Mercurial > repos > galaxyp > openms_idripper
diff IDRipper.xml @ 13:7960e660446e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
---|---|
date | Thu, 01 Dec 2022 19:15:32 +0000 |
parents | b017e7bd2316 |
children | e64214bd2f6e |
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--- a/IDRipper.xml Fri Nov 06 20:00:01 2020 +0000 +++ b/IDRipper.xml Thu Dec 01 19:15:32 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="IDRipper" name="IDRipper" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> - <description>Split protein/peptide identification file into several files according to annotated file origin.</description> +<tool id="IDRipper" name="IDRipper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> + <description>Split protein/peptide identification file into several files according to identification run and annotated file origin.</description> <macros> <token name="@EXECUTABLE@">IDRipper</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -18,7 +16,7 @@ ## Preprocessing mkdir in && ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && -mkdir out_path && +mkdir out && ## Main program call @@ -28,8 +26,8 @@ @EXECUTABLE@ -ini @EXECUTABLE@.ctd -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' --out_path -out_path/ +-out +out/ ## Postprocessing #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS @@ -40,11 +38,13 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/> + <param argument="-in" type="data" format="idxml" optional="false" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/> + <param argument="-numeric_filenames" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not infer output filenames from spectra_data or file_origin but use the input filename with numeric suffixes" help=""/> + <param argument="-split_ident_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Split different identification runs into separate files" help=""/> <expand macro="adv_opts_macro"> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> + <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -52,20 +52,91 @@ </param> </inputs> <outputs> - <collection type="list" name="out_path" label="${tool.name} on ${on_string}: out_path"> - <discover_datasets directory="out_path" format="idxml" pattern="_?(?P<designation>.*)\.[^.]*"/> + <collection type="list" name="out" label="${tool.name} on ${on_string}: out"> + <discover_datasets directory="out" recurse="true" format="idxml" pattern="_?(?P<designation>.*)\.[^.]*"/> </collection> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_IDRipper"/> - <expand macro="manutest_IDRipper"/> - </tests> - <help><![CDATA[Split protein/peptide identification file into several files according to annotated file origin. + <tests><!-- TOPP_IDRipper_1 --> + <!-- TOPP_IDRipper_2 --> + <!-- TOPP_IDRipper_2a --> + <!-- TOPP_IDRipper_3 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="test" value="true"/> + </section> + <param name="in" value="IDRipper_1_input.idXML"/> + <output_collection name="out" count="2"> + <element name="IDRipper_1_output_1" file="IDRipper_1_output1.idXML" ftype="idxml" compare="sim_size" delta="5700"/> + <element name="IDRipper_1_output_2" file="IDRipper_1_output2.idXML" ftype="idxml" compare="sim_size" delta="5700"/> + </output_collection> + <param name="numeric_filenames" value="false"/> + <param name="split_ident_runs" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test><test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="test" value="true"/> + </section> + <param name="in" value="IDRipper_2_input.idXML"/> + <output_collection name="out" count="3"> + <element name="IDRipper_2_input_idXML_0_0" file="IDRipper_2_input_0_0.idXML" ftype="idxml"/> + <element name="IDRipper_2_input_idXML_1_0" file="IDRipper_2_input_1_0.idXML" ftype="idxml"/> + <element name="IDRipper_2_input_idXML_2_1" file="IDRipper_2_input_2_1.idXML" ftype="idxml"/> + </output_collection> + <param name="numeric_filenames" value="true"/> + <param name="split_ident_runs" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test><test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="test" value="true"/> + </section> + <param name="in" value="IDRipper_2_input.idXML"/> + <output_collection name="out" count="2"> + <element name="IDRipper_2_input_idXML_0" file="IDRipper_2a_output_0.idXML" ftype="idxml"/> + <element name="IDRipper_2_input_idXML_1" file="IDRipper_2a_output_1.idXML" ftype="idxml"/> + </output_collection> + <param name="numeric_filenames" value="true"/> + <param name="split_ident_runs" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test><test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="test" value="true"/> + </section> + <param name="in" value="IDRipper_3_output.idXML"/> + <output_collection name="out" count="2"> + <element name="IDRipper_3_input1" file="IDRipper_3_input1.idXML" ftype="idxml"/> + <element name="IDRipper_3_input2" file="IDRipper_3_input2.idXML" ftype="idxml"/> + </output_collection> + <param name="numeric_filenames" value="false"/> + <param name="split_ident_runs" value="false"/> + <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[Split protein/peptide identification file into several files according to identification run and annotated file origin. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDRipper.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRipper.html]]></help> <expand macro="references"/> </tool>