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comparison maxquant_mqpar.xml @ 18:163452d1e255 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 9d6014f26ea5d3737320ec56749207e6fe602025
author galaxyp
date Sun, 13 Nov 2022 19:11:10 +0000
parents 1f39c833f65f
children 8934bc76bb52
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17:1f39c833f65f 18:163452d1e255
1 <tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@"> 1 <tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@" profile="21.05">
2 <macros> 2 <macros>
3 <xml name="output" token_format="tabular" token_label="default description" token_name="default"> 3 <xml name="output" token_format="tabular" token_label="default description" token_name="default">
4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> 4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
5 <filter>'@NAME@' in output</filter> 5 <filter>'@NAME@' in output</filter>
6 </data> 6 </data>
13 <import>macros.xml</import> 13 <import>macros.xml</import>
14 </macros> 14 </macros>
15 <expand macro="requirements"/> 15 <expand macro="requirements"/>
16 <expand macro="required_files"/> 16 <expand macro="required_files"/>
17 <command detect_errors="exit_code"><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
18 export COMPlus_EnableDiagnostics=0 &&
18 ## link galaxy datasets to filenames accepted by maxquant 19 ## link galaxy datasets to filenames accepted by maxquant
19 #import re 20 #import re
20 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $input_opts.infiles] 21 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $input_opts.infiles]
21 #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names] 22 #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names]
22 #for $target, $link in zip($infiles, $names_with_ext) 23 #for $target, $link in zip($infiles, $names_with_ext)
66 67
67 <inputs> 68 <inputs>
68 <conditional name="input_opts"> 69 <conditional name="input_opts">
69 <param name="ftype" type="select" label="choose the type of your input files"> 70 <param name="ftype" type="select" label="choose the type of your input files">
70 <option value=".thermo.raw">thermo.raw</option> 71 <option value=".thermo.raw">thermo.raw</option>
71 <option value=".mzxml">mzXML</option> 72 <option value=".mzxml">mzxml</option>
72 <option value=".mzml">mzML</option> 73 <option value=".mzml">mzml</option>
73 </param> 74 </param>
74 <when value=".thermo.raw"> 75 <when value=".thermo.raw">
75 <param multiple="true" name="infiles" type="data" 76 <param multiple="true" name="infiles" type="data"
76 format="thermo.raw" label="RAW Files" 77 format="thermo.raw" label="RAW Files"
77 help="Specify one or more Thermo RAW files" /> 78 help="Specify one or more Thermo RAW files" />
78 </when> 79 </when>
79 <when value=".mzxml"> 80 <when value=".mzxml">
80 <param multiple="true" name="infiles" type="data" 81 <param multiple="true" name="infiles" type="data"
81 format="mzXML" label="mzXML Files" 82 format="mzxml" label="mzXML Files"
82 help="Specify one or more mzXML files" /> 83 help="Specify one or more mzXML files" />
83 </when> 84 </when>
84 <when value=".mzml"> 85 <when value=".mzml">
85 <param multiple="true" name="infiles" type="data" 86 <param multiple="true" name="infiles" type="data"
86 format="mzML" label="mzML Files" 87 format="mzml" label="mzML Files"
87 help="Specify one or more mzML files" /> 88 help="Specify one or more mzML files" />
88 </when> 89 </when>
89 </conditional> 90 </conditional>
90 <param format="fasta" multiple="true" name="fasta_files" 91 <param format="fasta" multiple="true" name="fasta_files"
91 type="data" label="FASTA files" 92 type="data" label="FASTA files"
191 This tool is a wrapper for MaxQuant v@VERSION@. It gets its search parameters from a previously created parameter file (mqpar.xml). A similiar tool that allows the specification of search parameters directly through galaxy is available as well and should be preferred, if possible. 192 This tool is a wrapper for MaxQuant v@VERSION@. It gets its search parameters from a previously created parameter file (mqpar.xml). A similiar tool that allows the specification of search parameters directly through galaxy is available as well and should be preferred, if possible.
192 193
193 **Input files** 194 **Input files**
194 195
195 - Thermo raw file or mzXML file 196 - Thermo raw file or mzXML file
196 - The datatype has to be 'thermo.raw' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes) 197 - The datatype has to be 'thermo.raw' or 'mzxml'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
197 - mqpar.xml: 198 - mqpar.xml:
198 - MaxQuant parameters will be taken from the provided mqpar.xml file. This parameter file MUST be created using the same version of MaxQuant as is used by this tool. The correct version of MaxQuant can be obtained via the bioconda channel for the conda package manager. 199 - MaxQuant parameters will be taken from the provided mqpar.xml file. This parameter file MUST be created using the same version of MaxQuant as is used by this tool. The correct version of MaxQuant can be obtained via the bioconda channel for the conda package manager.
199 200
200 **Output files** 201 **Output files**
201 202