select" optional="false" label="Name of the configuration profile" help="">
         <option value="default" selected="true">default</option>
         <option value="qtof">qtof</option>
         <option value="orbitrap">orbitrap</option>
@@ -202,13 +202,13 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
       </param>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-ambiguity_resolution_mz_tolerance_unit" type="select" optional="false" display="radio" label="Unit of the ambiguity_resolution_mz_tolerance" help="">
+      <param argument="-ambiguity_resolution_mz_tolerance_unit" type="select" optional="false" label="Unit of the ambiguity_resolution_mz_tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="ambiguity_resolution_mz_tolerance_unit"/>
       </param>
       <param argument="-precursor_recalibration_window" type="float" optional="false" value="0.01" label="Tolerance window for precursor selection (Annotation of precursor mz and intensity)" help=""/>
-      <param argument="-precursor_recalibration_window_unit" type="select" optional="false" display="radio" label="Unit of the precursor_mz_tolerance_annotation" help="">
+      <param argument="-precursor_recalibration_window_unit" type="select" optional="false" label="Unit of the precursor_mz_tolerance_annotation" help="">
         <option value="Da" selected="true">Da</option>
         <option value="ppm">ppm</option>
         <expand macro="list_string_san" name="precursor_recalibration_window_unit"/>
diff --git a/tools/openms/BaselineFilter.xml b/tools/openms/BaselineFilter.xml
index 67062e980..0693c09a1 100644
--- a/tools/openms/BaselineFilter.xml
+++ b/tools/openms/BaselineFilter.xml
@@ -40,7 +40,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   <inputs>
     <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
     <param argument="-struc_elem_length" type="float" optional="false" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
-    <param argument="-struc_elem_unit" type="select" optional="false" display="radio" label="Unit of 'struc_elem_length' paramete" help="">
+    <param argument="-struc_elem_unit" type="select" optional="false" label="Unit of 'struc_elem_length' paramete" help="">
       <option value="Thomson" selected="true">Thomson</option>
       <option value="DataPoints">DataPoints</option>
       <expand macro="list_string_san" name="struc_elem_unit"/>
diff --git a/tools/openms/CometAdapter.xml b/tools/openms/CometAdapter.xml
index cc5beef35..cafe858de 100644
--- a/tools/openms/CometAdapter.xml
+++ b/tools/openms/CometAdapter.xml
@@ -67,7 +67,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/>
     <param argument="-default_params_file" type="data" format="txt" optional="true" label="Default Comet params file" help="All parameters of this take precedence. A template file can be generated using 'comet.exe -p' select txt data sets(s)"/>
     <param argument="-precursor_mass_tolerance" type="float" optional="false" value="10.0" label="Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance)" help="See also precursor_error_units to set the unit"/>
-    <param argument="-precursor_error_units" type="select" optional="false" display="radio" label="Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)" help="">
+    <param argument="-precursor_error_units" type="select" optional="false" label="Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)" help="">
       <option value="amu">amu</option>
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
@@ -83,12 +83,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <expand macro="list_string_san" name="isotope_error"/>
     </param>
     <param argument="-fragment_mass_tolerance" type="float" optional="false" min="0.0001" value="0.01" label="This is half the bin size, which is used to segment the MS/MS spectrum" help="Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size"/>
-    <param argument="-fragment_error_units" type="select" optional="false" display="radio" label="Fragment monoisotopic mass error units" help="">
+    <param argument="-fragment_error_units" type="select" optional="false" label="Fragment monoisotopic mass error units" help="">
       <option value="Da" selected="true">Da</option>
       <expand macro="list_string_san" name="fragment_error_units"/>
     </param>
     <param argument="-fragment_bin_offset" type="float" optional="false" min="0.0" max="1.0" value="0.0" label="Offset of fragment bins" help="Recommended by Comet: low-res: 0.4, high-res: 0.0"/>
-    <param argument="-instrument" type="select" optional="false" display="radio" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only" help="">
+    <param argument="-instrument" type="select" optional="false" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only" help="">
       <option value="low_res">low_res</option>
       <option value="high_res" selected="true">high_res</option>
       <expand macro="list_string_san" name="instrument"/>
@@ -108,7 +108,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Trypsin/P">Trypsin/P</option>
       <expand macro="list_string_san" name="enzyme"/>
     </param>
-    <param argument="-num_enzyme_termini" type="select" optional="false" display="radio" label="Specify the termini where the cleavage rule has to match" help="">
+    <param argument="-num_enzyme_termini" type="select" optional="false" label="Specify the termini where the cleavage rule has to match" help="">
       <option value="semi">semi</option>
       <option value="fully" selected="true">fully</option>
       <option value="C-term unspecific">C-term unspecific</option>
@@ -122,7 +122,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-precursor_charge" type="text" optional="false" value="0:0" label="Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3" help="">
       <expand macro="list_string_san" name="precursor_charge"/>
     </param>
-    <param argument="-override_charge" type="select" optional="false" display="radio" label="_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state" help="For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range">
+    <param argument="-override_charge" type="select" optional="false" label="_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state" help="For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range">
       <option value="keep any known">keep any known</option>
       <option value="ignore known">ignore known</option>
       <option value="ignore outside range">ignore outside range</option>
@@ -6084,12 +6084,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
         <expand macro="list_string_san" name="decoy_string"/>
       </param>
-      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="false" display="radio" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="false" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
         <option value="prefix" selected="true">prefix</option>
         <option value="suffix">suffix</option>
         <expand macro="list_string_san" name="decoy_string_position"/>
       </param>
-      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="false" display="radio" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="false" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
         <option value="error">error</option>
         <option value="warn" selected="true">warn</option>
         <option value="silent">silent</option>
@@ -6098,7 +6098,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
       <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
       <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
-      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="false" display="radio" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="false" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
         <option value="error" selected="true">error</option>
         <option value="warn">warn</option>
         <option value="remove">remove</option>
@@ -6146,7 +6146,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="PepsinA">PepsinA</option>
           <expand macro="list_string_san" name="name"/>
         </param>
-        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="false" display="radio" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="false" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
           <option value="auto" selected="true">auto</option>
           <option value="full">full</option>
           <option value="semi">semi</option>
@@ -6188,7 +6188,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
       <param argument="-minimum_peaks" type="integer" optional="false" value="10" label="Required minimum number of peaks in spectrum to search (default 10)" help=""/>
       <param argument="-minimum_intensity" type="float" optional="false" min="0.0" value="0.0" label="Minimum intensity value to read in" help=""/>
-      <param argument="-remove_precursor_peak" type="select" optional="false" display="radio" label="no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD)" help="phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance">
+      <param argument="-remove_precursor_peak" type="select" optional="false" label="no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD)" help="phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance">
         <option value="no" selected="true">no</option>
         <option value="yes">yes</option>
         <option value="charge_reduced">charge_reduced</option>
diff --git a/tools/openms/ConsensusID.xml b/tools/openms/ConsensusID.xml
index d6bd67555..77e0f88b9 100644
--- a/tools/openms/ConsensusID.xml
+++ b/tools/openms/ConsensusID.xml
@@ -82,7 +82,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param name="min_shared" argument="-PEPIons:min_shared" type="integer" optional="false" min="1" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help=""/>
     </section>
     <section name="PEPMatrix" title="PEPMatrix algorithm parameters" help="" expanded="false">
-      <param name="matrix" argument="-PEPMatrix:matrix" type="select" optional="false" display="radio" label="Substitution matrix to use for alignment-based similarity scoring" help="">
+      <param name="matrix" argument="-PEPMatrix:matrix" type="select" optional="false" label="Substitution matrix to use for alignment-based similarity scoring" help="">
         <option value="identity">identity</option>
         <option value="PAM30MS" selected="true">PAM30MS</option>
         <expand macro="list_string_san" name="matrix"/>
diff --git a/tools/openms/ConsensusMapNormalizer.xml b/tools/openms/ConsensusMapNormalizer.xml
index 447ac7167..5078c34bb 100644
--- a/tools/openms/ConsensusMapNormalizer.xml
+++ b/tools/openms/ConsensusMapNormalizer.xml
@@ -39,7 +39,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="consensusxml" optional="false" label="input file" help=" select consensusxml data sets(s)"/>
-    <param argument="-algorithm_type" type="select" optional="false" display="radio" label="The normalization algorithm that is applied" help="'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)">
+    <param argument="-algorithm_type" type="select" optional="false" label="The normalization algorithm that is applied" help="'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)">
       <option value="robust_regression" selected="true">robust_regression</option>
       <option value="median">median</option>
       <option value="median_shift">median_shift</option>
diff --git a/tools/openms/DatabaseFilter.xml b/tools/openms/DatabaseFilter.xml
index 943cb795f..2ebe231c2 100644
--- a/tools/openms/DatabaseFilter.xml
+++ b/tools/openms/DatabaseFilter.xml
@@ -44,7 +44,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   <inputs>
     <param argument="-in" type="data" format="fasta" optional="false" label="Input FASTA file, containing a database" help=" select fasta data sets(s)"/>
     <param argument="-id" type="data" format="idxml,mzid" optional="false" label="Input file containing identified peptides and proteins" help=" select idxml,mzid data sets(s)"/>
-    <param argument="-method" type="select" optional="false" display="radio" label="Switch between white-/blacklisting" help="">
+    <param argument="-method" type="select" optional="false" label="Switch between white-/blacklisting" help="">
       <option value="whitelist" selected="true">whitelist</option>
       <option value="blacklist">blacklist</option>
       <expand macro="list_string_san" name="method"/>
diff --git a/tools/openms/DecoyDatabase.xml b/tools/openms/DecoyDatabase.xml
index 70b2e6f60..b56a97b05 100644
--- a/tools/openms/DecoyDatabase.xml
+++ b/tools/openms/DecoyDatabase.xml
@@ -62,18 +62,18 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     <param argument="-decoy_string" type="text" optional="false" value="DECOY_" label="String that is combined with the accession of the protein identifier to indicate a decoy protein" help="">
       <expand macro="list_string_san" name="decoy_string"/>
     </param>
-    <param argument="-decoy_string_position" type="select" optional="false" display="radio" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="">
+    <param argument="-decoy_string_position" type="select" optional="false" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="">
       <option value="prefix" selected="true">prefix</option>
       <option value="suffix">suffix</option>
       <expand macro="list_string_san" name="decoy_string_position"/>
     </param>
     <param argument="-only_decoy" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write only decoy proteins to the output database instead of a combined database" help=""/>
-    <param argument="-type" type="select" optional="false" display="radio" label="Type of sequence" help="RNA sequences may contain modification codes, which will be handled correctly if this is set to 'RNA'">
+    <param argument="-type" type="select" optional="false" label="Type of sequence" help="RNA sequences may contain modification codes, which will be handled correctly if this is set to 'RNA'">
       <option value="protein" selected="true">protein</option>
       <option value="RNA">RNA</option>
       <expand macro="list_string_san" name="type"/>
     </param>
-    <param argument="-method" type="select" optional="false" display="radio" label="Method by which decoy sequences are generated from target sequences" help="Note that all sequences are shuffled using the same random seed, ensuring that identical sequences produce the same shuffled decoy sequences. Shuffled sequences that produce highly similar output sequences are shuffled again (see shuffle_sequence_identity_threshold)">
+    <param argument="-method" type="select" optional="false" label="Method by which decoy sequences are generated from target sequences" help="Note that all sequences are shuffled using the same random seed, ensuring that identical sequences produce the same shuffled decoy sequences. Shuffled sequences that produce highly similar output sequences are shuffled again (see shuffle_sequence_identity_threshold)">
       <option value="reverse" selected="true">reverse</option>
       <option value="shuffle">shuffle</option>
       <expand macro="list_string_san" name="method"/>
diff --git a/tools/openms/Digestor.xml b/tools/openms/Digestor.xml
index ba58260c4..68caa575b 100644
--- a/tools/openms/Digestor.xml
+++ b/tools/openms/Digestor.xml
@@ -39,7 +39,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="Set this if you cannot control the filename of 'out'" help="e.g., in TOPPAS">
+    <param argument="-out_type" type="select" optional="false" label="Set this if you cannot control the filename of 'out'" help="e.g., in TOPPAS">
       <option value="fasta">fasta</option>
       <option value="idXML">idxml</option>
       <expand macro="list_string_san" name="out_type"/>
@@ -84,13 +84,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <expand macro="list_string_san" name="enzyme"/>
     </param>
     <section name="FASTA" title="Options for FASTA output files" help="" expanded="false">
-      <param name="ID" argument="-FASTA:ID" type="select" optional="false" display="radio" label="Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)" help="">
+      <param name="ID" argument="-FASTA:ID" type="select" optional="false" label="Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)" help="">
         <option value="parent" selected="true">parent</option>
         <option value="number">number</option>
         <option value="both">both</option>
         <expand macro="list_string_san" name="ID"/>
       </param>
-      <param name="description" argument="-FASTA:description" type="select" optional="false" display="radio" label="Keep or remove the (possibly lengthy) FASTA header description" help="Keeping it can increase resulting FASTA file significantly">
+      <param name="description" argument="-FASTA:description" type="select" optional="false" label="Keep or remove the (possibly lengthy) FASTA header description" help="Keeping it can increase resulting FASTA file significantly">
         <option value="remove" selected="true">remove</option>
         <option value="keep">keep</option>
         <expand macro="list_string_san" name="description"/>
diff --git a/tools/openms/Epifany.xml b/tools/openms/Epifany.xml
index 3b68b80c0..d77dd3f35 100644
--- a/tools/openms/Epifany.xml
+++ b/tools/openms/Epifany.xml
@@ -68,13 +68,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </when>
     </conditional>
     <param argument="-exp_design" type="data" format="tabular" optional="true" label="(Currently unused) Input: experimental design" help=" select tabular data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="Output type: auto detected by file extension but can be overwritten here" help="">
+    <param argument="-out_type" type="select" optional="false" label="Output type: auto detected by file extension but can be overwritten here" help="">
       <option value="consensusXML">consensusxml</option>
       <option value="idXML">idxml</option>
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <param argument="-protein_fdr" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Additionally calculate the target-decoy FDR on protein-level based on the posteriors" help=""/>
-    <param argument="-greedy_group_resolution" type="select" optional="false" display="radio" label="Post-process inference output with greedy resolution of shared peptides based on the parent protein probabilities" help="Also adds the resolved ambiguity groups to output">
+    <param argument="-greedy_group_resolution" type="select" optional="false" label="Post-process inference output with greedy resolution of shared peptides based on the parent protein probabilities" help="Also adds the resolved ambiguity groups to output">
       <option value="none" selected="true">none</option>
       <option value="remove_associations_only">remove_associations_only</option>
       <option value="remove_proteins_wo_evidence">remove_proteins_wo_evidence</option>
@@ -98,7 +98,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="extended_model" argument="-algorithm:model_parameters:extended_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Uses information from different peptidoforms also across runs (automatically activated if an experimental design is given!)" help=""/>
       </section>
       <section name="loopy_belief_propagation" title="Settings for the loopy belief propagation algorithm" help="" expanded="false">
-        <param name="scheduling_type" argument="-algorithm:loopy_belief_propagation:scheduling_type" type="select" optional="false" display="radio" label="(Not used yet) How to pick the next message: priority = based on difference to last message (higher = more important)" help="fifo = first in first out. subtree = message passing follows a random spanning tree in each iteration">
+        <param name="scheduling_type" argument="-algorithm:loopy_belief_propagation:scheduling_type" type="select" optional="false" label="(Not used yet) How to pick the next message: priority = based on difference to last message (higher = more important)" help="fifo = first in first out. subtree = message passing follows a random spanning tree in each iteration">
           <option value="priority" selected="true">priority</option>
           <option value="fifo">fifo</option>
           <option value="subtree">subtree</option>
@@ -121,7 +121,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param argument="-picked_decoy_string" type="text" optional="true" value="" label="If using picked protein FDRs, which decoy string was used" help="Leave blank for auto-detection">
         <expand macro="list_string_san" name="picked_decoy_string"/>
       </param>
-      <param argument="-picked_decoy_prefix" type="select" optional="false" display="radio" label="If using picked protein FDRs, was the decoy string a prefix or suffix" help="Ignored during auto-detection">
+      <param argument="-picked_decoy_prefix" type="select" optional="false" label="If using picked protein FDRs, was the decoy string a prefix or suffix" help="Ignored during auto-detection">
         <option value="prefix" selected="true">prefix</option>
         <option value="suffix">suffix</option>
         <expand macro="list_string_san" name="picked_decoy_prefix"/>
diff --git a/tools/openms/FeatureFinderCentroided.xml b/tools/openms/FeatureFinderCentroided.xml
index 9b5fd2b19..e95f03911 100644
--- a/tools/openms/FeatureFinderCentroided.xml
+++ b/tools/openms/FeatureFinderCentroided.xml
@@ -97,13 +97,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="min_trace_score" argument="-algorithm:feature:min_trace_score" type="float" optional="false" min="0.0" max="1.0" value="0.5" label="Trace score threshold" help="Traces below this threshold are removed after the model fitting.. This parameter is important for features that overlap in m/z dimension"/>
         <param name="min_rt_span" argument="-algorithm:feature:min_rt_span" type="float" optional="false" min="0.0" max="1.0" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting" help=""/>
         <param name="max_rt_span" argument="-algorithm:feature:max_rt_span" type="float" optional="false" min="0.5" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have" help=""/>
-        <param name="rt_shape" argument="-algorithm:feature:rt_shape" type="select" optional="false" display="radio" label="Choose model used for RT profile fitting" help="If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used">
+        <param name="rt_shape" argument="-algorithm:feature:rt_shape" type="select" optional="false" label="Choose model used for RT profile fitting" help="If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used">
           <option value="symmetric" selected="true">symmetric</option>
           <option value="asymmetric">asymmetric</option>
           <expand macro="list_string_san" name="rt_shape"/>
         </param>
         <param name="max_intersection" argument="-algorithm:feature:max_intersection" type="float" optional="false" min="0.0" max="1.0" value="0.35" label="Maximum allowed intersection of features" help=""/>
-        <param name="reported_mz" argument="-algorithm:feature:reported_mz" type="select" optional="false" display="radio" label="The mass type that is reported for features" help="'maximum' returns the m/z value of the highest mass trace.. 'average' returns the intensity-weighted average m/z value of all contained peaks.. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model">
+        <param name="reported_mz" argument="-algorithm:feature:reported_mz" type="select" optional="false" label="The mass type that is reported for features" help="'maximum' returns the m/z value of the highest mass trace.. 'average' returns the intensity-weighted average m/z value of all contained peaks.. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model">
           <option value="maximum">maximum</option>
           <option value="average">average</option>
           <option value="monoisotopic" selected="true">monoisotopic</option>
diff --git a/tools/openms/FeatureFinderIdentification.xml b/tools/openms/FeatureFinderIdentification.xml
index 595267e9c..dd25422e3 100644
--- a/tools/openms/FeatureFinderIdentification.xml
+++ b/tools/openms/FeatureFinderIdentification.xml
@@ -130,7 +130,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <section name="svm" title="Parameters for scoring features using a support vector machine (SVM)" help="" expanded="false">
       <param name="samples" argument="-svm:samples" type="integer" optional="false" min="0" value="0" label="Number of observations to use for training ('0' for all)" help=""/>
       <param name="no_selection" argument="-svm:no_selection" type="boolean" truevalue="true" falsevalue="false" checked="false" label="By default, roughly the same number of positive and negative observations, with the same intensity distribution, are selected for training" help="This aims to reduce biases, but also reduces the amount of training data. Set this flag to skip this procedure and consider all available observations (subject to 'svm:samples')"/>
-      <param name="kernel" argument="-svm:kernel" type="select" optional="false" display="radio" label="SVM kernel" help="">
+      <param name="kernel" argument="-svm:kernel" type="select" optional="false" label="SVM kernel" help="">
         <option value="RBF" selected="true">RBF</option>
         <option value="linear">linear</option>
         <expand macro="list_string_san" name="kernel"/>
@@ -154,7 +154,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="min_prob" argument="-svm:min_prob" type="float" optional="false" min="0.0" max="1.0" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" help=""/>
     </section>
     <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="false" display="radio" label="Type of elution model to fit to features" help="">
+      <param name="type" argument="-model:type" type="select" optional="false" label="Type of elution model to fit to features" help="">
         <option value="symmetric" selected="true">symmetric</option>
         <option value="asymmetric">asymmetric</option>
         <option value="none">none</option>
diff --git a/tools/openms/FeatureFinderIsotopeWavelet.xml b/tools/openms/FeatureFinderIsotopeWavelet.xml
index d79c661b5..d3981cfa0 100644
--- a/tools/openms/FeatureFinderIsotopeWavelet.xml
+++ b/tools/openms/FeatureFinderIsotopeWavelet.xml
@@ -42,7 +42,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <section name="algorithm" title="Algorithm section" help="" expanded="false">
       <param name="max_charge" argument="-algorithm:max_charge" type="integer" optional="false" min="1" value="3" label="The maximal charge state to be considered" help=""/>
       <param name="intensity_threshold" argument="-algorithm:intensity_threshold" type="float" optional="false" value="-1.0" label="The final threshold t' is build upon the formula: t' = av+t*sd, where t is the intensity_threshold, av the average intensity within the wavelet transformed signal and sd the standard deviation of the transform" help="If you set intensity_threshold=-1, t' will be zero.. As the 'optimal' value for this parameter is highly data dependent, we would recommend to start with -1, which will also extract features with very low signal-to-noise ratio. Subsequently, one might increase the threshold to find an optimized trade-off between false positives and true positives. Depending on the dynamic range of your spectra, suitable value ranges include: -1, [0:10], and if your data features even very high intensity values, t can also adopt values up to around 30. Please note that this parameter is not of an integer type, s.t. you can also use t:=0.1, e.g"/>
-      <param name="intensity_type" argument="-algorithm:intensity_type" type="select" optional="false" display="radio" label="Determines the intensity type returned for the identified features" help="'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet)">
+      <param name="intensity_type" argument="-algorithm:intensity_type" type="select" optional="false" label="Determines the intensity type returned for the identified features" help="'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet)">
         <option value="ref" selected="true">ref</option>
         <option value="trans">trans</option>
         <option value="corrected">corrected</option>
