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do dot use checkboxes/radio for selects
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@bernt-matthias
bernt-matthias committed Jun 14, 2024
1 parent 1c32e81 commit 39d6e0d
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Showing 84 changed files with 291 additions and 291 deletions.
6 changes: 3 additions & 3 deletions tools/openms/AccurateMassSearch.xml
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Expand Up @@ -137,12 +137,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard
</section>
<section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
<param name="mass_error_value" argument="-algorithm:mass_error_value" type="float" optional="false" value="5.0" label="Tolerance allowed for accurate mass search" help=""/>
<param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="false" display="radio" label="Unit of mass error (ppm or Da)" help="">
<param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="false" label="Unit of mass error (ppm or Da)" help="">
<option value="ppm" selected="true">ppm</option>
<option value="Da">Da</option>
<expand macro="list_string_san" name="mass_error_unit"/>
</param>
<param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="false" display="radio" label="Positive or negative ionization mode" help="If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
<param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="false" label="Positive or negative ionization mode" help="If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
<option value="positive" selected="true">positive</option>
<option value="negative">negative</option>
<option value="auto">auto</option>
Expand All @@ -151,7 +151,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$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"/>
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16 changes: 8 additions & 8 deletions tools/openms/AssayGeneratorMetabo.xml
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Expand Up @@ -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"/>
Expand All @@ -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"/>
Expand All @@ -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"/>
Expand All @@ -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"/>
Expand All @@ -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>
Expand Down Expand Up @@ -202,13 +202,13 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
</param>
</section>
<expand macro="adv_opts_macro">
<param argument="-ambiguity_resolution_mz_tolerance_unit" type="select" optional="false" display="radio" label="Unit of the ambiguity_resolution_mz_tolerance" help="">
<param argument="-ambiguity_resolution_mz_tolerance_unit" type="select" optional="false" label="Unit of the ambiguity_resolution_mz_tolerance" help="">
<option value="ppm" selected="true">ppm</option>
<option value="Da">Da</option>
<expand macro="list_string_san" name="ambiguity_resolution_mz_tolerance_unit"/>
</param>
<param argument="-precursor_recalibration_window" type="float" optional="false" value="0.01" label="Tolerance window for precursor selection (Annotation of precursor mz and intensity)" help=""/>
<param argument="-precursor_recalibration_window_unit" type="select" optional="false" display="radio" label="Unit of the precursor_mz_tolerance_annotation" help="">
<param argument="-precursor_recalibration_window_unit" type="select" optional="false" label="Unit of the precursor_mz_tolerance_annotation" help="">
<option value="Da" selected="true">Da</option>
<option value="ppm">ppm</option>
<expand macro="list_string_san" name="precursor_recalibration_window_unit"/>
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2 changes: 1 addition & 1 deletion tools/openms/BaselineFilter.xml
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Expand Up @@ -40,7 +40,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$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"/>
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