Mercurial > repos > galaxyp > openms_mztabexporter
diff MzTabExporter.xml @ 14:748dfbdf2201 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:34:36 +0000 |
| parents | 2735db4dd8d9 |
| children |
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--- a/MzTabExporter.xml Thu Dec 01 19:23:13 2022 +0000 +++ b/MzTabExporter.xml Fri Jun 14 21:34:36 2024 +0000 @@ -1,8 +1,7 @@ -<?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]--> +<!--Proposed Tool Section: [File Converter]--> <tool id="MzTabExporter" name="MzTabExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Exports various XML formats to an mzTab file.</description> + <description>Exports various XML formats to an mzTab file</description> <macros> <token name="@EXECUTABLE@">MzTabExporter</token> <import>macros.xml</import> @@ -16,7 +15,7 @@ ## Preprocessing #if $in: mkdir in && - ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && + cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #end if mkdir out && @@ -44,7 +43,7 @@ </configfiles> <inputs> <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=""> + <param argument="-opt_columns" type="select" multiple="true" optional="false" 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" name="opt_columns"/> </param> @@ -52,7 +51,7 @@ <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=""> + <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> @@ -66,7 +65,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_MzTabExporter_1 --> + <tests> + <!-- TOPP_MzTabExporter_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="first_run_inference_only" value="false"/> @@ -75,7 +75,7 @@ <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"/> + <output name="out" value="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"> @@ -83,6 +83,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_MzTabExporter_2 --> <test expect_num_outputs="2"> @@ -93,7 +96,7 @@ <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"/> + <output name="out" value="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"> @@ -101,6 +104,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_MzTabExporter_3 --> <test expect_num_outputs="2"> @@ -111,7 +117,7 @@ <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"/> + <output name="out" value="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"> @@ -119,6 +125,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_MzTabExporter_4 --> <test expect_num_outputs="2"> @@ -129,7 +138,7 @@ <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"/> + <output name="out" value="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"> @@ -137,6 +146,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_MzTabExporter_5 --> <test expect_num_outputs="2"> @@ -147,7 +159,7 @@ <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"/> + <output name="out" value="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"> @@ -155,6 +167,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_MzTabExporter_6 --> <test expect_num_outputs="2"> @@ -165,7 +180,7 @@ <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"/> + <output name="out" value="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"> @@ -173,6 +188,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_MzTabExporter_7 --> <test expect_num_outputs="2"> @@ -183,7 +201,7 @@ <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"/> + <output name="out" value="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"> @@ -191,6 +209,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_MzTabExporter_8 --> <test expect_num_outputs="2"> @@ -201,7 +222,7 @@ <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"/> + <output name="out" value="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"> @@ -209,11 +230,14 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> </tests> <help><![CDATA[Exports various XML formats to an mzTab file. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MzTabExporter.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MzTabExporter.html]]></help> <expand macro="references"/> </tool>