Mercurial > repos > galaxyp > openms_openswathconfidencescoring

comparison OpenSwathConfidenceScoring.xml @ 13:c1809c05ae8c draft

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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
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equal deleted inserted replaced
12:1bf940c18d93 13:c1809c05ae8c
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Compute confidence scores for OpenSwath results</description> 5 <description>Compute confidence scores for OpenSwath results</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token> 7 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
51 <configfiles> 49 <configfiles>
52 <inputs name="args_json" data_style="paths"/> 50 <inputs name="args_json" data_style="paths"/>
53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
54 </configfiles> 52 </configfiles>
55 <inputs> 53 <inputs>
56 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/> 54 <param argument="-in" type="data" format="featurexml" optional="false" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/>
57 <param name="lib" argument="-lib" type="data" format="traml" optional="false" label="Assay library" help=" select traml data sets(s)"/> 55 <param argument="-lib" type="data" format="traml" optional="false" label="Assay library" help=" select traml data sets(s)"/>
58 <param name="trafo" argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/> 56 <param argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/>
59 <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 &quot;all&quot;)" help=""/> 57 <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 &quot;all&quot;)" help=""/>
60 <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 &quot;all&quot;)" help=""/> 58 <param argument="-transitions" type="integer" optional="true" min="0" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help=""/>
61 <section name="GLM" title="Parameters of the binomial GLM" help="" expanded="false"> 59 <section name="GLM" title="Parameters of the binomial GLM" help="" expanded="false">
62 <param name="intercept" argument="-GLM:intercept" type="float" optional="true" value="3.87333466" label="Intercept term" help=""/> 60 <param name="intercept" argument="-GLM:intercept" type="float" optional="true" value="3.87333466" label="Intercept term" help=""/>
63 <param name="delta_rt" argument="-GLM:delta_rt" type="float" optional="true" value="-0.02898629" label="Coefficient of retention time difference" help=""/> 61 <param name="delta_rt" argument="-GLM:delta_rt" type="float" optional="true" value="-0.02898629" label="Coefficient of retention time difference" help=""/>
64 <param name="dist_int" argument="-GLM:dist_int" type="float" optional="true" value="-7.75880768" label="Coefficient of intensity distance" help=""/> 62 <param name="dist_int" argument="-GLM:dist_int" type="float" optional="true" value="-7.75880768" label="Coefficient of intensity distance" help=""/>
65 </section> 63 </section>
66 <expand macro="adv_opts_macro"> 64 <expand macro="adv_opts_macro">
67 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 65 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
68 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 66 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
69 <expand macro="list_string_san"/> 67 <expand macro="list_string_san" name="test"/>
70 </param> 68 </param>
71 </expand> 69 </expand>
72 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 70 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
73 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 71 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
74 </param> 72 </param>
77 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> 75 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
78 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 76 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
79 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 77 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
80 </data> 78 </data>
81 </outputs> 79 </outputs>
82 <tests> 80 <tests><!-- TOPP_OpenSwathConfidenceScoring_1 -->
83 <expand macro="autotest_OpenSwathConfidenceScoring"/> 81 <test expect_num_outputs="2">
84 <expand macro="manutest_OpenSwathConfidenceScoring"/> 82 <section name="adv_opts">
83 <param name="force" value="false"/>
84 <param name="test" value="true"/>
85 </section>
86 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
87 <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
88 <output name="out" file="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
89 <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/>
90 <param name="decoys" value="1"/>
91 <param name="transitions" value="2"/>
92 <section name="GLM">
93 <param name="intercept" value="3.87333466"/>
94 <param name="delta_rt" value="-0.02898629"/>
95 <param name="dist_int" value="-7.75880768"/>
96 </section>
97 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
98 <output name="ctd_out" ftype="xml">
99 <assert_contents>
100 <is_valid_xml/>
101 </assert_contents>
102 </output>
103 </test>
85 </tests> 104 </tests>
86 <help><![CDATA[Compute confidence scores for OpenSwath results 105 <help><![CDATA[Compute confidence scores for OpenSwath results
87 106
88 107
89 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathConfidenceScoring.html]]></help> 108 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathConfidenceScoring.html]]></help>
90 <expand macro="references"/> 109 <expand macro="references"/>
91 </tool> 110 </tool>