diff --git a/tools/openms/FeatureFinderMetabo.xml b/tools/openms/FeatureFinderMetabo.xml
index 229859888..c25c03c15 100644
--- a/tools/openms/FeatureFinderMetabo.xml
+++ b/tools/openms/FeatureFinderMetabo.xml
@@ -61,13 +61,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="mtd" title="Mass Trace Detection parameters" help="" expanded="false">
         <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" optional="false" value="20.0" label="Allowed mass deviation (in ppm)" help=""/>
         <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/>
-        <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" optional="false" display="radio" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
+        <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" optional="false" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
           <option value="area" selected="true">area</option>
           <option value="median">median</option>
           <option value="max_height">max_height</option>
           <expand macro="list_string_san" name="quant_method"/>
         </param>
-        <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" optional="false" display="radio" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
+        <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" optional="false" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
           <option value="outlier" selected="true">outlier</option>
           <option value="sample_rate">sample_rate</option>
           <expand macro="list_string_san" name="trace_termination_criterion"/>
@@ -79,7 +79,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="epd" title="Elution Profile Detection (to separate isobaric Mass Traces by elution time)" help="" expanded="false">
         <param name="enabled" argument="-algorithm:epd:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable splitting of isobaric mass traces by chromatographic peak detection" help="Disable for direct injection"/>
-        <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" optional="false" display="radio" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
+        <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" optional="false" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
           <option value="off">off</option>
           <option value="fixed" selected="true">fixed</option>
           <option value="auto">auto</option>
@@ -96,7 +96,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="charge_upper_bound" argument="-algorithm:ffm:charge_upper_bound" type="integer" optional="false" value="3" label="Highest charge state to conside" help=""/>
         <param name="report_summed_ints" argument="-algorithm:ffm:report_summed_ints" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" help=""/>
         <param name="enable_RT_filtering" argument="-algorithm:ffm:enable_RT_filtering" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require sufficient overlap in RT while assembling mass traces" help="Disable for direct injection data"/>
-        <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" type="select" optional="false" display="radio" label="Remove/score candidate assemblies based on isotope intensities" help="SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device">
+        <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" type="select" optional="false" label="Remove/score candidate assemblies based on isotope intensities" help="SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device">
           <option value="metabolites (2% RMS)">metabolites (2% RMS)</option>
           <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option>
           <option value="peptides">peptides</option>
diff --git a/tools/openms/FeatureFinderMetaboIdent.xml b/tools/openms/FeatureFinderMetaboIdent.xml
index ac3e00653..4d1aa3174 100644
--- a/tools/openms/FeatureFinderMetaboIdent.xml
+++ b/tools/openms/FeatureFinderMetaboIdent.xml
@@ -99,7 +99,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" optional="false" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
     </section>
     <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="false" display="radio" label="Type of elution model to fit to features" help="">
+      <param name="type" argument="-model:type" type="select" optional="false" label="Type of elution model to fit to features" help="">
         <option value="symmetric" selected="true">symmetric</option>
         <option value="asymmetric">asymmetric</option>
         <option value="none">none</option>
diff --git a/tools/openms/FeatureFinderMultiplex.xml b/tools/openms/FeatureFinderMultiplex.xml
index 3c99ea56d..85ff41dd1 100644
--- a/tools/openms/FeatureFinderMultiplex.xml
+++ b/tools/openms/FeatureFinderMultiplex.xml
@@ -82,7 +82,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="rt_band" argument="-algorithm:rt_band" type="float" optional="false" min="0.0" value="0.0" label="The algorithm searches for characteristic isotopic peak patterns, spectrum by spectrum" help="For some low-intensity peptides, an important peak might be missing in one spectrum but be present in one of the neighbouring ones. The algorithm takes a bundle of neighbouring spectra with width rt_band into account. For example with rt_band = 0, all characteristic isotopic peaks have to be present in one and the same spectrum. As rt_band increases, the sensitivity of the algorithm but also the likelihood of false detections increases"/>
       <param name="rt_min" argument="-algorithm:rt_min" type="float" optional="false" min="0.0" value="2.0" label="Lower bound for the retention time [s]" help="(Any peptides seen for a shorter time period are not reported.)"/>
       <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="float" optional="false" min="0.0" value="6.0" label="m/z tolerance for search of peak patterns" help=""/>
-      <param name="mz_unit" argument="-algorithm:mz_unit" type="select" optional="false" display="radio" label="Unit of the 'mz_tolerance' paramete" help="">
+      <param name="mz_unit" argument="-algorithm:mz_unit" type="select" optional="false" label="Unit of the 'mz_tolerance' paramete" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_unit"/>
@@ -92,13 +92,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="averagine_similarity" argument="-algorithm:averagine_similarity" type="float" optional="false" min="-1.0" max="1.0" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" help="This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model"/>
       <param name="averagine_similarity_scaling" argument="-algorithm:averagine_similarity_scaling" type="float" optional="false" min="0.0" max="1.0" value="0.95" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -&gt; p' = p and x = 1 -&gt; p' = 1. (For knock_out = true, peptide doublets and singlets are detected simultaneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/>
       <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="false" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
-      <param name="spectrum_type" argument="-algorithm:spectrum_type" type="select" optional="false" display="radio" label="Type of MS1 spectra in input mzML file" help="'automatic' determines the spectrum type directly from the input mzML file">
+      <param name="spectrum_type" argument="-algorithm:spectrum_type" type="select" optional="false" label="Type of MS1 spectra in input mzML file" help="'automatic' determines the spectrum type directly from the input mzML file">
         <option value="profile">profile</option>
         <option value="centroid">centroid</option>
         <option value="automatic" selected="true">automatic</option>
         <expand macro="list_string_san" name="spectrum_type"/>
       </param>
-      <param name="averagine_type" argument="-algorithm:averagine_type" type="select" optional="false" display="radio" label="The type of averagine to use, currently RNA, DNA or peptide" help="">
+      <param name="averagine_type" argument="-algorithm:averagine_type" type="select" optional="false" label="The type of averagine to use, currently RNA, DNA or peptide" help="">
         <option value="peptide" selected="true">peptide</option>
         <option value="RNA">RNA</option>
         <option value="DNA">DNA</option>
diff --git a/tools/openms/FeatureLinkerUnlabeled.xml b/tools/openms/FeatureLinkerUnlabeled.xml
index 50e56465f..87787d671 100644
--- a/tools/openms/FeatureLinkerUnlabeled.xml
+++ b/tools/openms/FeatureLinkerUnlabeled.xml
@@ -81,7 +81,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </section>
       <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
         <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" optional="false" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
-        <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" optional="false" display="radio" label="Unit of the 'max_difference' paramete" help="">
+        <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" optional="false" label="Unit of the 'max_difference' paramete" help="">
           <option value="Da" selected="true">Da</option>
           <option value="ppm">ppm</option>
           <expand macro="list_string_san" name="unit"/>
@@ -92,7 +92,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
         <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="false" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
         <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="false" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
-        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" optional="false" display="radio" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
+        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" optional="false" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
           <option value="enabled">enabled</option>
           <option value="disabled" selected="true">disabled</option>
           <expand macro="list_string_san" name="log_transform"/>
diff --git a/tools/openms/FeatureLinkerUnlabeledKD.xml b/tools/openms/FeatureLinkerUnlabeledKD.xml
index 13eecbdfa..9eb31b4dd 100644
--- a/tools/openms/FeatureLinkerUnlabeledKD.xml
+++ b/tools/openms/FeatureLinkerUnlabeledKD.xml
@@ -70,7 +70,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
     <param argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="mz_unit" argument="-algorithm:mz_unit" type="select" optional="false" display="radio" label="Unit of m/z tolerance" help="">
+      <param name="mz_unit" argument="-algorithm:mz_unit" type="select" optional="false" label="Unit of m/z tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mz_unit"/>
@@ -87,13 +87,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <section name="link" title="" help="" expanded="false">
         <param name="rt_tol" argument="-algorithm:link:rt_tol" type="float" optional="false" min="0.0" value="30.0" label="Width of RT tolerance window (sec)" help=""/>
         <param name="mz_tol" argument="-algorithm:link:mz_tol" type="float" optional="false" min="0.0" value="10.0" label="m/z tolerance (in ppm or Da)" help=""/>
-        <param name="charge_merging" argument="-algorithm:link:charge_merging" type="select" optional="false" display="radio" label="whether to disallow charge mismatches (Identical), allow to link charge zero" help="(i.e., unknown charge state) with every charge state, or disregard charges (Any)">
+        <param name="charge_merging" argument="-algorithm:link:charge_merging" type="select" optional="false" label="whether to disallow charge mismatches (Identical), allow to link charge zero" help="(i.e., unknown charge state) with every charge state, or disregard charges (Any)">
           <option value="Identical">Identical</option>
           <option value="With_charge_zero" selected="true">With_charge_zero</option>
           <option value="Any">Any</option>
           <expand macro="list_string_san" name="charge_merging"/>
         </param>
-        <param name="adduct_merging" argument="-algorithm:link:adduct_merging" type="select" optional="false" display="radio" label="whether to only allow the same adduct for linking (Identical), also allow linking features with adduct-free ones, or disregard adducts (Any)" help="">
+        <param name="adduct_merging" argument="-algorithm:link:adduct_merging" type="select" optional="false" label="whether to only allow the same adduct for linking (Identical), also allow linking features with adduct-free ones, or disregard adducts (Any)" help="">
           <option value="Identical">Identical</option>
           <option value="With_unknown_adducts">With_unknown_adducts</option>
           <option value="Any" selected="true">Any</option>
@@ -111,7 +111,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
         <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="false" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
         <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="false" min="0.0" value="1.0" label="Final intensity distances are weighted by this facto" help=""/>
-        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" optional="false" display="radio" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
+        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" optional="false" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
           <option value="enabled" selected="true">enabled</option>
           <option value="disabled">disabled</option>
           <expand macro="list_string_san" name="log_transform"/>
@@ -121,13 +121,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="span" argument="-algorithm:LOWESS:span" type="float" optional="false" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
         <param name="num_iterations" argument="-algorithm:LOWESS:num_iterations" type="integer" optional="false" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
         <param name="delta" argument="-algorithm:LOWESS:delta" type="float" optional="false" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
-        <param name="interpolation_type" argument="-algorithm:LOWESS:interpolation_type" type="select" optional="false" display="radio" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
+        <param name="interpolation_type" argument="-algorithm:LOWESS:interpolation_type" type="select" optional="false" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-algorithm:LOWESS:extrapolation_type" type="select" optional="false" display="radio" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
+        <param name="extrapolation_type" argument="-algorithm:LOWESS:extrapolation_type" type="select" optional="false" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
           <option value="two-point-linear">two-point-linear</option>
           <option value="four-point-linear" selected="true">four-point-linear</option>
           <option value="global-linear">global-linear</option>
diff --git a/tools/openms/FeatureLinkerUnlabeledQT.xml b/tools/openms/FeatureLinkerUnlabeledQT.xml
index e754b7dfa..24a3109f8 100644
--- a/tools/openms/FeatureLinkerUnlabeledQT.xml
+++ b/tools/openms/FeatureLinkerUnlabeledQT.xml
@@ -84,7 +84,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </section>
       <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
         <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" optional="false" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
-        <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" optional="false" display="radio" label="Unit of the 'max_difference' paramete" help="">
+        <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" optional="false" label="Unit of the 'max_difference' paramete" help="">
           <option value="Da" selected="true">Da</option>
           <option value="ppm">ppm</option>
           <expand macro="list_string_san" name="unit"/>
@@ -95,7 +95,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
         <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="false" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
         <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="false" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
-        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" optional="false" display="radio" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
+        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" optional="false" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
           <option value="enabled">enabled</option>
           <option value="disabled" selected="true">disabled</option>
           <expand macro="list_string_san" name="log_transform"/>
diff --git a/tools/openms/FileConverter.xml b/tools/openms/FileConverter.xml
index b1ac30533..22371cf91 100644
--- a/tools/openms/FileConverter.xml
+++ b/tools/openms/FileConverter.xml
@@ -53,7 +53,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <expand macro="adv_opts_macro">
-      <param argument="-UID_postprocessing" type="select" optional="false" display="radio" label="unique ID post-processing for output data" help="'none' keeps current IDs even if invalid.. 'ensure' keeps current IDs but reassigns invalid ones.. 'reassign' assigns new unique IDs">
+      <param argument="-UID_postprocessing" type="select" optional="false" label="unique ID post-processing for output data" help="'none' keeps current IDs even if invalid.. 'ensure' keeps current IDs but reassigns invalid ones.. 'reassign' assigns new unique IDs">
         <option value="none">none</option>
         <option value="ensure" selected="true">ensure</option>
         <option value="reassign">reassign</option>
@@ -64,7 +64,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param argument="-force_MaxQuant_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help=""/>
       <param argument="-force_TPP_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help=""/>
       <param argument="-convert_to_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Assumes that the provided spectra represent data in SRM mode or targeted MS1 mode and converts them to chromatogram data" help=""/>
-      <param argument="-change_im_format" type="select" optional="false" display="radio" label="[mzML output only] How to store ion mobility scans (none: no change in format; multiple_spectra: store each IM frame as multiple scans (one per drift time value); concatenated: store whole frame as single scan with IM values in a FloatDataArray" help="">
+      <param argument="-change_im_format" type="select" optional="false" label="[mzML output only] How to store ion mobility scans (none: no change in format; multiple_spectra: store each IM frame as multiple scans (one per drift time value); concatenated: store whole frame as single scan with IM values in a FloatDataArray" help="">
         <option value="none" selected="true">none</option>
         <option value="concatenated">concatenated</option>
         <option value="multiple_spectra">multiple_spectra</option>
diff --git a/tools/openms/FileFilter.xml b/tools/openms/FileFilter.xml
index e8b036822..a69e0f829 100644
--- a/tools/openms/FileFilter.xml
+++ b/tools/openms/FileFilter.xml
@@ -63,7 +63,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="consensusxml,featurexml,mzml" optional="false" label="Input file" help=" select consensusxml,featurexml,mzml data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-out_type" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
       <option value="consensusXML">consensusxml</option>
       <option value="featureXML">featurexml</option>
       <option value="mzML">mzml</option>
@@ -97,12 +97,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="no_chromatograms" argument="-peak_options:no_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No conversion to space-saving real chromatograms" help="e.g. from SRM scans"/>
       <param name="remove_chromatograms" argument="-peak_options:remove_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes chromatograms stored in a file" help=""/>
       <param name="remove_empty" argument="-peak_options:remove_empty" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes spectra and chromatograms without peaks" help=""/>
-      <param name="mz_precision" argument="-peak_options:mz_precision" type="select" optional="false" display="radio" label="Store base64 encoded m/z data using 32 or 64 bit precision" help="">
+      <param name="mz_precision" argument="-peak_options:mz_precision" type="select" optional="false" label="Store base64 encoded m/z data using 32 or 64 bit precision" help="">
         <option value="32">32</option>
         <option value="64" selected="true">64</option>
         <expand macro="list_string_san" name="mz_precision"/>
       </param>
-      <param name="int_precision" argument="-peak_options:int_precision" type="select" optional="false" display="radio" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="">
+      <param name="int_precision" argument="-peak_options:int_precision" type="select" optional="false" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="">
         <option value="32" selected="true">32</option>
         <option value="64">64</option>
         <expand macro="list_string_san" name="int_precision"/>
@@ -110,7 +110,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="indexed_file" argument="-peak_options:indexed_file" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to add an index to the file when writing" help=""/>
       <param name="zlib_compression" argument="-peak_options:zlib_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to store data with zlib compression (lossless compression)" help=""/>
       <section name="numpress" title="Numpress compression for peak data" help="" expanded="false">
-        <param name="masstime" argument="-peak_options:numpress:masstime" type="select" optional="false" display="radio" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="">
+        <param name="masstime" argument="-peak_options:numpress:masstime" type="select" optional="false" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="">
           <option value="none" selected="true">none</option>
           <option value="linear">linear</option>
           <option value="pic">pic</option>
@@ -118,14 +118,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <expand macro="list_string_san" name="masstime"/>
         </param>
         <param name="lossy_mass_accuracy" argument="-peak_options:numpress:lossy_mass_accuracy" type="float" optional="false" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
-        <param name="intensity" argument="-peak_options:numpress:intensity" type="select" optional="false" display="radio" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="">
+        <param name="intensity" argument="-peak_options:numpress:intensity" type="select" optional="false" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="">
           <option value="none" selected="true">none</option>
           <option value="linear">linear</option>
           <option value="pic">pic</option>
           <option value="slof">slof</option>
           <expand macro="list_string_san" name="intensity"/>
         </param>
-        <param name="float_da" argument="-peak_options:numpress:float_da" type="select" optional="false" display="radio" label="Apply MS Numpress compression algorithms for the float data arrays (recommended: slof or pic)" help="">
+        <param name="float_da" argument="-peak_options:numpress:float_da" type="select" optional="false" label="Apply MS Numpress compression algorithms for the float data arrays (recommended: slof or pic)" help="">
           <option value="none" selected="true">none</option>
           <option value="linear">linear</option>
           <option value="pic">pic</option>
@@ -286,7 +286,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <expand macro="list_string_val" name="sequences_whitelist"/>
         <expand macro="list_string_san" name="sequences_whitelist"/>
       </param>
-      <param name="sequence_comparison_method" argument="-id:sequence_comparison_method" type="select" optional="false" display="radio" label="Comparison method used to determine if a feature is whitelisted" help="">
+      <param name="sequence_comparison_method" argument="-id:sequence_comparison_method" type="select" optional="false" label="Comparison method used to determine if a feature is whitelisted" help="">
         <option value="substring" selected="true">substring</option>
         <option value="exact">exact</option>
         <expand macro="list_string_san" name="sequence_comparison_method"/>
diff --git a/tools/openms/FileMerger.xml b/tools/openms/FileMerger.xml
index 05fa073a6..aca65032a 100644
--- a/tools/openms/FileMerger.xml
+++ b/tools/openms/FileMerger.xml
@@ -81,7 +81,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <option value="fasta">fasta</option>
     </param>
     <param argument="-annotate_file_origin" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" help=""/>
-    <param argument="-append_method" type="select" optional="false" display="radio" label="(ConsensusXML-only) Append quantitative information about features row-wise or column-wise" help="- 'append_rows' is usually used when the inputs come from the same MS run (e.g. caused by manual splitting or multiple algorithms on the same file). - 'append_cols' when you want to combine consensusXMLs from e.g. different fractions to be summarized in ProteinQuantifier or jointly exported with MzTabExporter">
+    <param argument="-append_method" type="select" optional="false" label="(ConsensusXML-only) Append quantitative information about features row-wise or column-wise" help="- 'append_rows' is usually used when the inputs come from the same MS run (e.g. caused by manual splitting or multiple algorithms on the same file). - 'append_cols' when you want to combine consensusXMLs from e.g. different fractions to be summarized in ProteinQuantifier or jointly exported with MzTabExporter">
       <option value="append_rows" selected="true">append_rows</option>
       <option value="append_cols">append_cols</option>
       <expand macro="list_string_san" name="append_method"/>
diff --git a/tools/openms/GNPSExport.xml b/tools/openms/GNPSExport.xml
index 405e899fa..3a5771039 100644
--- a/tools/openms/GNPSExport.xml
+++ b/tools/openms/GNPSExport.xml
@@ -91,7 +91,7 @@ ${' '.join(["'in_mzml_cond.in_mzml/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.elem
         <param argument="-in_mzml" type="data" format="mzml" multiple="false" optional="false" label="Original mzml files containing the ms2 spectra (aka peptide annotation)" help="Must be in order that the consensusXML file maps the original mzML files select mzml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-output_type" type="select" optional="false" display="radio" label="specificity of mgf output information" help="">
+    <param argument="-output_type" type="select" optional="false" label="specificity of mgf output information" help="">
       <option value="merged_spectra">merged_spectra</option>
       <option value="most_intense" selected="true">most_intense</option>
       <expand macro="list_string_san" name="output_type"/>
diff --git a/tools/openms/HighResPrecursorMassCorrector.xml b/tools/openms/HighResPrecursorMassCorrector.xml
index e9bd597c5..4387a0cde 100644
--- a/tools/openms/HighResPrecursorMassCorrector.xml
+++ b/tools/openms/HighResPrecursorMassCorrector.xml
@@ -63,7 +63,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <section name="feature" title="Use features for precursor mass correction" help="" expanded="false">
       <param name="in" argument="-feature:in" type="data" format="featurexml" optional="true" label="Features used to correct precursor masses" help=" select featurexml data sets(s)"/>
       <param name="mz_tolerance" argument="-feature:mz_tolerance" type="float" optional="false" value="5.0" label="The precursor mass tolerance" help="Used to determine matching to feature mass traces"/>
-      <param name="mz_tolerance_unit" argument="-feature:mz_tolerance_unit" type="select" optional="false" display="radio" label="Unit of precursor mass tolerance" help="">
+      <param name="mz_tolerance_unit" argument="-feature:mz_tolerance_unit" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_tolerance_unit"/>
