Mercurial > repos > galaxyp > openms_mrmpairfinder

comparison MRMPairFinder.xml @ 12:bd57c94d50fb 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 19:00:25 +0000
parents 482de0c17531
children e5ebdbc5e072
comparison
equal deleted inserted replaced
11:73be9c498aa8 12:bd57c94d50fb
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MRMPairFinder" name="MRMPairFinder" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MRMPairFinder" name="MRMPairFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description> 5 <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MRMPairFinder</token> 7 <token name="@EXECUTABLE@">MRMPairFinder</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@
56 <configfiles> 54 <configfiles>
57 <inputs name="args_json" data_style="paths"/> 55 <inputs name="args_json" data_style="paths"/>
58 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 56 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
59 </configfiles> 57 </configfiles>
60 <inputs> 58 <inputs>
61 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input featureXML file containing the features of the MRM experiment spectra" help=" select featurexml data sets(s)"/> 59 <param argument="-in" type="data" format="featurexml" optional="false" label="Input featureXML file containing the features of the MRM experiment spectra" help=" select featurexml data sets(s)"/>
62 <param name="pair_in" argument="-pair_in" type="data" format="csv" optional="false" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help=" select csv data sets(s)"/> 60 <param argument="-pair_in" type="data" format="csv" optional="false" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help=" select csv data sets(s)"/>
63 <expand macro="adv_opts_macro"> 61 <expand macro="adv_opts_macro">
64 <param name="mass_tolerance" argument="-mass_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/> 62 <param argument="-mass_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/>
65 <param name="RT_tolerance" argument="-RT_tolerance" type="float" optional="true" min="0.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/> 63 <param argument="-RT_tolerance" type="float" optional="true" min="0.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/>
66 <param name="RT_pair_tolerance" argument="-RT_pair_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have" help=""/> 64 <param argument="-RT_pair_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have" help=""/>
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="feature_out_FLAG">feature_out (Output featureXML file, only written if given, skipped otherwise)</option> 71 <option value="feature_out_FLAG">feature_out (Output featureXML file, only written if given, skipped otherwise)</option>
74 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 72 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
81 </data> 79 </data>
82 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 80 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
83 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 81 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
84 </data> 82 </data>
85 </outputs> 83 </outputs>
86 <tests> 84 <tests><!-- TODO no idea about a useful input for pair_in -->
87 <expand macro="autotest_MRMPairFinder"/> 85 </tests>
88 <expand macro="manutest_MRMPairFinder"/>
89 </tests>
90 <help><![CDATA[Util which can be used to evaluate labeled pair ratios on MRM features. 86 <help><![CDATA[Util which can be used to evaluate labeled pair ratios on MRM features.
91 87
92 88
93 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MRMPairFinder.html]]></help> 89 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MRMPairFinder.html]]></help>
94 <expand macro="references"/> 90 <expand macro="references"/>
95 </tool> 91 </tool>