Mercurial > repos > galaxyp > openms_mztabexporter
diff MzTabExporter.xml @ 13:2735db4dd8d9 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:23:13 +0000 |
| parents | 9bf4fbcf20c8 |
| children | 748dfbdf2201 |
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--- a/MzTabExporter.xml Fri Nov 06 20:25:38 2020 +0000 +++ b/MzTabExporter.xml Thu Dec 01 19:23:13 2022 +0000 @@ -1,13 +1,11 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [File Handling]--> -<tool id="MzTabExporter" name="MzTabExporter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="MzTabExporter" name="MzTabExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Exports various XML formats to an mzTab file.</description> <macros> <token name="@EXECUTABLE@">MzTabExporter</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -45,16 +43,17 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml,mzid" optional="true" label="Input files used to generate the mzTab file" help=" select consensusxml,featurexml,idxml,mzid data sets(s)"/> - <param name="opt_columns" argument="-opt_columns" multiple="true" type="select" optional="true" label="Add optional columns which are not part of the mzTab standard" help=""> + <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzid" optional="true" label="Input files used to generate the mzTab file" help=" select consensusxml,featurexml,idxml,mzid data sets(s)"/> + <param argument="-opt_columns" display="checkboxes" multiple="true" type="select" optional="true" label="Add optional columns which are not part of the mzTab standard" help=""> <option value="subfeatures" selected="true">subfeatures</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="opt_columns"/> </param> <expand macro="adv_opts_macro"> - <param name="first_run_inference_only" argument="-first_run_inference_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Does the first IdentificationRun in the file only represent (protein) inference results" help="If so, read peptide information only from second to last runs"/> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <param argument="-first_run_inference_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Does the first IdentificationRun in the file only represent (protein) inference results" help="If so, read peptide information only from second to last runs"/> + <param argument="-export_all_psms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Export all PSMs instead of only the best per spectrum" help=""/> + <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=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -67,13 +66,154 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_MzTabExporter"/> - <expand macro="manutest_MzTabExporter"/> + <tests><!-- TOPP_MzTabExporter_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="first_run_inference_only" value="false"/> + <param name="export_all_psms" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="MzTabExporter_1_input.consensusXML"/> + <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_MzTabExporter_2 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="first_run_inference_only" value="false"/> + <param name="export_all_psms" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="MzTabExporter_2_input.idXML"/> + <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_MzTabExporter_3 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="first_run_inference_only" value="false"/> + <param name="export_all_psms" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="MzTabExporter_3_input.featureXML"/> + <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_MzTabExporter_4 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="first_run_inference_only" value="false"/> + <param name="export_all_psms" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="Epifany_2_out.consensusXML"/> + <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_MzTabExporter_5 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="first_run_inference_only" value="true"/> + <param name="export_all_psms" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="MzTabExporter_5_in.consensusXML"/> + <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_MzTabExporter_6 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="first_run_inference_only" value="false"/> + <param name="export_all_psms" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="MzTabExporter_6_input.idXML"/> + <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_MzTabExporter_7 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="first_run_inference_only" value="false"/> + <param name="export_all_psms" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="MzTabExporter_7_input.consensusXML"/> + <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_MzTabExporter_8 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="first_run_inference_only" value="false"/> + <param name="export_all_psms" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="MzTabExporter_6_input.idXML"/> + <output name="out" file="MzTabExporter_8_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Exports various XML formats to an mzTab file. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MzTabExporter.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MzTabExporter.html]]></help> <expand macro="references"/> </tool>