@@ -76,7 +76,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <section name="nearest_peak" title="Use nearest centroided MS1 peak for precursor mass correction" help="" expanded="false">
       <param name="mz_tolerance" argument="-nearest_peak:mz_tolerance" type="float" optional="false" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(Disable method by setting value to 0.0)"/>
-      <param name="mz_tolerance_unit" argument="-nearest_peak:mz_tolerance_unit" type="select" optional="false" display="radio" label="Unit of precursor mass tolerance" help="">
+      <param name="mz_tolerance_unit" argument="-nearest_peak:mz_tolerance_unit" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_tolerance_unit"/>
@@ -84,7 +84,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <section name="highest_intensity_peak" title="Use centroided MS1 peak with the highest intensity in a certrain mass range - for precursor mass correction" help="" expanded="false">
       <param name="mz_tolerance" argument="-highest_intensity_peak:mz_tolerance" type="float" optional="false" value="0.0" label="The precursor mass tolerance to find the highest intensity MS1 peak" help="Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)"/>
-      <param name="mz_tolerance_unit" argument="-highest_intensity_peak:mz_tolerance_unit" type="select" optional="false" display="radio" label="Unit of precursor mass tolerance" help="">
+      <param name="mz_tolerance_unit" argument="-highest_intensity_peak:mz_tolerance_unit" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_tolerance_unit"/>
diff --git a/tools/openms/IDConflictResolver.xml b/tools/openms/IDConflictResolver.xml
index 50bc2b16e..a51bf7ac9 100644
--- a/tools/openms/IDConflictResolver.xml
+++ b/tools/openms/IDConflictResolver.xml
@@ -39,7 +39,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml data sets(s)"/>
-    <param argument="-resolve_between_features" type="select" optional="false" display="radio" label="A map may contain multiple features with both identical (possibly modified" help="i.e. not stripped) sequence and charge state. The feature with the 'highest intensity' is very likely the most reliable one. When switched on, the filter removes the sequence annotation from the lower intensity features, thereby resolving the multiplicity. Only the most reliable features for each (possibly modified i.e. not stripped) sequence maintain annotated with this peptide sequence">
+    <param argument="-resolve_between_features" type="select" optional="false" label="A map may contain multiple features with both identical (possibly modified" help="i.e. not stripped) sequence and charge state. The feature with the 'highest intensity' is very likely the most reliable one. When switched on, the filter removes the sequence annotation from the lower intensity features, thereby resolving the multiplicity. Only the most reliable features for each (possibly modified i.e. not stripped) sequence maintain annotated with this peptide sequence">
       <option value="off" selected="true">off</option>
       <option value="highest_intensity">highest_intensity</option>
       <expand macro="list_string_san" name="resolve_between_features"/>
diff --git a/tools/openms/IDFileConverter.xml b/tools/openms/IDFileConverter.xml
index 1506e295a..809c4d44f 100644
--- a/tools/openms/IDFileConverter.xml
+++ b/tools/openms/IDFileConverter.xml
@@ -62,14 +62,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <expand macro="list_string_san" name="mz_name"/>
     </param>
     <param argument="-peptideprophet_analyzed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" help="By default a 'raw' pepXML is produced that contains only search engine results"/>
-    <param argument="-score_type" type="select" optional="false" display="radio" label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" help="">
+    <param argument="-score_type" type="select" optional="false" label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" help="">
       <option value="qvalue" selected="true">qvalue</option>
       <option value="PEP">PEP</option>
       <option value="score">score</option>
       <expand macro="list_string_san" name="score_type"/>
     </param>
     <section name="fasta_to_mzml" title="[FASTA input + MzML output only] Parameters used to adjust simulation of the theoretical spectra" help="" expanded="false">
-      <param name="isotope_model" argument="-fasta_to_mzml:isotope_model" type="select" optional="false" display="radio" label="Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks" help="Note that adding isotopic peaks is very slow">
+      <param name="isotope_model" argument="-fasta_to_mzml:isotope_model" type="select" optional="false" label="Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks" help="Note that adding isotopic peaks is very slow">
         <option value="none" selected="true">none</option>
         <option value="coarse">coarse</option>
         <option value="fine">fine</option>
diff --git a/tools/openms/IDFilter.xml b/tools/openms/IDFilter.xml
index 69acc8021..95693f8fd 100644
--- a/tools/openms/IDFilter.xml
+++ b/tools/openms/IDFilter.xml
@@ -6096,7 +6096,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="unspecific cleavage">unspecific cleavage</option>
         <expand macro="list_string_san" name="enzyme"/>
       </param>
-      <param name="specificity" argument="-in_silico_digestion:specificity" type="select" optional="false" display="radio" label="Specificity of the filte" help="">
+      <param name="specificity" argument="-in_silico_digestion:specificity" type="select" optional="false" label="Specificity of the filte" help="">
         <option value="none">none</option>
         <option value="semi">semi</option>
         <option value="full" selected="true">full</option>
@@ -6152,7 +6152,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <section name="mz" title="Filtering by mass erro" help="" expanded="false">
       <param name="error" argument="-mz:error" type="float" optional="false" value="-1.0" label="Filtering by deviation to theoretical mass (disabled for negative values)" help=""/>
-      <param name="unit" argument="-mz:unit" type="select" optional="false" display="radio" label="Absolute or relative erro" help="">
+      <param name="unit" argument="-mz:unit" type="select" optional="false" label="Absolute or relative erro" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="unit"/>
diff --git a/tools/openms/IDMapper.xml b/tools/openms/IDMapper.xml
index 38068cf4a..e852065f1 100644
--- a/tools/openms/IDMapper.xml
+++ b/tools/openms/IDMapper.xml
@@ -54,12 +54,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-in" type="data" format="consensusxml,featurexml,mzq" optional="false" label="Feature map/consensus map file" help=" select consensusxml,featurexml,mzq data sets(s)"/>
     <param argument="-rt_tolerance" type="float" optional="false" min="0.0" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
     <param argument="-mz_tolerance" type="float" optional="false" min="0.0" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
-    <param argument="-mz_measure" type="select" optional="false" display="radio" label="Unit of 'mz_tolerance'" help="">
+    <param argument="-mz_measure" type="select" optional="false" label="Unit of 'mz_tolerance'" help="">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
       <expand macro="list_string_san" name="mz_measure"/>
     </param>
-    <param argument="-mz_reference" type="select" optional="false" display="radio" label="Source of m/z values for peptide identifications" help="If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',. masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)">
+    <param argument="-mz_reference" type="select" optional="false" label="Source of m/z values for peptide identifications" help="If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',. masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)">
       <option value="precursor">precursor</option>
       <option value="peptide" selected="true">peptide</option>
       <expand macro="list_string_san" name="mz_reference"/>
diff --git a/tools/openms/IDMerger.xml b/tools/openms/IDMerger.xml
index 3d4741e0f..0f151ec78 100644
--- a/tools/openms/IDMerger.xml
+++ b/tools/openms/IDMerger.xml
@@ -67,7 +67,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param argument="-in" type="data" format="idxml,sqlite" multiple="false" optional="false" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="Output file type (default: determined from file extension)" help="">
+    <param argument="-out_type" type="select" optional="false" label="Output file type (default: determined from file extension)" help="">
       <option value="idXML">idxml</option>
       <option value="oms">sqlite (oms)</option>
       <expand macro="list_string_san" name="out_type"/>
diff --git a/tools/openms/IDPosteriorErrorProbability.xml b/tools/openms/IDPosteriorErrorProbability.xml
index 6186e4244..07dcdfcf8 100644
--- a/tools/openms/IDPosteriorErrorProbability.xml
+++ b/tools/openms/IDPosteriorErrorProbability.xml
@@ -58,14 +58,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-prob_correct" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications" help=""/>
     <section name="fit_algorithm" title="Algorithm parameter subsection" help="" expanded="false">
       <param name="number_of_bins" argument="-fit_algorithm:number_of_bins" type="integer" optional="false" value="100" label="Number of bins used for visualization" help="Only needed if each iteration step of the EM-Algorithm will be visualized"/>
-      <param name="incorrectly_assigned" argument="-fit_algorithm:incorrectly_assigned" type="select" optional="false" display="radio" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="For 'Gauss', the Gauss distribution is used">
+      <param name="incorrectly_assigned" argument="-fit_algorithm:incorrectly_assigned" type="select" optional="false" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="For 'Gauss', the Gauss distribution is used">
         <option value="Gumbel" selected="true">Gumbel</option>
         <option value="Gauss">Gauss</option>
         <expand macro="list_string_san" name="incorrectly_assigned"/>
       </param>
       <param name="max_nr_iterations" argument="-fit_algorithm:max_nr_iterations" type="integer" optional="false" value="1000" label="Bounds the number of iterations for the EM algorithm when convergence is slow" help=""/>
       <param name="neg_log_delta" argument="-fit_algorithm:neg_log_delta" type="integer" optional="false" value="6" label="The negative logarithm of the convergence threshold for the likelihood increase" help=""/>
-      <param name="outlier_handling" argument="-fit_algorithm:outlier_handling" type="select" optional="false" display="radio" label="What to do with outliers:" help="- ignore_iqr_outliers: ignore outliers outside of 3*IQR from Q1/Q3 for fitting. - set_iqr_to_closest_valid: set IQR-based outliers to the last valid value for fitting. - ignore_extreme_percentiles: ignore everything outside 99th and 1st percentile (also removes equal values like potential censored max values in XTandem). - none: do nothing">
+      <param name="outlier_handling" argument="-fit_algorithm:outlier_handling" type="select" optional="false" label="What to do with outliers:" help="- ignore_iqr_outliers: ignore outliers outside of 3*IQR from Q1/Q3 for fitting. - set_iqr_to_closest_valid: set IQR-based outliers to the last valid value for fitting. - ignore_extreme_percentiles: ignore everything outside 99th and 1st percentile (also removes equal values like potential censored max values in XTandem). - none: do nothing">
         <option value="ignore_iqr_outliers" selected="true">ignore_iqr_outliers</option>
         <option value="set_iqr_to_closest_valid">set_iqr_to_closest_valid</option>
         <option value="ignore_extreme_percentiles">ignore_extreme_percentiles</option>
diff --git a/tools/openms/InternalCalibration.xml b/tools/openms/InternalCalibration.xml
index df265c019..32f411b0e 100644
--- a/tools/openms/InternalCalibration.xml
+++ b/tools/openms/InternalCalibration.xml
@@ -128,7 +128,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="lock_in" argument="-cal:lock_in" type="data" format="csv" optional="true" label="Input file containing reference m/z values (text file with each line as: m/z ms-level charge) which occur in all scans" help=" select csv data sets(s)"/>
       <param name="lock_require_mono" argument="-cal:lock_require_mono" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require all lock masses to be monoisotopic" help="i.e. not the iso1, iso2 etc ('charge' column is used to determine the spacing). Peaks which are not mono-isotopic are not used"/>
       <param name="lock_require_iso" argument="-cal:lock_require_iso" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require all lock masses to have at least the +1 isotope" help="Peaks without isotope pattern are not used"/>
-      <param name="model_type" argument="-cal:model_type" type="select" optional="false" display="radio" label="Type of function to be fitted to the calibration points" help="">
+      <param name="model_type" argument="-cal:model_type" type="select" optional="false" label="Type of function to be fitted to the calibration points" help="">
         <option value="linear">linear</option>
         <option value="linear_weighted" selected="true">linear_weighted</option>
         <option value="quadratic">quadratic</option>
diff --git a/tools/openms/LuciphorAdapter.xml b/tools/openms/LuciphorAdapter.xml
index 380a232b6..eb2072b99 100644
--- a/tools/openms/LuciphorAdapter.xml
+++ b/tools/openms/LuciphorAdapter.xml
@@ -44,13 +44,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   <inputs>
     <param argument="-in" type="data" format="mzml" optional="false" label="Input spectrum file" help=" select mzml data sets(s)"/>
     <param argument="-id" type="data" format="idxml" optional="false" label="Protein/peptide identifications file" help=" select idxml data sets(s)"/>
-    <param argument="-fragment_method" type="select" optional="false" display="radio" label="Fragmentation method" help="">
+    <param argument="-fragment_method" type="select" optional="false" label="Fragmentation method" help="">
       <option value="CID" selected="true">CID</option>
       <option value="HCD">HCD</option>
       <expand macro="list_string_san" name="fragment_method"/>
     </param>
     <param argument="-fragment_mass_tolerance" type="float" optional="false" value="0.5" label="Tolerance of the peaks in the fragment spectrum" help=""/>
-    <param argument="-fragment_error_units" type="select" optional="false" display="radio" label="Unit of fragment mass tolerance" help="">
+    <param argument="-fragment_error_units" type="select" optional="false" label="Unit of fragment mass tolerance" help="">
       <option value="Da" selected="true">Da</option>
       <option value="ppm">ppm</option>
       <expand macro="list_string_san" name="fragment_error_units"/>
@@ -3038,7 +3038,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-modeling_score_threshold" type="float" optional="false" min="0.0" value="0.95" label="Minimum score a PSM needs to be considered for modeling" help=""/>
     <param argument="-scoring_threshold" type="float" optional="false" min="0.0" value="0.0" label="PSMs below this value will be discarded" help=""/>
     <param argument="-min_num_psms_model" type="integer" optional="false" min="1" value="50" label="The minimum number of PSMs you need for any charge state in order to build a model for it" help=""/>
-    <param argument="-run_mode" type="select" optional="false" display="radio" label="Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported" help="">
+    <param argument="-run_mode" type="select" optional="false" label="Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported" help="">
       <option value="0" selected="true">0</option>
       <option value="1">1</option>
       <expand macro="list_string_san" name="run_mode"/>
diff --git a/tools/openms/MRMTransitionGroupPicker.xml b/tools/openms/MRMTransitionGroupPicker.xml
index 867b9e632..444d213ba 100644
--- a/tools/openms/MRMTransitionGroupPicker.xml
+++ b/tools/openms/MRMTransitionGroupPicker.xml
@@ -48,12 +48,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="stop_after_feature" argument="-algorithm:stop_after_feature" type="integer" optional="false" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
       <param name="stop_after_intensity_ratio" argument="-algorithm:stop_after_intensity_ratio" type="float" optional="false" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
       <param name="min_peak_width" argument="-algorithm:min_peak_width" type="float" optional="false" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
-      <param name="peak_integration" argument="-algorithm:peak_integration" type="select" optional="false" display="radio" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
+      <param name="peak_integration" argument="-algorithm:peak_integration" type="select" optional="false" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
         <option value="original" selected="true">original</option>
         <option value="smoothed">smoothed</option>
         <expand macro="list_string_san" name="peak_integration"/>
       </param>
-      <param name="background_subtraction" argument="-algorithm:background_subtraction" type="select" optional="false" display="radio" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
+      <param name="background_subtraction" argument="-algorithm:background_subtraction" type="select" optional="false" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
         <option value="none" selected="true">none</option>
         <option value="original">original</option>
         <option value="exact">exact</option>
@@ -68,7 +68,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="compute_peak_quality" argument="-algorithm:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
       <param name="compute_peak_shape_metrics" argument="-algorithm:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
       <param name="compute_total_mi" argument="-algorithm:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
-      <param name="boundary_selection_method" argument="-algorithm:boundary_selection_method" type="select" optional="false" display="radio" label="Method to use when selecting the best boundaries for peaks" help="">
+      <param name="boundary_selection_method" argument="-algorithm:boundary_selection_method" type="select" optional="false" label="Method to use when selecting the best boundaries for peaks" help="">
         <option value="largest" selected="true">largest</option>
         <option value="widest">widest</option>
         <expand macro="list_string_san" name="boundary_selection_method"/>
@@ -84,7 +84,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="sn_bin_count" argument="-algorithm:PeakPickerMRM:sn_bin_count" type="integer" optional="false" value="30" label="Signal to noise bin count" help=""/>
         <param name="write_sn_log_messages" argument="-algorithm:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
         <param name="remove_overlapping_peaks" argument="-algorithm:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/>
-        <param name="method" argument="-algorithm:PeakPickerMRM:method" type="select" optional="false" display="radio" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
+        <param name="method" argument="-algorithm:PeakPickerMRM:method" type="select" optional="false" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
           <option value="legacy">legacy</option>
           <option value="corrected" selected="true">corrected</option>
           <option value="crawdad">crawdad</option>
@@ -92,13 +92,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         </param>
       </section>
       <section name="PeakIntegrator" title="" help="" expanded="false">
-        <param name="integration_type" argument="-algorithm:PeakIntegrator:integration_type" type="select" optional="false" display="radio" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
+        <param name="integration_type" argument="-algorithm:PeakIntegrator:integration_type" type="select" optional="false" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
           <option value="intensity_sum" selected="true">intensity_sum</option>
           <option value="simpson">simpson</option>
           <option value="trapezoid">trapezoid</option>
           <expand macro="list_string_san" name="integration_type"/>
         </param>
-        <param name="baseline_type" argument="-algorithm:PeakIntegrator:baseline_type" type="select" optional="false" display="radio" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
+        <param name="baseline_type" argument="-algorithm:PeakIntegrator:baseline_type" type="select" optional="false" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
           <option value="base_to_base" selected="true">base_to_base</option>
           <option value="vertical_division">vertical_division</option>
           <option value="vertical_division_min">vertical_division_min</option>
diff --git a/tools/openms/MSFraggerAdapter.xml b/tools/openms/MSFraggerAdapter.xml
index 2ea43405b..e4bd4e8ec 100644
--- a/tools/openms/MSFraggerAdapter.xml
+++ b/tools/openms/MSFraggerAdapter.xml
@@ -55,7 +55,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"java_executable": "java", "executable": "/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-license" type="select" optional="false" display="radio" label="Set to yes, if you have read and agreed to the MSFragger license terms" help="">
+    <param argument="-license" type="select" optional="false" label="Set to yes, if you have read and agreed to the MSFragger license terms" help="">
       <option value="yes">yes</option>
       <option value="no">no</option>
       <expand macro="list_string_san" name="license"/>
@@ -67,24 +67,24 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <section name="tolerance" title="Search Tolerances" help="" expanded="false">
       <param name="precursor_mass_tolerance_lower" argument="-tolerance:precursor_mass_tolerance_lower" type="float" optional="false" min="0.0" value="20.0" label="Lower precursor mass tolerance" help=""/>
       <param name="precursor_mass_tolerance_upper" argument="-tolerance:precursor_mass_tolerance_upper" type="float" optional="false" min="0.0" value="20.0" label="Upper precursor mass tolerance" help=""/>
-      <param name="precursor_mass_unit" argument="-tolerance:precursor_mass_unit" type="select" optional="false" display="radio" label="Unit of precursor mass tolerance" help="">
+      <param name="precursor_mass_unit" argument="-tolerance:precursor_mass_unit" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="precursor_mass_unit"/>
       </param>
       <param name="precursor_true_tolerance" argument="-tolerance:precursor_true_tolerance" type="float" optional="false" min="0.0" value="0.0" label="True precursor mass tolerance (window is +/- this value)" help="Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches"/>
-      <param name="precursor_true_unit" argument="-tolerance:precursor_true_unit" type="select" optional="false" display="radio" label="Unit of precursor true tolerance" help="">
+      <param name="precursor_true_unit" argument="-tolerance:precursor_true_unit" type="select" optional="false" label="Unit of precursor true tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="precursor_true_unit"/>
       </param>
       <param name="fragment_mass_tolerance" argument="-tolerance:fragment_mass_tolerance" type="float" optional="false" min="0.0" value="20.0" label="Fragment mass tolerance (window is +/- this value)" help=""/>
-      <param name="fragment_mass_unit" argument="-tolerance:fragment_mass_unit" type="select" optional="false" display="radio" label="Unit of fragment mass tolerance" help="">
+      <param name="fragment_mass_unit" argument="-tolerance:fragment_mass_unit" type="select" optional="false" label="Unit of fragment mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="fragment_mass_unit"/>
       </param>
-      <param name="isotope_error" argument="-tolerance:isotope_error" type="select" optional="false" display="radio" label="Isotope correction for MS/MS events triggered on isotopic peaks" help="Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12">
+      <param name="isotope_error" argument="-tolerance:isotope_error" type="select" optional="false" label="Isotope correction for MS/MS events triggered on isotopic peaks" help="Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12">
         <option value="0" selected="true">0</option>
         <option value="1">1</option>
         <option value="2">2</option>
@@ -135,7 +135,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="search_enzyme_nocutbefore" argument="-digest:search_enzyme_nocutbefore" type="text" optional="false" value="P" label="Residues that the enzyme will not cut before" help="">
         <expand macro="list_string_san" name="search_enzyme_nocutbefore"/>
       </param>
-      <param name="num_enzyme_termini" argument="-digest:num_enzyme_termini" type="select" optional="false" display="radio" label="Number of enzyme termini (non-enzymatic (0), semi (1), fully (2)" help="">
+      <param name="num_enzyme_termini" argument="-digest:num_enzyme_termini" type="select" optional="false" label="Number of enzyme termini (non-enzymatic (0), semi (1), fully (2)" help="">
         <option value="non-enzymatic">non-enzymatic</option>
         <option value="semi">semi</option>
         <option value="fully" selected="true">fully</option>
@@ -187,7 +187,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="minimum_ratio" argument="-spectrum:minimum_ratio" type="float" optional="false" min="0.0" max="1.0" value="0.0" label="Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensity" help=""/>
       <param name="clear_mz_range_min" argument="-spectrum:clear_mz_range_min" type="float" optional="false" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (minimum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/>
       <param name="clear_mz_range_max" argument="-spectrum:clear_mz_range_max" type="float" optional="false" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (maximum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/>
-      <param name="max_fragment_charge" argument="-spectrum:max_fragment_charge" type="select" optional="false" display="radio" label="Maximum charge state for theoretical fragments to match" help="">
+      <param name="max_fragment_charge" argument="-spectrum:max_fragment_charge" type="select" optional="false" label="Maximum charge state for theoretical fragments to match" help="">
         <option value="1">1</option>
         <option value="2" selected="true">2</option>
         <option value="3">3</option>
@@ -243,12 +243,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
         <expand macro="list_string_san" name="decoy_string"/>
       </param>
-      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="false" display="radio" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="false" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
         <option value="prefix" selected="true">prefix</option>
         <option value="suffix">suffix</option>
         <expand macro="list_string_san" name="decoy_string_position"/>
       </param>
-      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="false" display="radio" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="false" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
         <option value="error">error</option>
         <option value="warn" selected="true">warn</option>
         <option value="silent">silent</option>
@@ -257,7 +257,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
       <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
       <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
-      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="false" display="radio" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="false" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
         <option value="error" selected="true">error</option>
         <option value="warn">warn</option>
         <option value="remove">remove</option>
@@ -305,7 +305,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Trypsin">Trypsin</option>
