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@@ -101,8 +101,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard | |
| <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | ||
| </configfiles> | ||
| <inputs> | ||
| <param argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="featureXML or consensusXML file" help=" select consensusxml,featurexml data sets(s)"/> | ||
| <param name="out_annotation_type" type="select" optional="false" label="File type of output out_annotation (A copy of the input file, annotated with matching hits from the database.)"> | ||
| <param argument="-in" type="data" format="consensusxml,featurexml" label="featureXML or consensusXML file" help=" select consensusxml,featurexml data sets(s)"/> | ||
| <param name="out_annotation_type" type="select" label="File type of output out_annotation (A copy of the input file, annotated with matching hits from the database.)"> | ||
| <option value="featureXML">featurexml</option> | ||
| <option value="consensusXML">consensusxml</option> | ||
| <option value="oms">sqlite (oms)</option> | ||
|
|
@@ -119,7 +119,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard | |
| <param name="mapping" argument="-db:mapping" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/> | ||
| </when> | ||
| <when value="yes"> | ||
| <param name="mapping" argument="-db:mapping" type="data" format="tabular" multiple="false" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/> | ||
| <param name="mapping" argument="-db:mapping" type="data" format="tabular" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/> | ||
| </when> | ||
| </conditional> | ||
| <conditional name="struct_cond"> | ||
|
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@@ -131,18 +131,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard | |
| <param name="struct" argument="-db:struct" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/> | ||
| </when> | ||
| <when value="yes"> | ||
| <param name="struct" argument="-db:struct" type="data" format="tabular" multiple="false" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/> | ||
| <param name="struct" argument="-db:struct" type="data" format="tabular" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/> | ||
| </when> | ||
| </conditional> | ||
| </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" label="Unit of mass error (ppm or Da)" help=""> | ||
| <param name="mass_error_value" argument="-algorithm:mass_error_value" type="float" value="5.0" label="Tolerance allowed for accurate mass search" help=""/> | ||
| <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" 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" 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" 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' '@[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" 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" 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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@@ -162,7 +162,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard | |
| </section> | ||
| <expand macro="adv_opts_macro"> | ||
| <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | ||
| <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | ||
| <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> | ||
| <expand macro="list_string_san" name="test"/> | ||
| </param> | ||
| </expand> | ||
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