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comparison OpenSwathConfidenceScoring.xml @ 14:e480a424b40f draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:43:51 +0000
parents c1809c05ae8c
children
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13:c1809c05ae8c 14:e480a424b40f
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
4 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Compute confidence scores for OpenSwath results</description> 4 <description>Compute confidence scores for OpenSwath results</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token> 6 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir lib && 18 mkdir lib &&
20 ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' && 19 cp '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' &&
21 mkdir out && 20 mkdir out &&
22 #if $trafo: 21 #if $trafo:
23 mkdir trafo && 22 mkdir trafo &&
24 ln -s '$trafo' 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)' && 23 cp '$trafo' 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)' &&
25 #end if 24 #end if
26 25
27 ## Main program call 26 ## Main program call
28 27
29 set -o pipefail && 28 set -o pipefail &&
49 <configfiles> 48 <configfiles>
50 <inputs name="args_json" data_style="paths"/> 49 <inputs name="args_json" data_style="paths"/>
51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 50 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
52 </configfiles> 51 </configfiles>
53 <inputs> 52 <inputs>
54 <param argument="-in" type="data" format="featurexml" optional="false" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/> 53 <param argument="-in" type="data" format="featurexml" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/>
55 <param argument="-lib" type="data" format="traml" optional="false" label="Assay library" help=" select traml data sets(s)"/> 54 <param argument="-lib" type="data" format="traml" label="Assay library" help=" select traml data sets(s)"/>
56 <param argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/> 55 <param argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/>
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=""/> 56 <param argument="-decoys" type="integer" min="0" value="1000" label="Number of decoy assays to select from the library for every true assay (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=""/> 57 <param argument="-transitions" type="integer" min="0" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help=""/>
59 <section name="GLM" title="Parameters of the binomial GLM" help="" expanded="false"> 58 <section name="GLM" title="Parameters of the binomial GLM" help="" expanded="false">
60 <param name="intercept" argument="-GLM:intercept" type="float" optional="true" value="3.87333466" label="Intercept term" help=""/> 59 <param name="intercept" argument="-GLM:intercept" type="float" value="3.87333466" label="Intercept term" help=""/>
61 <param name="delta_rt" argument="-GLM:delta_rt" type="float" optional="true" value="-0.02898629" label="Coefficient of retention time difference" help=""/> 60 <param name="delta_rt" argument="-GLM:delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help=""/>
62 <param name="dist_int" argument="-GLM:dist_int" type="float" optional="true" value="-7.75880768" label="Coefficient of intensity distance" help=""/> 61 <param name="dist_int" argument="-GLM:dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help=""/>
63 </section> 62 </section>
64 <expand macro="adv_opts_macro"> 63 <expand macro="adv_opts_macro">
65 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 64 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
66 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 65 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
67 <expand macro="list_string_san" name="test"/> 66 <expand macro="list_string_san" name="test"/>
68 </param> 67 </param>
69 </expand> 68 </expand>
70 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 69 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
71 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 70 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
75 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> 74 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
76 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 75 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
77 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 76 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
78 </data> 77 </data>
79 </outputs> 78 </outputs>
80 <tests><!-- TOPP_OpenSwathConfidenceScoring_1 --> 79 <tests>
80 <!-- TOPP_OpenSwathConfidenceScoring_1 -->
81 <test expect_num_outputs="2"> 81 <test expect_num_outputs="2">
82 <section name="adv_opts"> 82 <section name="adv_opts">
83 <param name="force" value="false"/> 83 <param name="force" value="false"/>
84 <param name="test" value="true"/> 84 <param name="test" value="true"/>
85 </section> 85 </section>
86 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> 86 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
87 <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/> 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"/> 88 <output name="out" value="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
89 <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/> 89 <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/>
90 <param name="decoys" value="1"/> 90 <param name="decoys" value="1"/>
91 <param name="transitions" value="2"/> 91 <param name="transitions" value="2"/>
92 <section name="GLM"> 92 <section name="GLM">
93 <param name="intercept" value="3.87333466"/> 93 <param name="intercept" value="3.87333466"/>
98 <output name="ctd_out" ftype="xml"> 98 <output name="ctd_out" ftype="xml">
99 <assert_contents> 99 <assert_contents>
100 <is_valid_xml/> 100 <is_valid_xml/>
101 </assert_contents> 101 </assert_contents>
102 </output> 102 </output>
103 <assert_stdout>
104 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
105 </assert_stdout>
103 </test> 106 </test>
104 </tests> 107 </tests>
105 <help><![CDATA[Compute confidence scores for OpenSwath results 108 <help><![CDATA[Compute confidence scores for OpenSwath results
106 109
107 110
108 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathConfidenceScoring.html]]></help> 111 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathConfidenceScoring.html]]></help>
109 <expand macro="references"/> 112 <expand macro="references"/>
110 </tool> 113 </tool>