           <expand macro="list_string_san" name="name"/>
         </param>
-        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="false" display="radio" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="false" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
           <option value="auto" selected="true">auto</option>
           <option value="full">full</option>
           <option value="semi">semi</option>
diff --git a/tools/openms/MSGFPlusAdapter.xml b/tools/openms/MSGFPlusAdapter.xml
index 7fc0a19e7..b7fbd0198 100644
--- a/tools/openms/MSGFPlusAdapter.xml
+++ b/tools/openms/MSGFPlusAdapter.xml
@@ -72,7 +72,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-in" type="data" format="mgf,ms2,mzml,mzxml" optional="false" label="Input file (MS-GF+ parameter '-s')" help=" select mgf,ms2,mzml,mzxml data sets(s)"/>
     <param argument="-database" type="data" format="fasta" optional="false" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/>
     <param argument="-precursor_mass_tolerance" type="float" optional="false" value="10.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help=""/>
-    <param argument="-precursor_error_units" type="select" optional="false" display="radio" label="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" help="">
+    <param argument="-precursor_error_units" type="select" optional="false" label="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" help="">
       <option value="Da">Da</option>
       <option value="ppm" selected="true">ppm</option>
       <expand macro="list_string_san" name="precursor_error_units"/>
@@ -80,14 +80,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-isotope_error_range" type="text" optional="false" value="0,1" label="Range of allowed isotope peak errors (MS-GF+ parameter '-ti')" help="Takes into account the error introduced by choosing a non-monoisotopic peak for fragmentation. Combined with 'precursor_mass_tolerance'/'precursor_error_units', this determines the actual precursor mass tolerance. E.g. for experimental mass 'exp' and calculated mass 'calc', '-precursor_mass_tolerance 20 -precursor_error_units ppm -isotope_error_range -1,2' tests '|exp - calc - n * 1.00335 Da| &lt; 20 ppm' for n = -1, 0, 1, 2">
       <expand macro="list_string_san" name="isotope_error_range"/>
     </param>
-    <param argument="-fragment_method" type="select" optional="false" display="radio" label="Fragmentation method ('from_spectrum' relies on spectrum meta data and uses CID as fallback option; MS-GF+ parameter '-m')" help="">
+    <param argument="-fragment_method" type="select" optional="false" label="Fragmentation method ('from_spectrum' relies on spectrum meta data and uses CID as fallback option; MS-GF+ parameter '-m')" help="">
       <option value="from_spectrum" selected="true">from_spectrum</option>
       <option value="CID">CID</option>
       <option value="ETD">ETD</option>
       <option value="HCD">HCD</option>
       <expand macro="list_string_san" name="fragment_method"/>
     </param>
-    <param argument="-instrument" type="select" optional="false" display="radio" label="Instrument that generated the data ('low_res'/'high_res' refer to LCQ and LTQ instruments; MS-GF+ parameter '-inst')" help="">
+    <param argument="-instrument" type="select" optional="false" label="Instrument that generated the data ('low_res'/'high_res' refer to LCQ and LTQ instruments; MS-GF+ parameter '-inst')" help="">
       <option value="low_res" selected="true">low_res</option>
       <option value="high_res">high_res</option>
       <option value="TOF">TOF</option>
@@ -116,7 +116,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="none">none</option>
       <expand macro="list_string_san" name="protocol"/>
     </param>
-    <param argument="-tryptic" type="select" optional="false" display="radio" label="Level of cleavage specificity required (MS-GF+ parameter '-ntt')" help="">
+    <param argument="-tryptic" type="select" optional="false" label="Level of cleavage specificity required (MS-GF+ parameter '-ntt')" help="">
       <option value="non">non</option>
       <option value="semi">semi</option>
       <option value="fully" selected="true">fully</option>
@@ -6071,12 +6071,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
         <expand macro="list_string_san" name="decoy_string"/>
       </param>
-      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="false" display="radio" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="false" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
         <option value="prefix" selected="true">prefix</option>
         <option value="suffix">suffix</option>
         <expand macro="list_string_san" name="decoy_string_position"/>
       </param>
-      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="false" display="radio" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="false" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
         <option value="error">error</option>
         <option value="warn" selected="true">warn</option>
         <option value="silent">silent</option>
@@ -6085,7 +6085,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
       <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
       <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
-      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="false" display="radio" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="false" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
         <option value="error" selected="true">error</option>
         <option value="warn">warn</option>
         <option value="remove">remove</option>
@@ -6133,7 +6133,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="proline endopeptidase">proline endopeptidase</option>
           <expand macro="list_string_san" name="name"/>
         </param>
-        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="false" display="radio" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="false" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
           <option value="auto" selected="true">auto</option>
           <option value="full">full</option>
           <option value="semi">semi</option>
diff --git a/tools/openms/MSstatsConverter.xml b/tools/openms/MSstatsConverter.xml
index a56e92f1d..34d271102 100644
--- a/tools/openms/MSstatsConverter.xml
+++ b/tools/openms/MSstatsConverter.xml
@@ -65,7 +65,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   <inputs>
     <param argument="-in" type="data" format="consensusxml" optional="false" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
     <param argument="-in_design" type="data" format="tabular" optional="false" label="Experimental Design file" help=" select tabular data sets(s)"/>
-    <param argument="-method" type="select" optional="false" display="radio" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help="">
+    <param argument="-method" type="select" optional="false" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help="">
       <option value="LFQ" selected="true">LFQ</option>
       <option value="ISO">ISO</option>
       <expand macro="list_string_san" name="method"/>
diff --git a/tools/openms/MapAlignerIdentification.xml b/tools/openms/MapAlignerIdentification.xml
index df073bc9a..a27cd9361 100644
--- a/tools/openms/MapAlignerIdentification.xml
+++ b/tools/openms/MapAlignerIdentification.xml
@@ -112,7 +112,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param name="use_adducts" argument="-algorithm:use_adducts" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If IDs contain adducts, treat differently adducted variants of the same molecule as different" help=""/>
     </section>
     <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="false" display="radio" label="Type of model" help="">
+      <param name="type" argument="-model:type" type="select" optional="false" label="Type of model" help="">
         <option value="linear">linear</option>
         <option value="b_spline" selected="true">b_spline</option>
         <option value="lowess">lowess</option>
@@ -121,14 +121,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </param>
       <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
         <param name="symmetric_regression" argument="-model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
-        <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="false" display="radio" label="Weight x values" help="">
+        <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="false" label="Weight x values" help="">
           <option value="1/x">1/x</option>
           <option value="1/x2">1/x2</option>
           <option value="ln(x)">ln(x)</option>
           <option value="x" selected="true">x</option>
           <expand macro="list_string_san" name="x_weight"/>
         </param>
-        <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="false" display="radio" label="Weight y values" help="">
+        <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="false" label="Weight y values" help="">
           <option value="1/y">1/y</option>
           <option value="1/y2">1/y2</option>
           <option value="ln(y)">ln(y)</option>
@@ -143,7 +143,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
         <param name="wavelength" argument="-model:b_spline:wavelength" type="float" optional="false" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
         <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" optional="false" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
-        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" optional="false" display="radio" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
+        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" optional="false" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
           <option value="linear" selected="true">linear</option>
           <option value="b_spline">b_spline</option>
           <option value="constant">constant</option>
@@ -156,13 +156,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="span" argument="-model:lowess:span" type="float" optional="false" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
         <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" optional="false" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
         <param name="delta" argument="-model:lowess:delta" type="float" optional="false" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
-        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" optional="false" display="radio" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
+        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" optional="false" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" optional="false" display="radio" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
+        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" optional="false" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
           <option value="two-point-linear">two-point-linear</option>
           <option value="four-point-linear" selected="true">four-point-linear</option>
           <option value="global-linear">global-linear</option>
@@ -170,13 +170,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         </param>
       </section>
       <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
-        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="false" display="radio" label="Type of interpolation to apply" help="">
+        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="false" label="Type of interpolation to apply" help="">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" optional="false" display="radio" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
+        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" optional="false" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
           <option value="two-point-linear" selected="true">two-point-linear</option>
           <option value="four-point-linear">four-point-linear</option>
           <option value="global-linear">global-linear</option>
diff --git a/tools/openms/MapAlignerPoseClustering.xml b/tools/openms/MapAlignerPoseClustering.xml
index 36f8e80f9..9a494506d 100644
--- a/tools/openms/MapAlignerPoseClustering.xml
+++ b/tools/openms/MapAlignerPoseClustering.xml
@@ -118,7 +118,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         </section>
         <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
           <param name="max_difference" argument="-algorithm:pairfinder:distance_MZ:max_difference" type="float" optional="false" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
-          <param name="unit" argument="-algorithm:pairfinder:distance_MZ:unit" type="select" optional="false" display="radio" label="Unit of the 'max_difference' paramete" help="">
+          <param name="unit" argument="-algorithm:pairfinder:distance_MZ:unit" type="select" optional="false" label="Unit of the 'max_difference' paramete" help="">
             <option value="Da" selected="true">Da</option>
             <option value="ppm">ppm</option>
             <expand macro="list_string_san" name="unit"/>
@@ -129,7 +129,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
           <param name="exponent" argument="-algorithm:pairfinder:distance_intensity:exponent" type="float" optional="false" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
           <param name="weight" argument="-algorithm:pairfinder:distance_intensity:weight" type="float" optional="false" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
-          <param name="log_transform" argument="-algorithm:pairfinder:distance_intensity:log_transform" type="select" optional="false" display="radio" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
+          <param name="log_transform" argument="-algorithm:pairfinder:distance_intensity:log_transform" type="select" optional="false" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
             <option value="enabled">enabled</option>
             <option value="disabled" selected="true">disabled</option>
             <expand macro="list_string_san" name="log_transform"/>
diff --git a/tools/openms/MapAlignerSpectrum.xml b/tools/openms/MapAlignerSpectrum.xml
index cb4755e4d..339da48cc 100644
--- a/tools/openms/MapAlignerSpectrum.xml
+++ b/tools/openms/MapAlignerSpectrum.xml
@@ -87,14 +87,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param name="bucketsize" argument="-algorithm:bucketsize" type="integer" optional="false" min="1" value="100" label="Defines the numbers of buckets" help="It is a quantize of the interval of those points, which defines the main alignment (match points). These points have to filtered, to reduce the amount of points for the calculating a smoother spline curve"/>
       <param name="anchorpoints" argument="-algorithm:anchorpoints" type="integer" optional="false" min="1" max="100" value="100" label="Defines the percent of numbers of match points which a selected from one bucket" help="The high score pairs are previously selected. The reduction of match points helps to get a smoother spline curve"/>
       <param name="mismatchscore" argument="-algorithm:mismatchscore" type="float" optional="false" max="0.0" value="-5.0" label="Defines the score of two spectra if they have no similarity to each othe" help=""/>
-      <param name="scorefunction" argument="-algorithm:scorefunction" type="select" optional="false" display="radio" label="The score function is the core of an alignment" help="The success of an alignment depends mostly of the elected score function. The score function return the similarity of two spectra. The score influence defines later the way of possible traceback. There are multiple spectra similarity scores available">
+      <param name="scorefunction" argument="-algorithm:scorefunction" type="select" optional="false" label="The score function is the core of an alignment" help="The success of an alignment depends mostly of the elected score function. The score function return the similarity of two spectra. The score influence defines later the way of possible traceback. There are multiple spectra similarity scores available">
         <option value="SteinScottImproveScore" selected="true">SteinScottImproveScore</option>
         <option value="ZhangSimilarityScore">ZhangSimilarityScore</option>
         <expand macro="list_string_san" name="scorefunction"/>
       </param>
     </section>
     <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="false" display="radio" label="Type of model" help="">
+      <param name="type" argument="-model:type" type="select" optional="false" label="Type of model" help="">
         <option value="linear">linear</option>
         <option value="b_spline">b_spline</option>
         <option value="lowess">lowess</option>
@@ -103,14 +103,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </param>
       <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
         <param name="symmetric_regression" argument="-model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
-        <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="false" display="radio" label="Weight x values" help="">
+        <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="false" label="Weight x values" help="">
           <option value="1/x">1/x</option>
           <option value="1/x2">1/x2</option>
           <option value="ln(x)">ln(x)</option>
           <option value="x" selected="true">x</option>
           <expand macro="list_string_san" name="x_weight"/>
         </param>
-        <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="false" display="radio" label="Weight y values" help="">
+        <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="false" label="Weight y values" help="">
           <option value="1/y">1/y</option>
           <option value="1/y2">1/y2</option>
           <option value="ln(y)">ln(y)</option>
@@ -125,7 +125,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
         <param name="wavelength" argument="-model:b_spline:wavelength" type="float" optional="false" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
         <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" optional="false" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
-        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" optional="false" display="radio" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
+        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" optional="false" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
           <option value="linear" selected="true">linear</option>
           <option value="b_spline">b_spline</option>
           <option value="constant">constant</option>
@@ -138,13 +138,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="span" argument="-model:lowess:span" type="float" optional="false" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
         <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" optional="false" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
         <param name="delta" argument="-model:lowess:delta" type="float" optional="false" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
-        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" optional="false" display="radio" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
+        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" optional="false" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" optional="false" display="radio" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
+        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" optional="false" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
           <option value="two-point-linear">two-point-linear</option>
           <option value="four-point-linear" selected="true">four-point-linear</option>
           <option value="global-linear">global-linear</option>
@@ -152,13 +152,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         </param>
       </section>
       <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
-        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="false" display="radio" label="Type of interpolation to apply" help="">
+        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="false" label="Type of interpolation to apply" help="">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" optional="false" display="radio" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
+        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" optional="false" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
           <option value="two-point-linear" selected="true">two-point-linear</option>
           <option value="four-point-linear">four-point-linear</option>
           <option value="global-linear">global-linear</option>
diff --git a/tools/openms/MapAlignerTreeGuided.xml b/tools/openms/MapAlignerTreeGuided.xml
index 4ee2ff20a..ea0884dfa 100644
--- a/tools/openms/MapAlignerTreeGuided.xml
+++ b/tools/openms/MapAlignerTreeGuided.xml
@@ -81,7 +81,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </when>
     </conditional>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="model_type" argument="-algorithm:model_type" type="select" optional="false" display="radio" label="Options to control the modeling of retention time transformations from data" help="">
+      <param name="model_type" argument="-algorithm:model_type" type="select" optional="false" label="Options to control the modeling of retention time transformations from data" help="">
         <option value="linear">linear</option>
         <option value="b_spline" selected="true">b_spline</option>
         <option value="lowess">lowess</option>
@@ -89,7 +89,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <expand macro="list_string_san" name="model_type"/>
       </param>
       <section name="model" title="" help="" expanded="false">
-        <param name="type" argument="-algorithm:model:type" type="select" optional="false" display="radio" label="Type of model" help="">
+        <param name="type" argument="-algorithm:model:type" type="select" optional="false" label="Type of model" help="">
           <option value="linear">linear</option>
           <option value="b_spline" selected="true">b_spline</option>
           <option value="lowess">lowess</option>
@@ -98,14 +98,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         </param>
         <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
           <param name="symmetric_regression" argument="-algorithm:model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
-          <param name="x_weight" argument="-algorithm:model:linear:x_weight" type="select" optional="false" display="radio" label="Weight x values" help="">
+          <param name="x_weight" argument="-algorithm:model:linear:x_weight" type="select" optional="false" label="Weight x values" help="">
             <option value="1/x">1/x</option>
             <option value="1/x2">1/x2</option>
             <option value="ln(x)">ln(x)</option>
             <option value="x" selected="true">x</option>
             <expand macro="list_string_san" name="x_weight"/>
           </param>
-          <param name="y_weight" argument="-algorithm:model:linear:y_weight" type="select" optional="false" display="radio" label="Weight y values" help="">
+          <param name="y_weight" argument="-algorithm:model:linear:y_weight" type="select" optional="false" label="Weight y values" help="">
             <option value="1/y">1/y</option>
             <option value="1/y2">1/y2</option>
             <option value="ln(y)">ln(y)</option>
@@ -120,7 +120,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
           <param name="wavelength" argument="-algorithm:model:b_spline:wavelength" type="float" optional="false" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
           <param name="num_nodes" argument="-algorithm:model:b_spline:num_nodes" type="integer" optional="false" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
-          <param name="extrapolate" argument="-algorithm:model:b_spline:extrapolate" type="select" optional="false" display="radio" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
+          <param name="extrapolate" argument="-algorithm:model:b_spline:extrapolate" type="select" optional="false" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
             <option value="linear" selected="true">linear</option>
             <option value="b_spline">b_spline</option>
             <option value="constant">constant</option>
@@ -133,13 +133,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <param name="span" argument="-algorithm:model:lowess:span" type="float" optional="false" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
           <param name="num_iterations" argument="-algorithm:model:lowess:num_iterations" type="integer" optional="false" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
           <param name="delta" argument="-algorithm:model:lowess:delta" type="float" optional="false" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
-          <param name="interpolation_type" argument="-algorithm:model:lowess:interpolation_type" type="select" optional="false" display="radio" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
+          <param name="interpolation_type" argument="-algorithm:model:lowess:interpolation_type" type="select" optional="false" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
             <option value="linear">linear</option>
             <option value="cspline" selected="true">cspline</option>
             <option value="akima">akima</option>
             <expand macro="list_string_san" name="interpolation_type"/>
           </param>
-          <param name="extrapolation_type" argument="-algorithm:model:lowess:extrapolation_type" type="select" optional="false" display="radio" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
+          <param name="extrapolation_type" argument="-algorithm:model:lowess:extrapolation_type" type="select" optional="false" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
             <option value="two-point-linear">two-point-linear</option>
             <option value="four-point-linear" selected="true">four-point-linear</option>
             <option value="global-linear">global-linear</option>
@@ -147,13 +147,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           </param>
         </section>
         <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
-          <param name="interpolation_type" argument="-algorithm:model:interpolated:interpolation_type" type="select" optional="false" display="radio" label="Type of interpolation to apply" help="">
+          <param name="interpolation_type" argument="-algorithm:model:interpolated:interpolation_type" type="select" optional="false" label="Type of interpolation to apply" help="">
             <option value="linear">linear</option>
             <option value="cspline" selected="true">cspline</option>
             <option value="akima">akima</option>
             <expand macro="list_string_san" name="interpolation_type"/>
           </param>
-          <param name="extrapolation_type" argument="-algorithm:model:interpolated:extrapolation_type" type="select" optional="false" display="radio" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
+          <param name="extrapolation_type" argument="-algorithm:model:interpolated:extrapolation_type" type="select" optional="false" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
             <option value="two-point-linear" selected="true">two-point-linear</option>
             <option value="four-point-linear">four-point-linear</option>
             <option value="global-linear">global-linear</option>
diff --git a/tools/openms/MapRTTransformer.xml b/tools/openms/MapRTTransformer.xml
index 4f4562dc2..a91f92427 100644
--- a/tools/openms/MapRTTransformer.xml
+++ b/tools/openms/MapRTTransformer.xml
@@ -80,14 +80,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
       <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
         <param name="symmetric_regression" argument="-model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
-        <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="false" display="radio" label="Weight x values" help="">
