Mercurial > repos > galaxyp > openms_openswathconfidencescoring
diff OpenSwathConfidenceScoring.xml @ 13:c1809c05ae8c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
---|---|
date | Thu, 01 Dec 2022 19:01:26 +0000 |
parents | fa73919cc97e |
children | e480a424b40f |
line wrap: on
line diff
--- a/OpenSwathConfidenceScoring.xml Fri Nov 06 20:04:09 2020 +0000 +++ b/OpenSwathConfidenceScoring.xml Thu Dec 01 19:01:26 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="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Compute confidence scores for OpenSwath results</description> <macros> <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -53,20 +51,20 @@ <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="featurexml" optional="false" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/> - <param name="lib" argument="-lib" type="data" format="traml" optional="false" label="Assay library" help=" select traml data sets(s)"/> - <param name="trafo" argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/> - <param name="decoys" argument="-decoys" type="integer" optional="true" min="0" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for "all")" help=""/> - <param name="transitions" argument="-transitions" type="integer" optional="true" min="0" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for "all")" help=""/> + <param argument="-in" type="data" format="featurexml" optional="false" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/> + <param argument="-lib" type="data" format="traml" optional="false" label="Assay library" help=" select traml data sets(s)"/> + <param argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/> + <param argument="-decoys" type="integer" optional="true" min="0" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for "all")" help=""/> + <param argument="-transitions" type="integer" optional="true" min="0" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for "all")" help=""/> <section name="GLM" title="Parameters of the binomial GLM" help="" expanded="false"> <param name="intercept" argument="-GLM:intercept" type="float" optional="true" value="3.87333466" label="Intercept term" help=""/> <param name="delta_rt" argument="-GLM:delta_rt" type="float" optional="true" value="-0.02898629" label="Coefficient of retention time difference" help=""/> <param name="dist_int" argument="-GLM:dist_int" type="float" optional="true" value="-7.75880768" label="Coefficient of intensity distance" help=""/> </section> <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"> @@ -79,13 +77,34 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_OpenSwathConfidenceScoring"/> - <expand macro="manutest_OpenSwathConfidenceScoring"/> + <tests><!-- TOPP_OpenSwathConfidenceScoring_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> + <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/> + <output name="out" file="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/> + <param name="decoys" value="1"/> + <param name="transitions" value="2"/> + <section name="GLM"> + <param name="intercept" value="3.87333466"/> + <param name="delta_rt" value="-0.02898629"/> + <param name="dist_int" value="-7.75880768"/> + </section> + <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[Compute confidence scores for OpenSwath results -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathConfidenceScoring.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathConfidenceScoring.html]]></help> <expand macro="references"/> </tool>