Mercurial > repos > galaxyp > openms_idextractor
diff IDExtractor.xml @ 15:589bf635f424 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
---|---|
date | Thu, 01 Dec 2022 19:07:40 +0000 |
parents | 2a2fa2b57306 |
children | a6124b08daff |
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--- a/IDExtractor.xml Fri Nov 06 19:40:34 2020 +0000 +++ b/IDExtractor.xml Thu Dec 01 19:07:40 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: [Utilities]--> -<tool id="IDExtractor" name="IDExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="IDExtractor" name="IDExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Extracts 'n' peptides randomly or best 'n' from idXML files.</description> <macros> <token name="@EXECUTABLE@">IDExtractor</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -41,14 +39,14 @@ <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" help=" select idxml data sets(s)"/> - <param name="number_of_peptides" argument="-number_of_peptides" type="integer" optional="true" min="1" value="10" label="Number of randomly chosen peptides" help=""/> - <param name="number_of_rand_invokations" argument="-number_of_rand_invokations" type="integer" optional="true" min="0" value="0" label="Number of rand invocations before random draw" help=""/> - <param name="best_hits" argument="-best_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the best n peptides are chosen" help=""/> + <param argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/> + <param argument="-number_of_peptides" type="integer" optional="true" min="1" value="10" label="Number of randomly chosen peptides" help=""/> + <param argument="-number_of_rand_invokations" type="integer" optional="true" min="0" value="0" label="Number of rand invocations before random draw (basically a seed)" help=""/> + <param argument="-best_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the best n peptides are chosen" 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"> @@ -61,13 +59,17 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_IDExtractor"/> - <expand macro="manutest_IDExtractor"/> - </tests> + <tests><test expect_num_outputs="1"><!-- --> + <param name="adv_opts|test" value="true"/> + <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/> + <param name="best_hits" value="true"/> + <param name="number_of_peptides" value="1"/> + <output name="out" value="IDExtractor.idXML" compare="sim_size"/> + </test> +</tests> <help><![CDATA[Extracts 'n' peptides randomly or best 'n' from idXML files. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_IDExtractor.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDExtractor.html]]></help> <expand macro="references"/> </tool>