+        <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="false" label="Weight x values" help="">
           <option value="1/x">1/x</option>
           <option value="1/x2">1/x2</option>
           <option value="ln(x)">ln(x)</option>
           <option value="x" selected="true">x</option>
           <expand macro="list_string_san" name="x_weight"/>
         </param>
-        <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="false" display="radio" label="Weight y values" help="">
+        <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="false" label="Weight y values" help="">
           <option value="1/y">1/y</option>
           <option value="1/y2">1/y2</option>
           <option value="ln(y)">ln(y)</option>
@@ -102,7 +102,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
         <param name="wavelength" argument="-model:b_spline:wavelength" type="float" optional="false" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
         <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" optional="false" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
-        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" optional="false" display="radio" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
+        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" optional="false" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
           <option value="linear" selected="true">linear</option>
           <option value="b_spline">b_spline</option>
           <option value="constant">constant</option>
@@ -115,13 +115,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="span" argument="-model:lowess:span" type="float" optional="false" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
         <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" optional="false" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
         <param name="delta" argument="-model:lowess:delta" type="float" optional="false" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
-        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" optional="false" display="radio" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
+        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" optional="false" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" optional="false" display="radio" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
+        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" optional="false" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
           <option value="two-point-linear">two-point-linear</option>
           <option value="four-point-linear" selected="true">four-point-linear</option>
           <option value="global-linear">global-linear</option>
@@ -129,13 +129,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         </param>
       </section>
       <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
-        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="false" display="radio" label="Type of interpolation to apply" help="">
+        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="false" label="Type of interpolation to apply" help="">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" optional="false" display="radio" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
+        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" optional="false" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
           <option value="two-point-linear" selected="true">two-point-linear</option>
           <option value="four-point-linear">four-point-linear</option>
           <option value="global-linear">global-linear</option>
diff --git a/tools/openms/MascotAdapter.xml b/tools/openms/MascotAdapter.xml
index 4a8d24f29..372a78d82 100644
--- a/tools/openms/MascotAdapter.xml
+++ b/tools/openms/MascotAdapter.xml
@@ -39,7 +39,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="mascotxml,mzdata" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="output file type (for TOPPAS)" help="">
+    <param argument="-out_type" type="select" optional="false" label="output file type (for TOPPAS)" help="">
       <option value="idXML">idxml</option>
       <option value="mgf">mgf</option>
       <expand macro="list_string_san" name="out_type"/>
@@ -170,7 +170,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-boundary" type="text" optional="true" value="" label="MIME boundary for mascot output format" help="">
       <expand macro="list_string_san" name="boundary"/>
     </param>
-    <param argument="-mass_type" type="select" optional="false" display="radio" label="mass type" help="">
+    <param argument="-mass_type" type="select" optional="false" label="mass type" help="">
       <option value="Monoisotopic" selected="true">Monoisotopic</option>
       <option value="Average">Average</option>
       <expand macro="list_string_san" name="mass_type"/>
diff --git a/tools/openms/MascotAdapterOnline.xml b/tools/openms/MascotAdapterOnline.xml
index 9e995e93e..b3a6881ec 100644
--- a/tools/openms/MascotAdapterOnline.xml
+++ b/tools/openms/MascotAdapterOnline.xml
@@ -43,7 +43,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="database" argument="-Mascot_parameters:database" type="text" optional="false" value="MSDB" label="Name of the sequence database" help="">
         <expand macro="list_string_san" name="database"/>
       </param>
-      <param name="search_type" argument="-Mascot_parameters:search_type" type="select" optional="false" display="radio" label="Name of the search type for the query" help="">
+      <param name="search_type" argument="-Mascot_parameters:search_type" type="select" optional="false" label="Name of the search type for the query" help="">
         <option value="MIS" selected="true">MIS</option>
         <option value="SQ">SQ</option>
         <option value="PMF">PMF</option>
@@ -57,7 +57,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
       <param name="missed_cleavages" argument="-Mascot_parameters:missed_cleavages" type="integer" optional="false" min="0" value="1" label="Number of missed cleavages allowed for the enzyme" help=""/>
       <param name="precursor_mass_tolerance" argument="-Mascot_parameters:precursor_mass_tolerance" type="float" optional="false" min="0.0" value="3.0" label="Tolerance of the precursor peaks" help=""/>
-      <param name="precursor_error_units" argument="-Mascot_parameters:precursor_error_units" type="select" optional="false" display="radio" label="Units of the precursor mass tolerance" help="">
+      <param name="precursor_error_units" argument="-Mascot_parameters:precursor_error_units" type="select" optional="false" label="Units of the precursor mass tolerance" help="">
         <option value="%">%</option>
         <option value="ppm">ppm</option>
         <option value="mmu">mmu</option>
@@ -65,7 +65,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <expand macro="list_string_san" name="precursor_error_units"/>
       </param>
       <param name="fragment_mass_tolerance" argument="-Mascot_parameters:fragment_mass_tolerance" type="float" optional="false" min="0.0" value="0.3" label="Tolerance of the peaks in the fragment spectrum" help=""/>
-      <param name="fragment_error_units" argument="-Mascot_parameters:fragment_error_units" type="select" optional="false" display="radio" label="Units of the fragment peaks tolerance" help="">
+      <param name="fragment_error_units" argument="-Mascot_parameters:fragment_error_units" type="select" optional="false" label="Units of the fragment peaks tolerance" help="">
         <option value="mmu">mmu</option>
         <option value="Da" selected="true">Da</option>
         <expand macro="list_string_san" name="fragment_error_units"/>
@@ -6013,7 +6013,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="special_modifications" argument="-Mascot_parameters:special_modifications" type="text" optional="false" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)" label="Modifications with specificity groups that are used by Mascot and have to be treated specially" help="">
         <expand macro="list_string_san" name="special_modifications"/>
       </param>
-      <param name="mass_type" argument="-Mascot_parameters:mass_type" type="select" optional="false" display="radio" label="Defines the mass type, either monoisotopic or average" help="">
+      <param name="mass_type" argument="-Mascot_parameters:mass_type" type="select" optional="false" label="Defines the mass type, either monoisotopic or average" help="">
         <option value="monoisotopic" selected="true">monoisotopic</option>
         <option value="average">average</option>
         <expand macro="list_string_san" name="mass_type"/>
diff --git a/tools/openms/MassCalculator.xml b/tools/openms/MassCalculator.xml
index f158b0e92..982216956 100644
--- a/tools/openms/MassCalculator.xml
+++ b/tools/openms/MassCalculator.xml
@@ -59,7 +59,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-charge" type="text" optional="false" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_integer_valsan" name="charge"/>
     </param>
-    <param argument="-format" type="select" optional="false" display="radio" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="">
+    <param argument="-format" type="select" optional="false" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="">
       <option value="list" selected="true">list</option>
       <option value="table">table</option>
       <option value="mass_only">mass_only</option>
diff --git a/tools/openms/MassTraceExtractor.xml b/tools/openms/MassTraceExtractor.xml
index 02d8dfdf4..145d57a19 100644
--- a/tools/openms/MassTraceExtractor.xml
+++ b/tools/openms/MassTraceExtractor.xml
@@ -39,7 +39,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="mzml" optional="false" label="input centroided mzML file" help=" select mzml data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="output file type -- default: determined from file extension or content" help="">
+    <param argument="-out_type" type="select" optional="false" label="output file type -- default: determined from file extension or content" help="">
       <option value="consensusXML">consensusxml</option>
       <option value="featureXML">featurexml</option>
       <expand macro="list_string_san" name="out_type"/>
@@ -53,13 +53,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="mtd" title="" help="" expanded="false">
         <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" optional="false" value="20.0" label="Allowed mass deviation (in ppm)" help=""/>
         <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/>
-        <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" optional="false" display="radio" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
+        <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" optional="false" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
           <option value="area" selected="true">area</option>
           <option value="median">median</option>
           <option value="max_height">max_height</option>
           <expand macro="list_string_san" name="quant_method"/>
         </param>
-        <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" optional="false" display="radio" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
+        <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" optional="false" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
           <option value="outlier" selected="true">outlier</option>
           <option value="sample_rate">sample_rate</option>
           <expand macro="list_string_san" name="trace_termination_criterion"/>
@@ -70,7 +70,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" optional="false" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/>
       </section>
       <section name="epd" title="" help="" expanded="false">
-        <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" optional="false" display="radio" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
+        <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" optional="false" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
           <option value="off">off</option>
           <option value="fixed" selected="true">fixed</option>
           <option value="auto">auto</option>
diff --git a/tools/openms/MetaProSIP.xml b/tools/openms/MetaProSIP.xml
index 4d686581c..67e716b6f 100644
--- a/tools/openms/MetaProSIP.xml
+++ b/tools/openms/MetaProSIP.xml
@@ -60,7 +60,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-xic_threshold" type="float" optional="false" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
     <param argument="-decomposition_threshold" type="float" optional="false" value="0.7" label="Minimum R-squared of decomposition that must be achieved for a peptide to be reported" help=""/>
     <param argument="-weight_merge_window" type="float" optional="false" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help=""/>
-    <param argument="-plot_extension" type="select" optional="false" display="radio" label="Extension used for plots (png|svg|pdf)" help="">
+    <param argument="-plot_extension" type="select" optional="false" label="Extension used for plots (png|svg|pdf)" help="">
       <option value="png" selected="true">png</option>
       <option value="svg">svg</option>
       <option value="pdf">pdf</option>
@@ -69,7 +69,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-qc_output_directory" type="text" optional="true" value="" label="Output directory for the quality report" help="">
       <expand macro="list_string_san" name="qc_output_directory"/>
     </param>
-    <param argument="-labeling_element" type="select" optional="false" display="radio" label="Which element (single letter code) is labeled" help="">
+    <param argument="-labeling_element" type="select" optional="false" label="Which element (single letter code) is labeled" help="">
       <option value="C" selected="true">C</option>
       <option value="N">N</option>
       <option value="H">H</option>
@@ -91,7 +91,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param argument="-observed_peak_fraction" type="float" optional="false" value="0.5" label="Fraction of observed/expected peaks" help=""/>
       <param argument="-min_consecutive_isotopes" type="integer" optional="false" value="2" label="Minimum number of consecutive isotopic intensities needed" help=""/>
       <param argument="-score_plot_yaxis_min" type="float" optional="false" value="0.0" label="The minimum value of the score axis" help="Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/>
-      <param argument="-collect_method" type="select" optional="false" display="radio" label="How RIAs are collected" help="">
+      <param argument="-collect_method" type="select" optional="false" label="How RIAs are collected" help="">
         <option value="correlation_maximum" selected="true">correlation_maximum</option>
         <option value="decomposition_maximum">decomposition_maximum</option>
         <expand macro="list_string_san" name="collect_method"/>
diff --git a/tools/openms/MetaboliteSpectralMatcher.xml b/tools/openms/MetaboliteSpectralMatcher.xml
index 3a24e5848..2edbe0c17 100644
--- a/tools/openms/MetaboliteSpectralMatcher.xml
+++ b/tools/openms/MetaboliteSpectralMatcher.xml
@@ -60,17 +60,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <param name="prec_mass_error_value" argument="-algorithm:prec_mass_error_value" type="float" optional="false" value="100.0" label="Error allowed for precursor ion mass" help=""/>
       <param name="frag_mass_error_value" argument="-algorithm:frag_mass_error_value" type="float" optional="false" value="500.0" label="Error allowed for product ions" help=""/>
-      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="false" display="radio" label="Unit of mass error (ppm or Da)" help="">
+      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="false" label="Unit of mass error (ppm or Da)" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_error_unit"/>
       </param>
-      <param name="report_mode" argument="-algorithm:report_mode" type="select" optional="false" display="radio" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="">
+      <param name="report_mode" argument="-algorithm:report_mode" type="select" optional="false" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="">
         <option value="top3" selected="true">top3</option>
         <option value="best">best</option>
         <expand macro="list_string_san" name="report_mode"/>
       </param>
-      <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="false" display="radio" label="Positive or negative ionization mode?" help="">
+      <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="false" label="Positive or negative ionization mode?" help="">
         <option value="positive" selected="true">positive</option>
         <option value="negative">negative</option>
         <expand macro="list_string_san" name="ionization_mode"/>
diff --git a/tools/openms/MzMLSplitter.xml b/tools/openms/MzMLSplitter.xml
index b88e9c55d..7eb19fa36 100644
--- a/tools/openms/MzMLSplitter.xml
+++ b/tools/openms/MzMLSplitter.xml
@@ -40,7 +40,7 @@ out/
     <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
     <param argument="-parts" type="integer" optional="false" min="1" value="1" label="Number of parts to split into (takes precedence over 'size' if set)" help=""/>
     <param argument="-size" type="integer" optional="false" min="0" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help=""/>
-    <param argument="-unit" type="select" optional="false" display="radio" label="Unit for 'size' (base 1024)" help="">
+    <param argument="-unit" type="select" optional="false" label="Unit for 'size' (base 1024)" help="">
       <option value="KB">KB</option>
       <option value="MB" selected="true">MB</option>
       <option value="GB">GB</option>
diff --git a/tools/openms/NoiseFilterGaussian.xml b/tools/openms/NoiseFilterGaussian.xml
index a86ec47b3..c6c198886 100644
--- a/tools/openms/NoiseFilterGaussian.xml
+++ b/tools/openms/NoiseFilterGaussian.xml
@@ -46,7 +46,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="write_log_messages" argument="-algorithm:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="true: Warn if no signal was found by the Gauss filter algorithm" help=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-processOption" type="select" optional="false" display="radio" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
+      <param argument="-processOption" type="select" optional="false" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
         <option value="inmemory" selected="true">inmemory</option>
         <option value="lowmemory">lowmemory</option>
         <expand macro="list_string_san" name="processOption"/>
diff --git a/tools/openms/NoiseFilterSGolay.xml b/tools/openms/NoiseFilterSGolay.xml
index 3c3a0ea27..166394973 100644
--- a/tools/openms/NoiseFilterSGolay.xml
+++ b/tools/openms/NoiseFilterSGolay.xml
@@ -44,7 +44,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="polynomial_order" argument="-algorithm:polynomial_order" type="integer" optional="false" value="4" label="Order or the polynomial that is fitted" help=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-processOption" type="select" optional="false" display="radio" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
+      <param argument="-processOption" type="select" optional="false" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
         <option value="inmemory" selected="true">inmemory</option>
         <option value="lowmemory">lowmemory</option>
         <expand macro="list_string_san" name="processOption"/>
diff --git a/tools/openms/NovorAdapter.xml b/tools/openms/NovorAdapter.xml
index eb2e3b822..4e6ade2d6 100644
--- a/tools/openms/NovorAdapter.xml
+++ b/tools/openms/NovorAdapter.xml
@@ -47,16 +47,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
-    <param argument="-enzyme" type="select" optional="false" display="radio" label="Digestion enzyme - currently only Trypsin is supported" help="">
+    <param argument="-enzyme" type="select" optional="false" label="Digestion enzyme - currently only Trypsin is supported" help="">
       <option value="Trypsin" selected="true">Trypsin</option>
       <expand macro="list_string_san" name="enzyme"/>
     </param>
-    <param argument="-fragmentation" type="select" optional="false" display="radio" label="Fragmentation method" help="">
+    <param argument="-fragmentation" type="select" optional="false" label="Fragmentation method" help="">
       <option value="CID" selected="true">CID</option>
       <option value="HCD">HCD</option>
       <expand macro="list_string_san" name="fragmentation"/>
     </param>
-    <param argument="-massAnalyzer" type="select" optional="false" display="radio" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
+    <param argument="-massAnalyzer" type="select" optional="false" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
       <option value="Trap" selected="true">Trap</option>
       <option value="TOF">TOF</option>
       <option value="FT">FT</option>
@@ -64,7 +64,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </param>
     <param argument="-fragment_mass_tolerance" type="float" optional="false" value="0.5" label="Fragmentation error tolerance  (Da)" help=""/>
     <param argument="-precursor_mass_tolerance" type="float" optional="false" value="15.0" label="Precursor error tolerance  (ppm or Da)" help=""/>
-    <param argument="-precursor_error_units" type="select" optional="false" display="radio" label="Unit of precursor mass tolerance" help="">
+    <param argument="-precursor_error_units" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
       <expand macro="list_string_san" name="precursor_error_units"/>
@@ -127,7 +127,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Trimethyl (RK)">Trimethyl (RK)</option>
       <expand macro="list_string_san" name="fixed_modifications"/>
     </param>
-    <param argument="-forbiddenResidues" type="select" optional="true" multiple="true" display="checkboxes" label="Forbidden Resiudes" help="">
+    <param argument="-forbiddenResidues" type="select" optional="true" multiple="true" label="Forbidden Resiudes" help="">
       <option value="I">I</option>
       <option value="U">U</option>
       <expand macro="list_string_san" name="forbiddenResidues"/>
diff --git a/tools/openms/NucleicAcidSearchEngine.xml b/tools/openms/NucleicAcidSearchEngine.xml
index 0881c4797..bf1c0c00f 100644
--- a/tools/openms/NucleicAcidSearchEngine.xml
+++ b/tools/openms/NucleicAcidSearchEngine.xml
@@ -122,7 +122,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-digest" type="data" format="sqlite" optional="true" label="Input file: pre-digested sequence database" help="Can be used instead of 'database'. Sets all 'oligo:...' parameters select sqlite data sets(s)"/>
     <section name="precursor" title="Precursor (parent ion) options" help="" expanded="false">
       <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="false" value="10.0" label="Precursor mass tolerance (+/- around uncharged precursor mass)" help=""/>
-      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="false" display="radio" label="Unit of precursor mass tolerance" help="">
+      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
@@ -142,7 +142,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <section name="fragment" title="Fragment (Product Ion) Options" help="" expanded="false">
       <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="false" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/>
-      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="false" display="radio" label="Unit of fragment mass tolerance" help="">
+      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="false" label="Unit of fragment mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
diff --git a/tools/openms/OpenPepXL.xml b/tools/openms/OpenPepXL.xml
index 28172b02d..ffb233475 100644
--- a/tools/openms/OpenPepXL.xml
+++ b/tools/openms/OpenPepXL.xml
@@ -106,7 +106,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-decoy_prefix" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Set to true, if the decoy_string is a prefix of accessions in the protein database" help="Otherwise it is a suffix"/>
     <section name="precursor" title="Precursor filtering settings" help="" expanded="false">
       <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="false" value="10.0" label="Width of precursor mass tolerance window" help=""/>
-      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="false" display="radio" label="Unit of precursor mass tolerance" help="">
+      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
@@ -120,7 +120,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <section name="fragment" title="Fragment peak matching settings" help="" expanded="false">
       <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="false" value="20.0" label="Fragment mass tolerance" help=""/>
       <param name="mass_tolerance_xlinks" argument="-fragment:mass_tolerance_xlinks" type="float" optional="false" value="20.0" label="Fragment mass tolerance for cross-link ions" help=""/>
-      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="false" display="radio" label="Unit of fragment m" help="">
+      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="false" label="Unit of fragment m" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
@@ -6123,7 +6123,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <section name="algorithm" title="Additional algorithm settings" help="" expanded="false">
       <param name="number_top_hits" argument="-algorithm:number_top_hits" type="integer" optional="false" value="1" label="Number of top hits reported for each spectrum pai" help=""/>
-      <param name="deisotope" argument="-algorithm:deisotope" type="select" optional="false" display="radio" label="Set to true, if the input spectra should be deisotoped before any other processing steps" help="If set to auto the spectra will be deisotoped, if the fragment mass tolerance is &lt; 0.1 Da or &lt; 100 ppm (0.1 Da at a mass of 1000)">
+      <param name="deisotope" argument="-algorithm:deisotope" type="select" optional="false" label="Set to true, if the input spectra should be deisotoped before any other processing steps" help="If set to auto the spectra will be deisotoped, if the fragment mass tolerance is &lt; 0.1 Da or &lt; 100 ppm (0.1 Da at a mass of 1000)">
         <option value="true">true</option>
         <option value="false">false</option>
         <option value="auto" selected="true">auto</option>
diff --git a/tools/openms/OpenPepXLLF.xml b/tools/openms/OpenPepXLLF.xml
index 985575d83..285ef9998 100644
--- a/tools/openms/OpenPepXLLF.xml
+++ b/tools/openms/OpenPepXLLF.xml
@@ -101,7 +101,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-decoy_prefix" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Set to true, if the decoy_string is a prefix of accessions in the protein database" help="Otherwise it is a suffix"/>
     <section name="precursor" title="Precursor filtering settings" help="" expanded="false">
       <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="false" value="10.0" label="Width of precursor mass tolerance window" help=""/>
-      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="false" display="radio" label="Unit of precursor mass tolerance" help="">
+      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
@@ -115,7 +115,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <section name="fragment" title="Fragment peak matching settings" help="" expanded="false">
       <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="false" value="20.0" label="Fragment mass tolerance" help=""/>
       <param name="mass_tolerance_xlinks" argument="-fragment:mass_tolerance_xlinks" type="float" optional="false" value="20.0" label="Fragment mass tolerance for cross-link ions" help=""/>
-      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="false" display="radio" label="Unit of fragment m" help="">
+      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="false" label="Unit of fragment m" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
@@ -6117,7 +6117,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <section name="algorithm" title="Additional algorithm settings" help="" expanded="false">
