Mercurial > repos > galaxyp > openms_mrmpairfinder

comparison MRMPairFinder.xml @ 13:e5ebdbc5e072 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 21:43:58 +0000
parents bd57c94d50fb
children
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12:bd57c94d50fb 13:e5ebdbc5e072
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: [Utilities]--> 2 <!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
4 <tool id="MRMPairFinder" name="MRMPairFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Util which can be used to evaluate labeled pair ratios on MRM features</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">MRMPairFinder</token> 6 <token name="@EXECUTABLE@">MRMPairFinder</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
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($in.ext)' &&
19 mkdir pair_in && 18 mkdir pair_in &&
20 ln -s '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' && 19 cp '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' &&
21 mkdir out && 20 mkdir out &&
22 #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 21 #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir feature_out && 22 mkdir feature_out &&
24 #end if 23 #end if
25 24
54 <configfiles> 53 <configfiles>
55 <inputs name="args_json" data_style="paths"/> 54 <inputs name="args_json" data_style="paths"/>
56 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 55 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
57 </configfiles> 56 </configfiles>
58 <inputs> 57 <inputs>
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)"/> 58 <param argument="-in" type="data" format="featurexml" label="Input featureXML file containing the features of the MRM experiment spectra" help=" select featurexml 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)"/> 59 <param argument="-pair_in" type="data" format="csv" 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)"/>
61 <expand macro="adv_opts_macro"> 60 <expand macro="adv_opts_macro">
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=""/> 61 <param argument="-mass_tolerance" type="float" 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=""/>
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=""/> 62 <param argument="-RT_tolerance" type="float" 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=""/>
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=""/> 63 <param argument="-RT_pair_tolerance" type="float" 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=""/>
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="feature_out_FLAG">feature_out (Output featureXML file, only written if given, skipped otherwise)</option> 70 <option value="feature_out_FLAG">feature_out (Output featureXML file, only written if given, skipped otherwise)</option>
79 </data> 78 </data>
80 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 79 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
81 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 80 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
82 </data> 81 </data>
83 </outputs> 82 </outputs>
84 <tests><!-- TODO no idea about a useful input for pair_in --> 83 <tests>
85 </tests> 84 <!-- TODO no idea about a useful input for pair_in -->
85 </tests>
86 <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.
87 87
88 88
89 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MRMPairFinder.html]]></help> 89 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MRMPairFinder.html]]></help>
90 <expand macro="references"/> 90 <expand macro="references"/>
91 </tool> 91 </tool>