Mercurial > repos > galaxyp > openms_openswathrewritetofeaturexml
diff OpenSwathRewriteToFeatureXML.xml @ 13:b956337a7473 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:23:47 +0000 |
| parents | 5ad2d341fb2f |
| children | 77f01ffce2b7 |
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--- a/OpenSwathRewriteToFeatureXML.xml Fri Nov 06 20:19:28 2020 +0000 +++ b/OpenSwathRewriteToFeatureXML.xml Thu Dec 01 19:23:47 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: [Targeted Experiments]--> -<tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description> <macros> <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -49,13 +47,13 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="csv" argument="-csv" type="data" format="csv" optional="true" label="mProphet tsv output file: "all_peakgroups.xls"" help=" select csv data sets(s)"/> - <param name="featureXML" argument="-featureXML" type="data" format="featurexml" optional="false" label="input featureXML file" help=" select featurexml data sets(s)"/> - <param name="FDR_cutoff" argument="-FDR_cutoff" type="float" optional="true" value="-1.0" label="FDR cutoff" help="(e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/> + <param argument="-csv" type="data" format="csv" optional="true" label="mProphet tsv output file: "all_peakgroups.xls"" help=" select csv data sets(s)"/> + <param argument="-featureXML" type="data" format="featurexml" optional="false" label="input featureXML file" help=" select featurexml data sets(s)"/> + <param argument="-FDR_cutoff" type="float" optional="true" value="-1.0" label="FDR cutoff" help="(e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/> <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"> @@ -68,13 +66,15 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_OpenSwathRewriteToFeatureXML"/> - <expand macro="manutest_OpenSwathRewriteToFeatureXML"/> - </tests> + <tests><test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> + <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> + <param name="adv_opts|test" value="true"/> + <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/> + </test> +</tests> <help><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_OpenSwathRewriteToFeatureXML.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathRewriteToFeatureXML.html]]></help> <expand macro="references"/> </tool>