       <param name="number_top_hits" argument="-algorithm:number_top_hits" type="integer" optional="false" value="1" label="Number of top hits reported for each spectrum pai" help=""/>
-      <param name="deisotope" argument="-algorithm:deisotope" type="select" optional="false" display="radio" label="Set to true, if the input spectra should be deisotoped before any other processing steps" help="If set to auto the spectra will be deisotoped, if the fragment mass tolerance is &lt; 0.1 Da or &lt; 100 ppm (0.1 Da at a mass of 1000)">
+      <param name="deisotope" argument="-algorithm:deisotope" type="select" optional="false" label="Set to true, if the input spectra should be deisotoped before any other processing steps" help="If set to auto the spectra will be deisotoped, if the fragment mass tolerance is &lt; 0.1 Da or &lt; 100 ppm (0.1 Da at a mass of 1000)">
         <option value="true">true</option>
         <option value="false">false</option>
         <option value="auto" selected="true">auto</option>
diff --git a/tools/openms/OpenSwathAnalyzer.xml b/tools/openms/OpenSwathAnalyzer.xml
index d94fe04e8..17729663e 100644
--- a/tools/openms/OpenSwathAnalyzer.xml
+++ b/tools/openms/OpenSwathAnalyzer.xml
@@ -85,7 +85,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </conditional>
     <param argument="-min_upper_edge_dist" type="float" optional="false" value="0.0" label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/>
     <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="false" display="radio" label="Type of model" help="">
+      <param name="type" argument="-model:type" type="select" optional="false" label="Type of model" help="">
         <option value="linear" selected="true">linear</option>
         <option value="b_spline">b_spline</option>
         <option value="interpolated">interpolated</option>
@@ -100,7 +100,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="rt_normalization_factor" argument="-algorithm:rt_normalization_factor" type="float" optional="false" value="1.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
       <param name="quantification_cutoff" argument="-algorithm:quantification_cutoff" type="float" optional="false" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
       <param name="write_convex_hull" argument="-algorithm:write_convex_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write out all points of all features into the featureXML" help=""/>
-      <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" type="select" optional="false" display="radio" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
+      <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" type="select" optional="false" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
         <option value="simple" selected="true">simple</option>
         <option value="resample">resample</option>
         <expand macro="list_string_san" name="spectrum_addition_method"/>
@@ -109,7 +109,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="spacing_for_spectra_resampling" argument="-algorithm:spacing_for_spectra_resampling" type="float" optional="false" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
       <param name="uis_threshold_sn" argument="-algorithm:uis_threshold_sn" type="integer" optional="false" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
       <param name="uis_threshold_peak_area" argument="-algorithm:uis_threshold_peak_area" type="integer" optional="false" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
-      <param name="scoring_model" argument="-algorithm:scoring_model" type="select" optional="false" display="radio" label="Scoring model to use" help="">
+      <param name="scoring_model" argument="-algorithm:scoring_model" type="select" optional="false" label="Scoring model to use" help="">
         <option value="default" selected="true">default</option>
         <option value="single_transition">single_transition</option>
         <expand macro="list_string_san" name="scoring_model"/>
@@ -120,12 +120,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" optional="false" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
         <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" optional="false" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
         <param name="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" optional="false" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
-        <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" type="select" optional="false" display="radio" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
+        <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" type="select" optional="false" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
           <option value="original" selected="true">original</option>
           <option value="smoothed">smoothed</option>
           <expand macro="list_string_san" name="peak_integration"/>
         </param>
-        <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" type="select" optional="false" display="radio" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
+        <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" type="select" optional="false" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
           <option value="none" selected="true">none</option>
           <option value="original">original</option>
           <option value="exact">exact</option>
@@ -140,7 +140,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="compute_peak_quality" argument="-algorithm:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
         <param name="compute_peak_shape_metrics" argument="-algorithm:TransitionGroupPicker:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
         <param name="compute_total_mi" argument="-algorithm:TransitionGroupPicker:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
-        <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" type="select" optional="false" display="radio" label="Method to use when selecting the best boundaries for peaks" help="">
+        <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" type="select" optional="false" label="Method to use when selecting the best boundaries for peaks" help="">
           <option value="largest" selected="true">largest</option>
           <option value="widest">widest</option>
           <expand macro="list_string_san" name="boundary_selection_method"/>
@@ -156,7 +156,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="sn_bin_count" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count" type="integer" optional="false" value="30" label="Signal to noise bin count" help=""/>
           <param name="write_sn_log_messages" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
           <param name="remove_overlapping_peaks" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/>
-          <param name="method" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:method" type="select" optional="false" display="radio" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
+          <param name="method" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:method" type="select" optional="false" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
             <option value="legacy">legacy</option>
             <option value="corrected" selected="true">corrected</option>
             <option value="crawdad">crawdad</option>
@@ -164,13 +164,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           </param>
         </section>
         <section name="PeakIntegrator" title="" help="" expanded="false">
-          <param name="integration_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" optional="false" display="radio" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
+          <param name="integration_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" optional="false" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
             <option value="intensity_sum" selected="true">intensity_sum</option>
             <option value="simpson">simpson</option>
             <option value="trapezoid">trapezoid</option>
             <expand macro="list_string_san" name="integration_type"/>
           </param>
-          <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" optional="false" display="radio" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
+          <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" optional="false" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
             <option value="base_to_base" selected="true">base_to_base</option>
             <option value="vertical_division">vertical_division</option>
             <option value="vertical_division_min">vertical_division_min</option>
@@ -182,7 +182,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="DIAScoring" title="" help="" expanded="false">
         <param name="dia_extraction_window" argument="-algorithm:DIAScoring:dia_extraction_window" type="float" optional="false" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
-        <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" optional="false" display="radio" label="DIA extraction window unit" help="">
+        <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" optional="false" label="DIA extraction window unit" help="">
           <option value="Th" selected="true">Th</option>
           <option value="ppm">ppm</option>
           <expand macro="list_string_san" name="dia_extraction_unit"/>
diff --git a/tools/openms/OpenSwathAssayGenerator.xml b/tools/openms/OpenSwathAssayGenerator.xml
index 6141c7d26..1ebae847d 100644
--- a/tools/openms/OpenSwathAssayGenerator.xml
+++ b/tools/openms/OpenSwathAssayGenerator.xml
@@ -55,7 +55,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-out_type" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
       <option value="TraML">traml</option>
       <option value="pqp">pqp</option>
       <option value="tsv">tabular (tsv)</option>
diff --git a/tools/openms/OpenSwathChromatogramExtractor.xml b/tools/openms/OpenSwathChromatogramExtractor.xml
index 755027619..3c39b4890 100644
--- a/tools/openms/OpenSwathChromatogramExtractor.xml
+++ b/tools/openms/OpenSwathChromatogramExtractor.xml
@@ -81,7 +81,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     <param argument="-is_swath" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if the data is SWATH data" help=""/>
     <param argument="-extract_MS1" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)" help=""/>
     <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="false" display="radio" label="Type of model" help="">
+      <param name="type" argument="-model:type" type="select" optional="false" label="Type of model" help="">
         <option value="linear" selected="true">linear</option>
         <option value="b_spline">b_spline</option>
         <option value="interpolated">interpolated</option>
@@ -91,7 +91,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-extraction_function" type="select" optional="false" display="radio" label="Function used to extract the signal" help="">
+      <param argument="-extraction_function" type="select" optional="false" label="Function used to extract the signal" help="">
         <option value="tophat" selected="true">tophat</option>
         <option value="bartlett">bartlett</option>
         <expand macro="list_string_san" name="extraction_function"/>
diff --git a/tools/openms/OpenSwathDecoyGenerator.xml b/tools/openms/OpenSwathDecoyGenerator.xml
index 1cc5d570b..42a340640 100644
--- a/tools/openms/OpenSwathDecoyGenerator.xml
+++ b/tools/openms/OpenSwathDecoyGenerator.xml
@@ -39,13 +39,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-out_type" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
       <option value="TraML">traml</option>
       <option value="pqp">pqp</option>
       <option value="tsv">tabular (tsv)</option>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-method" type="select" optional="false" display="radio" label="Decoy generation method" help="">
+    <param argument="-method" type="select" optional="false" label="Decoy generation method" help="">
       <option value="shuffle" selected="true">shuffle</option>
       <option value="pseudo-reverse">pseudo-reverse</option>
       <option value="reverse">reverse</option>
diff --git a/tools/openms/OpenSwathMzMLFileCacher.xml b/tools/openms/OpenSwathMzMLFileCacher.xml
index 1d9960a2b..284e13084 100644
--- a/tools/openms/OpenSwathMzMLFileCacher.xml
+++ b/tools/openms/OpenSwathMzMLFileCacher.xml
@@ -39,7 +39,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="mzml,sqmass" optional="false" label="Input mzML file" help=" select mzml,sqmass data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
+    <param argument="-out_type" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
       <option value="mzML">mzml</option>
       <option value="sqMass">sqmass</option>
       <expand macro="list_string_san" name="out_type"/>
diff --git a/tools/openms/OpenSwathRTNormalizer.xml b/tools/openms/OpenSwathRTNormalizer.xml
index 78687a283..3674b432d 100644
--- a/tools/openms/OpenSwathRTNormalizer.xml
+++ b/tools/openms/OpenSwathRTNormalizer.xml
@@ -77,7 +77,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     <param argument="-min_coverage" type="float" optional="false" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/>
     <param argument="-estimateBestPeptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization" help="Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (e.g. due to them being endogenous peptides or using a less curated list of peptides)"/>
     <section name="RTNormalization" title="Parameters for the RTNormalization" help="RT normalization and outlier detection can be done iteratively (by default) which removes one outlier per iteration or using the RANSAC algorithm" expanded="false">
-      <param name="outlierMethod" argument="-RTNormalization:outlierMethod" type="select" optional="false" display="radio" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
+      <param name="outlierMethod" argument="-RTNormalization:outlierMethod" type="select" optional="false" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
         <option value="iter_residual" selected="true">iter_residual</option>
         <option value="iter_jackknife">iter_jackknife</option>
         <option value="ransac">ransac</option>
@@ -95,7 +95,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param name="rt_normalization_factor" argument="-algorithm:rt_normalization_factor" type="float" optional="false" value="1.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
       <param name="quantification_cutoff" argument="-algorithm:quantification_cutoff" type="float" optional="false" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
       <param name="write_convex_hull" argument="-algorithm:write_convex_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write out all points of all features into the featureXML" help=""/>
-      <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" type="select" optional="false" display="radio" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
+      <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" type="select" optional="false" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
         <option value="simple" selected="true">simple</option>
         <option value="resample">resample</option>
         <expand macro="list_string_san" name="spectrum_addition_method"/>
@@ -104,7 +104,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param name="spacing_for_spectra_resampling" argument="-algorithm:spacing_for_spectra_resampling" type="float" optional="false" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
       <param name="uis_threshold_sn" argument="-algorithm:uis_threshold_sn" type="integer" optional="false" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
       <param name="uis_threshold_peak_area" argument="-algorithm:uis_threshold_peak_area" type="integer" optional="false" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
-      <param name="scoring_model" argument="-algorithm:scoring_model" type="select" optional="false" display="radio" label="Scoring model to use" help="">
+      <param name="scoring_model" argument="-algorithm:scoring_model" type="select" optional="false" label="Scoring model to use" help="">
         <option value="default" selected="true">default</option>
         <option value="single_transition">single_transition</option>
         <expand macro="list_string_san" name="scoring_model"/>
@@ -115,12 +115,12 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" optional="false" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
         <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" optional="false" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
         <param name="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" optional="false" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
-        <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" type="select" optional="false" display="radio" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
+        <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" type="select" optional="false" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
           <option value="original" selected="true">original</option>
           <option value="smoothed">smoothed</option>
           <expand macro="list_string_san" name="peak_integration"/>
         </param>
-        <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" type="select" optional="false" display="radio" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
+        <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" type="select" optional="false" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
           <option value="none" selected="true">none</option>
           <option value="original">original</option>
           <option value="exact">exact</option>
@@ -135,7 +135,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="compute_peak_quality" argument="-algorithm:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
         <param name="compute_peak_shape_metrics" argument="-algorithm:TransitionGroupPicker:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
         <param name="compute_total_mi" argument="-algorithm:TransitionGroupPicker:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
-        <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" type="select" optional="false" display="radio" label="Method to use when selecting the best boundaries for peaks" help="">
+        <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" type="select" optional="false" label="Method to use when selecting the best boundaries for peaks" help="">
           <option value="largest" selected="true">largest</option>
           <option value="widest">widest</option>
           <expand macro="list_string_san" name="boundary_selection_method"/>
@@ -151,7 +151,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <param name="sn_bin_count" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count" type="integer" optional="false" value="30" label="Signal to noise bin count" help=""/>
           <param name="write_sn_log_messages" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
           <param name="remove_overlapping_peaks" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/>
-          <param name="method" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:method" type="select" optional="false" display="radio" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
+          <param name="method" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:method" type="select" optional="false" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
             <option value="legacy">legacy</option>
             <option value="corrected" selected="true">corrected</option>
             <option value="crawdad">crawdad</option>
@@ -159,13 +159,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           </param>
         </section>
         <section name="PeakIntegrator" title="" help="" expanded="false">
-          <param name="integration_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" optional="false" display="radio" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
+          <param name="integration_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" optional="false" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
             <option value="intensity_sum" selected="true">intensity_sum</option>
             <option value="simpson">simpson</option>
             <option value="trapezoid">trapezoid</option>
             <expand macro="list_string_san" name="integration_type"/>
           </param>
-          <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" optional="false" display="radio" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
+          <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" optional="false" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
             <option value="base_to_base" selected="true">base_to_base</option>
             <option value="vertical_division">vertical_division</option>
             <option value="vertical_division_min">vertical_division_min</option>
@@ -177,7 +177,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </section>
       <section name="DIAScoring" title="" help="" expanded="false">
         <param name="dia_extraction_window" argument="-algorithm:DIAScoring:dia_extraction_window" type="float" optional="false" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
-        <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" optional="false" display="radio" label="DIA extraction window unit" help="">
+        <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" optional="false" label="DIA extraction window unit" help="">
           <option value="Th" selected="true">Th</option>
           <option value="ppm">ppm</option>
           <expand macro="list_string_san" name="dia_extraction_unit"/>
diff --git a/tools/openms/OpenSwathWorkflow.xml b/tools/openms/OpenSwathWorkflow.xml
index d3aa9e2d9..6ad283b02 100644
--- a/tools/openms/OpenSwathWorkflow.xml
+++ b/tools/openms/OpenSwathWorkflow.xml
@@ -161,7 +161,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-im_extraction_window_ms1" type="float" optional="false" value="-1.0" label="Extraction window in ion mobility dimension for MS1 (in 1/k0 or milliseconds depending on library)" help="-1 means this is not ion mobility data"/>
     <section name="Calibration" title="Parameters for the m/z and ion mobility calibration" help="" expanded="false">
       <param name="ms1_im_calibration" argument="-Calibration:ms1_im_calibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use MS1 precursor data for the ion mobility calibration (default = false, uses MS2 / fragment ions for calibration)" help=""/>
-      <param name="im_correction_function" argument="-Calibration:im_correction_function" type="select" optional="false" display="radio" label="Type of normalization function for IM calibration" help="">
+      <param name="im_correction_function" argument="-Calibration:im_correction_function" type="select" optional="false" label="Type of normalization function for IM calibration" help="">
         <option value="none">none</option>
         <option value="linear" selected="true">linear</option>
         <expand macro="list_string_san" name="im_correction_function"/>
@@ -174,7 +174,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
     </section>
     <section name="Library" title="Library parameters section" help="" expanded="false">
-      <param name="retentionTimeInterpretation" argument="-Library:retentionTimeInterpretation" type="select" optional="false" display="radio" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">
+      <param name="retentionTimeInterpretation" argument="-Library:retentionTimeInterpretation" type="select" optional="false" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">
         <option value="iRT" selected="true">iRT</option>
         <option value="seconds">seconds</option>
         <option value="minutes">minutes</option>
@@ -184,14 +184,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="force_invalid_mods" argument="-Library:force_invalid_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help=""/>
     </section>
     <section name="RTNormalization" title="Parameters for the RTNormalization for iRT petides" help="This specifies how the RT alignment is performed and how outlier detection is applied. Outlier detection can be done iteratively (by default) which removes one outlier per iteration or using the RANSAC algorithm" expanded="false">
-      <param name="alignmentMethod" argument="-RTNormalization:alignmentMethod" type="select" optional="false" display="radio" label="How to perform the alignment to the normalized RT space using anchor points" help="'linear': perform linear regression (for few anchor points). 'interpolated': Interpolate between anchor points (for few, noise-free anchor points). 'lowess' Use local regression (for many, noisy anchor points). 'b_spline' use b splines for smoothing">
+      <param name="alignmentMethod" argument="-RTNormalization:alignmentMethod" type="select" optional="false" label="How to perform the alignment to the normalized RT space using anchor points" help="'linear': perform linear regression (for few anchor points). 'interpolated': Interpolate between anchor points (for few, noise-free anchor points). 'lowess' Use local regression (for many, noisy anchor points). 'b_spline' use b splines for smoothing">
         <option value="linear" selected="true">linear</option>
         <option value="interpolated">interpolated</option>
         <option value="lowess">lowess</option>
         <option value="b_spline">b_spline</option>
         <expand macro="list_string_san" name="alignmentMethod"/>
       </param>
-      <param name="outlierMethod" argument="-RTNormalization:outlierMethod" type="select" optional="false" display="radio" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
+      <param name="outlierMethod" argument="-RTNormalization:outlierMethod" type="select" optional="false" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
         <option value="iter_residual" selected="true">iter_residual</option>
         <option value="iter_jackknife">iter_jackknife</option>
         <option value="ransac">ransac</option>
@@ -220,7 +220,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="rt_normalization_factor" argument="-Scoring:rt_normalization_factor" type="float" optional="false" value="100.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
       <param name="quantification_cutoff" argument="-Scoring:quantification_cutoff" type="float" optional="false" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
       <param name="write_convex_hull" argument="-Scoring:write_convex_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write out all points of all features into the featureXML" help=""/>
-      <param name="spectrum_addition_method" argument="-Scoring:spectrum_addition_method" type="select" optional="false" display="radio" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
+      <param name="spectrum_addition_method" argument="-Scoring:spectrum_addition_method" type="select" optional="false" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
         <option value="simple" selected="true">simple</option>
         <option value="resample">resample</option>
         <expand macro="list_string_san" name="spectrum_addition_method"/>
@@ -229,7 +229,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="spacing_for_spectra_resampling" argument="-Scoring:spacing_for_spectra_resampling" type="float" optional="false" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
       <param name="uis_threshold_sn" argument="-Scoring:uis_threshold_sn" type="integer" optional="false" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
       <param name="uis_threshold_peak_area" argument="-Scoring:uis_threshold_peak_area" type="integer" optional="false" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
-      <param name="scoring_model" argument="-Scoring:scoring_model" type="select" optional="false" display="radio" label="Scoring model to use" help="">
+      <param name="scoring_model" argument="-Scoring:scoring_model" type="select" optional="false" label="Scoring model to use" help="">
         <option value="default" selected="true">default</option>
         <option value="single_transition">single_transition</option>
         <expand macro="list_string_san" name="scoring_model"/>
@@ -239,12 +239,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="TransitionGroupPicker" title="" help="" expanded="false">
         <param name="stop_after_feature" argument="-Scoring:TransitionGroupPicker:stop_after_feature" type="integer" optional="false" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
         <param name="min_peak_width" argument="-Scoring:TransitionGroupPicker:min_peak_width" type="float" optional="false" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
-        <param name="peak_integration" argument="-Scoring:TransitionGroupPicker:peak_integration" type="select" optional="false" display="radio" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
+        <param name="peak_integration" argument="-Scoring:TransitionGroupPicker:peak_integration" type="select" optional="false" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
           <option value="original" selected="true">original</option>
           <option value="smoothed">smoothed</option>
           <expand macro="list_string_san" name="peak_integration"/>
         </param>
-        <param name="background_subtraction" argument="-Scoring:TransitionGroupPicker:background_subtraction" type="select" optional="false" display="radio" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
+        <param name="background_subtraction" argument="-Scoring:TransitionGroupPicker:background_subtraction" type="select" optional="false" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
           <option value="none" selected="true">none</option>
           <option value="original">original</option>
           <option value="exact">exact</option>
@@ -259,7 +259,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="compute_peak_quality" argument="-Scoring:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
         <param name="compute_peak_shape_metrics" argument="-Scoring:TransitionGroupPicker:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
         <param name="compute_total_mi" argument="-Scoring:TransitionGroupPicker:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
-        <param name="boundary_selection_method" argument="-Scoring:TransitionGroupPicker:boundary_selection_method" type="select" optional="false" display="radio" label="Method to use when selecting the best boundaries for peaks" help="">
+        <param name="boundary_selection_method" argument="-Scoring:TransitionGroupPicker:boundary_selection_method" type="select" optional="false" label="Method to use when selecting the best boundaries for peaks" help="">
           <option value="largest" selected="true">largest</option>
           <option value="widest">widest</option>
           <expand macro="list_string_san" name="boundary_selection_method"/>
@@ -273,7 +273,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="signal_to_noise" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" optional="false" min="0.0" value="0.1" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
           <param name="write_sn_log_messages" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
           <param name="remove_overlapping_peaks" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Try to remove overlapping peaks during peak picking" help=""/>
-          <param name="method" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:method" type="select" optional="false" display="radio" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
+          <param name="method" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:method" type="select" optional="false" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
             <option value="legacy">legacy</option>
             <option value="corrected" selected="true">corrected</option>
             <option value="crawdad">crawdad</option>
@@ -281,13 +281,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           </param>
         </section>
         <section name="PeakIntegrator" title="" help="" expanded="false">
-          <param name="integration_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" optional="false" display="radio" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
+          <param name="integration_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" optional="false" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
             <option value="intensity_sum" selected="true">intensity_sum</option>
             <option value="simpson">simpson</option>
             <option value="trapezoid">trapezoid</option>
             <expand macro="list_string_san" name="integration_type"/>
           </param>
-          <param name="baseline_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" optional="false" display="radio" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
+          <param name="baseline_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" optional="false" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
             <option value="base_to_base" selected="true">base_to_base</option>
             <option value="vertical_division">vertical_division</option>
             <option value="vertical_division_min">vertical_division_min</option>
@@ -299,7 +299,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="DIAScoring" title="" help="" expanded="false">
         <param name="dia_extraction_window" argument="-Scoring:DIAScoring:dia_extraction_window" type="float" optional="false" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
-        <param name="dia_extraction_unit" argument="-Scoring:DIAScoring:dia_extraction_unit" type="select" optional="false" display="radio" label="DIA extraction window unit" help="">
+        <param name="dia_extraction_unit" argument="-Scoring:DIAScoring:dia_extraction_unit" type="select" optional="false" label="DIA extraction window unit" help="">
           <option value="Th" selected="true">Th</option>
           <option value="ppm">ppm</option>
           <expand macro="list_string_san" name="dia_extraction_unit"/>
@@ -348,12 +348,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
       <param argument="-min_upper_edge_dist" type="float" optional="false" value="0.0" label="Minimal distance to the upper edge of a Swath window to still consider a precursor, in Thomson" help=""/>
       <param argument="-extra_rt_extraction_window" type="float" optional="false" min="0.0" value="0.0" label="Output an XIC with a RT-window by this much large" help="(e.g. to visually inspect a larger area of the chromatogram)"/>
-      <param argument="-mz_extraction_window_unit" type="select" optional="false" display="radio" label="Unit for mz extraction" help="">
+      <param argument="-mz_extraction_window_unit" type="select" optional="false" label="Unit for mz extraction" help="">
         <option value="Th">Th</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_extraction_window_unit"/>
       </param>
-      <param argument="-mz_extraction_window_ms1_unit" type="select" optional="false" display="radio" label="Unit of the MS1 m/z extraction window" help="">
+      <param argument="-mz_extraction_window_ms1_unit" type="select" optional="false" label="Unit of the MS1 m/z extraction window" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Th">Th</option>
         <expand macro="list_string_san" name="mz_extraction_window_ms1_unit"/>
@@ -361,7 +361,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param argument="-use_ms1_ion_mobility" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Also perform precursor extraction using the same ion mobility window as for fragment ion extraction" help=""/>
       <param argument="-matching_window_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assume the input data is targeted / PRM-like data with potentially overlapping DIA windows" help="Will only attempt to extract each assay from the *best* matching DIA window (instead of all matching windows)"/>
       <param argument="-irt_mz_extraction_window" type="float" optional="false" min="0.0" value="50.0" label="Extraction window used for iRT and m/z correction in Thomson or ppm (see irt_mz_extraction_window_unit)" help=""/>
-      <param argument="-irt_mz_extraction_window_unit" type="select" optional="false" display="radio" label="Unit for mz extraction" help="">
+      <param argument="-irt_mz_extraction_window_unit" type="select" optional="false" label="Unit for mz extraction" help="">
         <option value="Th">Th</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="irt_mz_extraction_window_unit"/>
@@ -371,7 +371,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param argument="-min_coverage" type="float" optional="false" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/>
       <param argument="-split_file_input" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The input files each contain one single SWATH (alternatively: all SWATH are in separate files)" help=""/>
       <param argument="-use_elution_model_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Turn on elution model score (EMG fit to peak)" help=""/>
-      <param argument="-readOptions" type="select" optional="false" display="radio" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first" help="If you choose cache, make sure to also set tempDirectory">
+      <param argument="-readOptions" type="select" optional="false" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first" help="If you choose cache, make sure to also set tempDirectory">
         <option value="normal" selected="true">normal</option>
         <option value="cache">cache</option>
         <option value="cacheWorkingInMemory">cacheWorkingInMemory</option>
@@ -389,7 +389,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="quadratic_regression_delta_ppm">quadratic_regression_delta_ppm</option>
         <expand macro="list_string_san" name="mz_correction_function"/>
       </param>
-      <param argument="-extraction_function" type="select" optional="false" display="radio" label="Function used to extract the signal" help="">
+      <param argument="-extraction_function" type="select" optional="false" label="Function used to extract the signal" help="">
         <option value="tophat" selected="true">tophat</option>
         <option value="bartlett">bartlett</option>
         <expand macro="list_string_san" name="extraction_function"/>
diff --git a/tools/openms/PSMFeatureExtractor.xml b/tools/openms/PSMFeatureExtractor.xml
index f512faaa3..8171bec4b 100644
--- a/tools/openms/PSMFeatureExtractor.xml
+++ b/tools/openms/PSMFeatureExtractor.xml
@@ -59,7 +59,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param argument="-in" type="data" format="idxml,mzid" multiple="false" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-out_type" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
       <option value="idXML">idxml</option>
       <option value="mzid">mzid</option>
       <expand macro="list_string_san" name="out_type"/>
diff --git a/tools/openms/PeakPickerHiRes.xml b/tools/openms/PeakPickerHiRes.xml
index 1d1987471..d8e006f41 100644
--- a/tools/openms/PeakPickerHiRes.xml
+++ b/tools/openms/PeakPickerHiRes.xml
@@ -51,7 +51,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         </expand>
       </param>
       <param name="report_FWHM" argument="-algorithm:report_FWHM" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help=""/>
-      <param name="report_FWHM_unit" argument="-algorithm:report_FWHM_unit" type="select" optional="false" display="radio" label="Unit of FWHM" help="Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)">
+      <param name="report_FWHM_unit" argument="-algorithm:report_FWHM_unit" type="select" optional="false" label="Unit of FWHM" help="Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)">
         <option value="relative" selected="true">relative</option>
         <option value="absolute">absolute</option>
         <expand macro="list_string_san" name="report_FWHM_unit"/>
@@ -69,7 +69,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-processOption" type="select" optional="false" display="radio" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
+      <param argument="-processOption" type="select" optional="false" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
         <option value="inmemory" selected="true">inmemory</option>
         <option value="lowmemory">lowmemory</option>
         <expand macro="list_string_san" name="processOption"/>
diff --git a/tools/openms/PeptideIndexer.xml b/tools/openms/PeptideIndexer.xml
index 508d20752..ca16c2749 100644
--- a/tools/openms/PeptideIndexer.xml
+++ b/tools/openms/PeptideIndexer.xml
@@ -51,12 +51,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
       <expand macro="list_string_san" name="decoy_string"/>
     </param>
-    <param argument="-decoy_string_position" type="select" optional="false" display="radio" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+    <param argument="-decoy_string_position" type="select" optional="false" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
       <option value="prefix" selected="true">prefix</option>
       <option value="suffix">suffix</option>
       <expand macro="list_string_san" name="decoy_string_position"/>
     </param>
-    <param argument="-missing_decoy_action" type="select" optional="false" display="radio" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+    <param argument="-missing_decoy_action" type="select" optional="false" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
       <option value="error" selected="true">error</option>
       <option value="warn">warn</option>
       <option value="silent">silent</option>
@@ -65,7 +65,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
     <param argument="-write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
     <param argument="-keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
-    <param argument="-unmatched_action" type="select" optional="false" display="radio" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+    <param argument="-unmatched_action" type="select" optional="false" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
       <option value="error" selected="true">error</option>
       <option value="warn">warn</option>
       <option value="remove">remove</option>
@@ -113,7 +113,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="proline endopeptidase">proline endopeptidase</option>
         <expand macro="list_string_san" name="name"/>
       </param>
-      <param name="specificity" argument="-enzyme:specificity" type="select" optional="false" display="radio" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+      <param name="specificity" argument="-enzyme:specificity" type="select" optional="false" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
         <option value="auto" selected="true">auto</option>
         <option value="full">full</option>
         <option value="semi">semi</option>
diff --git a/tools/openms/PercolatorAdapter.xml b/tools/openms/PercolatorAdapter.xml
index 2c4e9e049..e8c338cbd 100644
--- a/tools/openms/PercolatorAdapter.xml
+++ b/tools/openms/PercolatorAdapter.xml
@@ -184,7 +184,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </when>
     </conditional>
     <param argument="-in_osw" type="data" format="osw" optional="true" label="Input file in OSW format" help=" select osw data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-out_type" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
       <option value="idXML">idxml</option>
       <option value="mzid">mzid</option>
       <option value="osw">osw</option>
@@ -208,13 +208,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </param>
     <param argument="-peptide_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate peptide-level FDRs instead of PSM-level FDRs" help=""/>
     <param argument="-protein_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the picked protein-level FDR to infer protein probabilities" help="Use the -fasta option and -decoy_pattern to set the Fasta file and decoy pattern"/>
-    <param argument="-osw_level" type="select" optional="false" display="radio" label="OSW: the data level selected for scoring" help="">
+    <param argument="-osw_level" type="select" optional="false" label="OSW: the data level selected for scoring" help="">
       <option value="ms1">ms1</option>
       <option value="ms2" selected="true">ms2</option>
       <option value="transition">transition</option>
       <expand macro="list_string_san" name="osw_level"/>
     </param>
-    <param argument="-score_type" type="select" optional="false" display="radio" label="Type of the peptide main score" help="">
+    <param argument="-score_type" type="select" optional="false" label="Type of the peptide main score" help="">
       <option value="q-value" selected="true">q-value</option>
       <option value="pep">pep</option>
       <option value="svm">svm</option>
diff --git a/tools/openms/PhosphoScoring.xml b/tools/openms/PhosphoScoring.xml
index 57641810d..4905ef3e7 100644
--- a/tools/openms/PhosphoScoring.xml
+++ b/tools/openms/PhosphoScoring.xml
@@ -45,7 +45,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-in" type="data" format="mzml" optional="false" label="Input file with MS/MS spectra" help=" select mzml data sets(s)"/>
     <param argument="-id" type="data" format="idxml" optional="false" label="Identification input file which contains a search against a concatenated sequence database" help=" select idxml data sets(s)"/>
     <param argument="-fragment_mass_tolerance" type="float" optional="false" min="0.0" value="0.05" label="Fragment mass tolerance for spectrum comparisons" help=""/>
-    <param argument="-fragment_mass_unit" type="select" optional="false" display="radio" label="Unit of fragment mass tolerance" help="">
+    <param argument="-fragment_mass_unit" type="select" optional="false" label="Unit of fragment mass tolerance" help="">
       <option value="Da" selected="true">Da</option>
       <option value="ppm">ppm</option>
       <expand macro="list_string_san" name="fragment_mass_unit"/>
diff --git a/tools/openms/ProteinInference.xml b/tools/openms/ProteinInference.xml
index 53ba89e25..fc31198ec 100644
--- a/tools/openms/ProteinInference.xml
+++ b/tools/openms/ProteinInference.xml
@@ -59,12 +59,12 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="false" label="input file(s)" help=" select consensusxml,idxml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="output file type" help="">
+    <param argument="-out_type" type="select" optional="false" label="output file type" help="">
       <option value="consensusXML">consensusxml</option>
       <option value="idXML">idxml</option>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-merge_runs" type="select" optional="false" display="radio" label="If your idXML contains multiple runs, merge them beforehand" help="Otherwise performs inference separately per run">
+    <param argument="-merge_runs" type="select" optional="false" label="If your idXML contains multiple runs, merge them beforehand" help="Otherwise performs inference separately per run">
       <option value="no">no</option>
       <option value="all" selected="true">all</option>
       <expand macro="list_string_san" name="merge_runs"/>
@@ -76,7 +76,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     </section>
     <section name="Algorithm" title="" help="" expanded="false">
       <param name="min_peptides_per_protein" argument="-Algorithm:min_peptides_per_protein" type="integer" optional="false" min="0" value="1" label="Minimal number of peptides needed for a protein identification" help="If set to zero, unmatched proteins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept"/>
-      <param name="score_aggregation_method" argument="-Algorithm:score_aggregation_method" type="select" optional="false" display="radio" label="How to aggregate scores of peptides matching to the same protein?" help="">
+      <param name="score_aggregation_method" argument="-Algorithm:score_aggregation_method" type="select" optional="false" label="How to aggregate scores of peptides matching to the same protein?" help="">
         <option value="best" selected="true">best</option>
         <option value="product">product</option>
         <option value="sum">sum</option>
@@ -96,7 +96,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param argument="-picked_decoy_string" type="text" optional="true" value="" label="If using picked protein FDRs, which decoy string was used" help="Leave blank for auto-detection">
         <expand macro="list_string_san" name="picked_decoy_string"/>
       </param>
-      <param argument="-picked_decoy_prefix" type="select" optional="false" display="radio" label="If using picked protein FDRs, was the decoy string a prefix or suffix" help="Ignored during auto-detection">
+      <param argument="-picked_decoy_prefix" type="select" optional="false" label="If using picked protein FDRs, was the decoy string a prefix or suffix" help="Ignored during auto-detection">
         <option value="prefix" selected="true">prefix</option>
         <option value="suffix">suffix</option>
         <expand macro="list_string_san" name="picked_decoy_prefix"/>
diff --git a/tools/openms/ProteinQuantifier.xml b/tools/openms/ProteinQuantifier.xml
index 14153054f..a7373ac77 100644
--- a/tools/openms/ProteinQuantifier.xml
+++ b/tools/openms/ProteinQuantifier.xml
@@ -86,7 +86,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
     <param argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. via the ProteinInference tool).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/>
     <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
-    <param argument="-method" type="select" optional="false" display="radio" label="- top - quantify based on three most abundant peptides (number can be changed in 'top')" help="- iBAQ (intensity based absolute quantification), calculate the sum of all peptide peak intensities divided by the number of theoretically observable tryptic peptides (https://rdcu.be/cND1J). Warning: only consensusXML or featureXML input is allowed!">
+    <param argument="-method" type="select" optional="false" label="- top - quantify based on three most abundant peptides (number can be changed in 'top')" help="- iBAQ (intensity based absolute quantification), calculate the sum of all peptide peak intensities divided by the number of theoretically observable tryptic peptides (https://rdcu.be/cND1J). Warning: only consensusXML or featureXML input is allowed!">
       <option value="top" selected="true">top</option>
       <option value="iBAQ">iBAQ</option>
       <expand macro="list_string_san" name="method"/>
@@ -97,7 +97,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/>
     <section name="top" title="Additional options for custom quantification using top N peptides" help="" expanded="false">
       <param name="N" argument="-top:N" type="integer" optional="false" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/>
-      <param name="aggregate" argument="-top:aggregate" type="select" optional="false" display="radio" label="Aggregation method used to compute protein abundances from peptide abundances" help="">
+      <param name="aggregate" argument="-top:aggregate" type="select" optional="false" label="Aggregation method used to compute protein abundances from peptide abundances" help="">
         <option value="median" selected="true">median</option>
         <option value="mean">mean</option>
         <option value="weighted_mean">weighted_mean</option>
@@ -114,7 +114,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="">
         <expand macro="list_string_san" name="separator"/>
       </param>
-      <param name="quoting" argument="-format:quoting" type="select" optional="false" display="radio" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
+      <param name="quoting" argument="-format:quoting" type="select" optional="false" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
         <option value="none">none</option>
         <option value="double" selected="true">double</option>
         <option value="escape">escape</option>
diff --git a/tools/openms/ProteinResolver.xml b/tools/openms/ProteinResolver.xml
index 132ca29c8..f0299cb87 100644
--- a/tools/openms/ProteinResolver.xml
+++ b/tools/openms/ProteinResolver.xml
@@ -122,7 +122,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <section name="resolver" title="Additional options for algorithm" help="" expanded="false">
       <param name="missed_cleavages" argument="-resolver:missed_cleavages" type="integer" optional="false" min="0" value="2" label="Number of allowed missed cleavages" help=""/>
       <param name="min_length" argument="-resolver:min_length" type="integer" optional="false" min="1" value="6" label="Minimum length of peptide" help=""/>
-      <param name="enzyme" argument="-resolver:enzyme" type="select" optional="false" display="radio" label="Digestion enzyme" help="">
+      <param name="enzyme" argument="-resolver:enzyme" type="select" optional="false" label="Digestion enzyme" help="">
         <option value="Trypsin" selected="true">Trypsin</option>
         <expand macro="list_string_san" name="enzyme"/>
       </param>
@@ -134,7 +134,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="file" argument="-designer:file" type="text" optional="false" value="File" label="Identifier for the file name" help="">
         <expand macro="list_string_san" name="file"/>
       </param>
-      <param name="separator" argument="-designer:separator" type="select" optional="false" display="radio" label="Separator, which should be used to split a row into columns" help="">
+      <param name="separator" argument="-designer:separator" type="select" optional="false" label="Separator, which should be used to split a row into columns" help="">
         <option value="tab" selected="true">tab</option>
         <option value="semi-colon">semi-colon</option>
         <option value="comma">comma</option>
diff --git a/tools/openms/QCCalculator.xml b/tools/openms/QCCalculator.xml
index 1e1327bed..1413916cf 100644
--- a/tools/openms/QCCalculator.xml
+++ b/tools/openms/QCCalculator.xml
@@ -63,7 +63,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="mzml" optional="false" label="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help=" select mzml data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-out_type" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
       <option value="mzQC">mzqc</option>
       <option value="qcML">qcml</option>
       <expand macro="list_string_san" name="out_type"/>
diff --git a/tools/openms/QualityControl.xml b/tools/openms/QualityControl.xml
index 7b5968eaa..83519f423 100644
--- a/tools/openms/QualityControl.xml
+++ b/tools/openms/QualityControl.xml
@@ -181,7 +181,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <expand macro="list_string_san" name="out_msms"/>
     </param>
     <section name="FragmentMassError" title="Fragment Mass Error settings" help="" expanded="false">
-      <param name="unit" argument="-FragmentMassError:unit" type="select" optional="false" display="radio" label="Unit for mass tolerance" help="'auto' uses information from FeatureXML">
+      <param name="unit" argument="-FragmentMassError:unit" type="select" optional="false" label="Unit for mass tolerance" help="'auto' uses information from FeatureXML">
         <option value="auto" selected="true">auto</option>
         <option value="ppm">ppm</option>
         <option value="da">da</option>
diff --git a/tools/openms/RNPxlSearch.xml b/tools/openms/RNPxlSearch.xml
index 7263fa995..6de417793 100644
--- a/tools/openms/RNPxlSearch.xml
+++ b/tools/openms/RNPxlSearch.xml
@@ -59,7 +59,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-database" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/>
     <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
       <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="false" value="10.0" label="Precursor mass tolerance (+/- around precursor m/z)" help=""/>
-      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="false" display="radio" label="Unit of precursor mass tolerance" help="">
+      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
@@ -72,7 +72,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false">
       <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="false" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/>
-      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="false" display="radio" label="Unit of fragment m" help="">
+      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="false" label="Unit of fragment m" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
@@ -6087,7 +6087,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <expand macro="list_string_val" name="modifications"/>
         <expand macro="list_string_san" name="modifications"/>
       </param>
-      <param name="scoring" argument="-RNPxl:scoring" type="select" optional="false" display="radio" label="Scoring algorithm used in prescoring (fast: total-loss, slow: all losses)" help="">
+      <param name="scoring" argument="-RNPxl:scoring" type="select" optional="false" label="Scoring algorithm used in prescoring (fast: total-loss, slow: all losses)" help="">
         <option value="fast" selected="true">fast</option>
         <option value="slow">slow</option>
         <expand macro="list_string_san" name="scoring"/>
diff --git a/tools/openms/SageAdapter.xml b/tools/openms/SageAdapter.xml
index 93ce05f95..ca7e71ed1 100644
--- a/tools/openms/SageAdapter.xml
+++ b/tools/openms/SageAdapter.xml
@@ -70,14 +70,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     <param argument="-batch_size" type="integer" optional="false" value="0" label="Number of files to load and search in parallel (default = # of CPUs/2)" help=""/>
     <param argument="-precursor_tol_left" type="float" optional="false" value="-6.0" label="Start (left side) of the precursor tolerance window w.r.t" help="precursor location. Usually used with negative values smaller or equal to the 'right' counterpart"/>
     <param argument="-precursor_tol_right" type="float" optional="false" value="6.0" label="End (right side) of the precursor tolerance window w.r.t" help="precursor location. Usually used with positive values larger or equal to the 'left' counterpart"/>
-    <param argument="-precursor_tol_unit" type="select" optional="false" display="radio" label="Unit of precursor tolerance (ppm or Da)" help="">
+    <param argument="-precursor_tol_unit" type="select" optional="false" label="Unit of precursor tolerance (ppm or Da)" help="">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
       <expand macro="list_string_san" name="precursor_tol_unit"/>
     </param>
     <param argument="-fragment_tol_left" type="float" optional="false" value="-20.0" label="Start (left side) of the fragment tolerance window w.r.t" help="precursor location. Usually used with negative values smaller or equal to the 'right' counterpart"/>
     <param argument="-fragment_tol_right" type="float" optional="false" value="20.0" label="End (right side) of the fragment tolerance window w.r.t" help="precursor location. Usually used with positive values larger or equal to the 'left' counterpart"/>
-    <param argument="-fragment_tol_unit" type="select" optional="false" display="radio" label="Unit of fragment tolerance (ppm or Da)" help="">
+    <param argument="-fragment_tol_unit" type="select" optional="false" label="Unit of fragment tolerance (ppm or Da)" help="">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
       <expand macro="list_string_san" name="fragment_tol_unit"/>
@@ -6057,12 +6057,12 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
         <expand macro="list_string_san" name="decoy_string"/>
       </param>
-      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="false" display="radio" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="false" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
         <option value="prefix" selected="true">prefix</option>
         <option value="suffix">suffix</option>
         <expand macro="list_string_san" name="decoy_string_position"/>
       </param>
-      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="false" display="radio" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="false" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
         <option value="error">error</option>
         <option value="warn" selected="true">warn</option>
         <option value="silent">silent</option>
@@ -6071,7 +6071,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
       <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
       <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
-      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="false" display="radio" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="false" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
         <option value="error" selected="true">error</option>
         <option value="warn">warn</option>
         <option value="remove">remove</option>
@@ -6119,7 +6119,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <option value="staphylococcal protease/D">staphylococcal protease/D</option>
           <expand macro="list_string_san" name="name"/>
         </param>
-        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="false" display="radio" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="false" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
           <option value="auto" selected="true">auto</option>
           <option value="full">full</option>
           <option value="semi">semi</option>
diff --git a/tools/openms/SimpleSearchEngine.xml b/tools/openms/SimpleSearchEngine.xml
index d39cfecf3..b4b9fa0eb 100644
--- a/tools/openms/SimpleSearchEngine.xml
+++ b/tools/openms/SimpleSearchEngine.xml
@@ -84,7 +84,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="decoys" argument="-Search:decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Should decoys be generated?" help=""/>
       <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
         <param name="mass_tolerance" argument="-Search:precursor:mass_tolerance" type="float" optional="false" value="10.0" label="+/- tolerance for precursor mass" help=""/>
-        <param name="mass_tolerance_unit" argument="-Search:precursor:mass_tolerance_unit" type="select" optional="false" display="radio" label="Unit of precursor mass tolerance" help="">
+        <param name="mass_tolerance_unit" argument="-Search:precursor:mass_tolerance_unit" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
           <option value="ppm" selected="true">ppm</option>
           <option value="Da">Da</option>
           <expand macro="list_string_san" name="mass_tolerance_unit"/>
@@ -97,7 +97,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false">
         <param name="mass_tolerance" argument="-Search:fragment:mass_tolerance" type="float" optional="false" value="10.0" label="Fragment mass tolerance" help=""/>
-        <param name="mass_tolerance_unit" argument="-Search:fragment:mass_tolerance_unit" type="select" optional="false" display="radio" label="Unit of fragment m" help="">
+        <param name="mass_tolerance_unit" argument="-Search:fragment:mass_tolerance_unit" type="select" optional="false" label="Unit of fragment m" help="">
           <option value="ppm" selected="true">ppm</option>
           <option value="Da">Da</option>
           <expand macro="list_string_san" name="mass_tolerance_unit"/>
diff --git a/tools/openms/SiriusAdapter.xml b/tools/openms/SiriusAdapter.xml
index 8c77cae8c..2bf81a8c5 100644
--- a/tools/openms/SiriusAdapter.xml
+++ b/tools/openms/SiriusAdapter.xml
@@ -99,7 +99,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <section name="preprocessing" title="" help="" expanded="false">
       <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="false" min="1" value="1" label="Number of mass traces each feature has to have to be included" help="To use this parameter, setting the feature_only flag is necessary"/>
       <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="false" value="10.0" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
-      <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" optional="false" display="radio" label="Unit of the precursor_mz_tolerance" help="">
+      <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" optional="false" label="Unit of the precursor_mz_tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/>
@@ -123,7 +123,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="false" min="0" value="100" label="Time out in seconds per fragmentation tree computations" help="0 for an infinite amount of time"/>
       <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="false" min="0" value="100" label="Maximal computation time in seconds for a single compound" help="0 for an infinite amount of time"/>
       <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable recalibration of input spectra" help=""/>
-      <param name="profile" argument="-sirius:profile" type="select" optional="false" display="radio" label="Name of the configuration profile" help="">
+      <param name="profile" argument="-sirius:profile" type="select" optional="false" label="Name of the configuration profile" help="">
         <option value="default" selected="true">default</option>
         <option value="qtof">qtof</option>
         <option value="orbitrap">orbitrap</option>
diff --git a/tools/openms/SpecLibSearcher.xml b/tools/openms/SpecLibSearcher.xml
index 55ae0544f..cd237eded 100644
--- a/tools/openms/SpecLibSearcher.xml
+++ b/tools/openms/SpecLibSearcher.xml
@@ -76,7 +76,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
     </param>
     <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
       <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="false" value="10.0" label="Width of precursor mass tolerance window" help=""/>
-      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="false" display="radio" label="Unit of precursor mass tolerance" help="">
+      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
diff --git a/tools/openms/SpectraFilterNormalizer.xml b/tools/openms/SpectraFilterNormalizer.xml
index ce6fa07ec..d59186bce 100644
--- a/tools/openms/SpectraFilterNormalizer.xml
+++ b/tools/openms/SpectraFilterNormalizer.xml
@@ -40,7 +40,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   <inputs>
     <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
-      <param name="method" argument="-algorithm:method" type="select" optional="false" display="radio" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="intensity of one ('to_one') per spectrum">
+      <param name="method" argument="-algorithm:method" type="select" optional="false" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="intensity of one ('to_one') per spectrum">
         <option value="to_one" selected="true">to_one</option>
         <option value="to_TIC">to_TIC</option>
         <expand macro="list_string_san" name="method"/>
diff --git a/tools/openms/SpectraFilterWindowMower.xml b/tools/openms/SpectraFilterWindowMower.xml
index 4a6e5f42e..754e5c6fd 100644
--- a/tools/openms/SpectraFilterWindowMower.xml
+++ b/tools/openms/SpectraFilterWindowMower.xml
@@ -42,7 +42,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
       <param name="windowsize" argument="-algorithm:windowsize" type="float" optional="false" value="50.0" label="The size of the sliding window along the m/z axis" help=""/>
       <param name="peakcount" argument="-algorithm:peakcount" type="integer" optional="false" value="2" label="The number of peaks that should be kept" help=""/>
-      <param name="movetype" argument="-algorithm:movetype" type="select" optional="false" display="radio" label="Whether sliding window (one peak steps) or jumping window (window size steps) should be used" help="">
+      <param name="movetype" argument="-algorithm:movetype" type="select" optional="false" label="Whether sliding window (one peak steps) or jumping window (window size steps) should be used" help="">
         <option value="slide" selected="true">slide</option>
         <option value="jump">jump</option>
         <expand macro="list_string_san" name="movetype"/>
diff --git a/tools/openms/SpectraMerger.xml b/tools/openms/SpectraMerger.xml
index 3f59ab326..a80b670fd 100644
--- a/tools/openms/SpectraMerger.xml
+++ b/tools/openms/SpectraMerger.xml
@@ -39,7 +39,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="mzml" optional="false" label="Input mzML file" help=" select mzml data sets(s)"/>
-    <param argument="-merging_method" type="select" optional="false" display="radio" label="Method of merging which should be used" help="">
+    <param argument="-merging_method" type="select" optional="false" label="Method of merging which should be used" help="">
       <option value="average_gaussian" selected="true">average_gaussian</option>
       <option value="average_tophat">average_tophat</option>
       <option value="precursor_method">precursor_method</option>
@@ -48,18 +48,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </param>
     <section name="algorithm" title="Algorithm section for merging spectra" help="" expanded="false">
       <param name="mz_binning_width" argument="-algorithm:mz_binning_width" type="float" optional="false" min="0.0" value="5.0" label="minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct" help="Closer data points or peaks will be merged"/>
-      <param name="mz_binning_width_unit" argument="-algorithm:mz_binning_width_unit" type="select" optional="false" display="radio" label="Unit in which the distance between two data points or peaks is given" help="">
+      <param name="mz_binning_width_unit" argument="-algorithm:mz_binning_width_unit" type="select" optional="false" label="Unit in which the distance between two data points or peaks is given" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_binning_width_unit"/>
       </param>
-      <param name="sort_blocks" argument="-algorithm:sort_blocks" type="select" optional="false" display="radio" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="">
+      <param name="sort_blocks" argument="-algorithm:sort_blocks" type="select" optional="false" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="">
         <option value="RT_ascending" selected="true">RT_ascending</option>
         <option value="RT_descending">RT_descending</option>
         <expand macro="list_string_san" name="sort_blocks"/>
       </param>
       <section name="average_gaussian" title="" help="" expanded="false">
-        <param name="spectrum_type" argument="-algorithm:average_gaussian:spectrum_type" type="select" optional="false" display="radio" label="Spectrum type of the MS level to be averaged" help="">
+        <param name="spectrum_type" argument="-algorithm:average_gaussian:spectrum_type" type="select" optional="false" label="Spectrum type of the MS level to be averaged" help="">
           <option value="profile">profile</option>
           <option value="centroid">centroid</option>
           <option value="automatic" selected="true">automatic</option>
@@ -72,7 +72,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="precursor_max_charge" argument="-algorithm:average_gaussian:precursor_max_charge" type="integer" optional="false" min="1" value="1" label="Possible maximum precursor ion charge" help="Effective only when average_gaussian:precursor_mass_tol option is active"/>
       </section>
       <section name="average_tophat" title="" help="" expanded="false">
-        <param name="spectrum_type" argument="-algorithm:average_tophat:spectrum_type" type="select" optional="false" display="radio" label="Spectrum type of the MS level to be averaged" help="">
+        <param name="spectrum_type" argument="-algorithm:average_tophat:spectrum_type" type="select" optional="false" label="Spectrum type of the MS level to be averaged" help="">
           <option value="profile">profile</option>
           <option value="centroid">centroid</option>
           <option value="automatic" selected="true">automatic</option>
@@ -80,7 +80,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         </param>
         <param name="ms_level" argument="-algorithm:average_tophat:ms_level" type="integer" optional="false" min="0" value="1" label="If set to be 0, each MS level will be merged from 1 to max" help="Otherwise, average spectra of this level. All other spectra remain unchanged"/>
         <param name="rt_range" argument="-algorithm:average_tophat:rt_range" type="float" optional="false" min="0.0" max="100000000000.0" value="5.0" label="RT range to be averaged ove" help="i.e. +/-(RT range)/2 from each spectrum"/>
-        <param name="rt_unit" argument="-algorithm:average_tophat:rt_unit" type="select" optional="false" display="radio" label="Unit for RT range" help="">
+        <param name="rt_unit" argument="-algorithm:average_tophat:rt_unit" type="select" optional="false" label="Unit for RT range" help="">
           <option value="scans" selected="true">scans</option>
           <option value="seconds">seconds</option>
           <expand macro="list_string_san" name="rt_unit"/>
diff --git a/tools/openms/SpectraSTSearchAdapter.xml b/tools/openms/SpectraSTSearchAdapter.xml
index a5e18d854..5a1eb6cf2 100644
--- a/tools/openms/SpectraSTSearchAdapter.xml
+++ b/tools/openms/SpectraSTSearchAdapter.xml
@@ -101,7 +101,7 @@ ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(omsext)s' 'output_files/%(bn
     </param>
     <param argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/>
     <param argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta data sets(s)"/>
-    <param argument="-sequence_database_type" type="select" optional="false" display="radio" label="Specify type of sequence database" help="">
+    <param argument="-sequence_database_type" type="select" optional="false" label="Specify type of sequence database" help="">
       <option value="DNA">DNA</option>
       <option value="AA" selected="true">AA</option>
       <expand macro="list_string_san" name="sequence_database_type"/>
diff --git a/tools/openms/StaticModification.xml b/tools/openms/StaticModification.xml
index d9cc734de..02833d7be 100644
--- a/tools/openms/StaticModification.xml
+++ b/tools/openms/StaticModification.xml
@@ -3006,7 +3006,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="ZQG (K)">ZQG (K)</option>
       <expand macro="list_string_san" name="mods"/>
     </param>
-    <param argument="-presets" type="select" optional="false" display="radio" label="Add predefined sets, as shortcut to manually specifying a lot of modifications" help="">
+    <param argument="-presets" type="select" optional="false" label="Add predefined sets, as shortcut to manually specifying a lot of modifications" help="">
       <option value="none" selected="true">none</option>
       <option value="N15">N15</option>
       <expand macro="list_string_san" name="presets"/>
diff --git a/tools/openms/TargetedFileConverter.xml b/tools/openms/TargetedFileConverter.xml
index 2346d2c17..dfc8508f6 100644
--- a/tools/openms/TargetedFileConverter.xml
+++ b/tools/openms/TargetedFileConverter.xml
@@ -39,14 +39,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file to convert" help="See http://www.openms.de/current_doxygen/html/TOPP_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file select mrm,pqp,tabular,traml data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="Output file type -- default: determined from file extension or content" help="Note: not all conversion paths work or make sense">
+    <param argument="-out_type" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: not all conversion paths work or make sense">
       <option value="TraML">traml</option>
       <option value="pqp">pqp</option>
       <option value="tsv">tabular (tsv)</option>
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="retentionTimeInterpretation" argument="-algorithm:retentionTimeInterpretation" type="select" optional="false" display="radio" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">
+      <param name="retentionTimeInterpretation" argument="-algorithm:retentionTimeInterpretation" type="select" optional="false" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">
         <option value="iRT" selected="true">iRT</option>
         <option value="seconds">seconds</option>
         <option value="minutes">minutes</option>
diff --git a/tools/openms/TextExporter.xml b/tools/openms/TextExporter.xml
index a0ba7b927..1596c0c5e 100644
--- a/tools/openms/TextExporter.xml
+++ b/tools/openms/TextExporter.xml
@@ -72,7 +72,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" display="radio" label="Output file type -- default: determined from file extension, ambiguous file extensions are interpreted as tsv" help="">
+    <param argument="-out_type" type="select" optional="false" label="Output file type -- default: determined from file extension, ambiguous file extensions are interpreted as tsv" help="">
       <option value="csv">csv</option>
       <option value="tsv">tabular (tsv)</option>
       <option value="txt">txt</option>
@@ -81,7 +81,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-replacement" type="text" optional="false" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="">
       <expand macro="list_string_san" name="replacement"/>
     </param>
-    <param argument="-quoting" type="select" optional="false" display="radio" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
+    <param argument="-quoting" type="select" optional="false" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
       <option value="none" selected="true">none</option>
       <option value="double">double</option>
       <option value="escape">escape</option>
diff --git a/tools/openms/XTandemAdapter.xml b/tools/openms/XTandemAdapter.xml
index faa0f1ae7..bd1ee019d 100644
--- a/tools/openms/XTandemAdapter.xml
+++ b/tools/openms/XTandemAdapter.xml
@@ -75,12 +75,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-ignore_adapter_param" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this to use the configuration given in 'default_config_file' exclusively, ignoring other parameters (apart from 'in', 'out', 'database', 'xtandem_executable') set via this adapte" help=""/>
     <param argument="-precursor_mass_tolerance" type="float" optional="false" value="10.0" label="Precursor mass tolerance" help=""/>
     <param argument="-fragment_mass_tolerance" type="float" optional="false" value="0.3" label="Fragment mass erro" help=""/>
-    <param argument="-precursor_error_units" type="select" optional="false" display="radio" label="Parent monoisotopic mass error units" help="">
+    <param argument="-precursor_error_units" type="select" optional="false" label="Parent monoisotopic mass error units" help="">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
       <expand macro="list_string_san" name="precursor_error_units"/>
     </param>
-    <param argument="-fragment_error_units" type="select" optional="false" display="radio" label="Fragment monoisotopic mass error units" help="">
+    <param argument="-fragment_error_units" type="select" optional="false" label="Fragment monoisotopic mass error units" help="">
       <option value="ppm">ppm</option>
       <option value="Da" selected="true">Da</option>
       <expand macro="list_string_san" name="fragment_error_units"/>
@@ -6051,7 +6051,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </param>
     <param argument="-missed_cleavages" type="integer" optional="false" value="1" label="Number of possible cleavage sites missed by the enzyme" help=""/>
     <param argument="-semi_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require only peptide end to have a valid cleavage site, not both" help=""/>
-    <param argument="-output_results" type="select" optional="false" display="radio" label="Which hits should be reported" help="All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)">
+    <param argument="-output_results" type="select" optional="false" label="Which hits should be reported" help="All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)">
       <option value="all" selected="true">all</option>
       <option value="valid">valid</option>
       <option value="stochastic">stochastic</option>
@@ -6063,12 +6063,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
         <expand macro="list_string_san" name="decoy_string"/>
       </param>
-      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="false" display="radio" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="false" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
         <option value="prefix" selected="true">prefix</option>
         <option value="suffix">suffix</option>
         <expand macro="list_string_san" name="decoy_string_position"/>
       </param>
-      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="false" display="radio" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="false" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
         <option value="error">error</option>
         <option value="warn" selected="true">warn</option>
         <option value="silent">silent</option>
@@ -6077,7 +6077,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
       <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
       <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
-      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="false" display="radio" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="false" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
         <option value="error" selected="true">error</option>
         <option value="warn">warn</option>
         <option value="remove">remove</option>
@@ -6090,11 +6090,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="enzyme" title="" help="" expanded="false">
         <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" optional="false" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
           <option value="auto" selected="true">auto</option>
-          <option value="PepsinA + P">PepsinA + P</option>
-          <option value="cyanogen-bromide">cyanogen-bromide</option>
-          <option value="Clostripain/P">Clostripain/P</option>
-          <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
-          <option value="no cleavage">no cleavage</option>
+          <option value="2-iodobenzoate">2-iodobenzoate</option>
+          <option value="iodosobenzoate">iodosobenzoate</option>
+          <option value="staphylococcal protease/D">staphylococcal protease/D</option>
+          <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
+          <option value="Glu-C+P">Glu-C+P</option>
           <option value="Chymotrypsin">Chymotrypsin</option>
           <option value="Chymotrypsin/P">Chymotrypsin/P</option>
           <option value="CNBr">CNBr</option>
@@ -6107,14 +6107,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Trypsin/P">Trypsin/P</option>
           <option value="Lys-C/P">Lys-C/P</option>
           <option value="PepsinA">PepsinA</option>
+          <option value="PepsinA + P">PepsinA + P</option>
+          <option value="cyanogen-bromide">cyanogen-bromide</option>
+          <option value="Clostripain/P">Clostripain/P</option>
+          <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+          <option value="no cleavage">no cleavage</option>
           <option value="Asp-N">Asp-N</option>
           <option value="Asp-N/B">Asp-N/B</option>
           <option value="Asp-N_ambic">Asp-N_ambic</option>
-          <option value="2-iodobenzoate">2-iodobenzoate</option>
-          <option value="iodosobenzoate">iodosobenzoate</option>
-          <option value="staphylococcal protease/D">staphylococcal protease/D</option>
-          <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
-          <option value="Glu-C+P">Glu-C+P</option>
           <option value="Arg-C">Arg-C</option>
           <option value="Arg-C/P">Arg-C/P</option>
           <option value="V8-DE">V8-DE</option>
@@ -6125,7 +6125,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Lys-N">Lys-N</option>
           <expand macro="list_string_san" name="name"/>
         </param>
-        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="false" display="radio" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="false" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
           <option value="auto" selected="true">auto</option>
           <option value="full">full</option>
           <option value="semi">semi</option>