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comparison maxquant_mqpar.xml @ 20:5d013f405259 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
author galaxyp
date Mon, 19 Jun 2023 17:01:43 +0000
parents acb539867086
children
comparison
equal deleted inserted replaced
19:ef25c9c04aee 20:5d013f405259
1 <tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@" profile="21.05"> 1 <tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@" profile="@PROFILE@">
2 <macros> 2 <macros>
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@">
5 <filter>'@NAME@' in output</filter>
6 </data>
7 </xml>
8 <xml name="output_from_wdir" token_ext="txt" token_format="tabular" token_label="default description" token_name="default">
9 <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="@LABEL@ for ${on_string}" name="@NAME@">
10 <filter>'@NAME@' in output</filter>
11 </data>
12 </xml>
13 <import>macros.xml</import> 3 <import>macros.xml</import>
14 </macros> 4 </macros>
15 <expand macro="requirements"/> 5 <expand macro="requirements"/>
16 <expand macro="required_files"/> 6 <expand macro="required_files"/>
17 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
48 #if 'output_all' in $output: 38 #if 'output_all' in $output:
49 && 39 &&
50 tar -zcf '$output_all' ./combined/txt 40 tar -zcf '$output_all' ./combined/txt
51 #end if 41 #end if
52 42
53 #if $qc.do_it: 43 #if $qc.do_it == 'true':
54 && 44 &&
55 Rscript '$qr' '$qr_yaml' 45 Rscript '$qr' '$qr_yaml'
56 #if 'log' in $output: 46 #if 'log' in $output:
57 >> '$log' 2>&1 47 >> '$log' 2>&1
58 #end if 48 #end if
146 <param name="infiles" value="BSA_min_22,BSA_min_21.mzXML" /> 136 <param name="infiles" value="BSA_min_22,BSA_min_21.mzXML" />
147 <param name="fasta_files" value="bsa.fasta" /> 137 <param name="fasta_files" value="bsa.fasta" />
148 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 138 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
149 <param name="description_parse_rule" value="&gt;(.*)" /> 139 <param name="description_parse_rule" value="&gt;(.*)" />
150 <param name="mqpar_input" value="mqpar/mqpar.xml" /> 140 <param name="mqpar_input" value="mqpar/mqpar.xml" />
151 <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" /> 141 <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" />
152 <output name="evidence"> 142 <output name="evidence">
153 <assert_contents> 143 <assert_contents>
154 <has_text text="AEFVEVTK" /> 144 <has_text text="AEFVEVTK" />
155 </assert_contents> 145 </assert_contents>
156 </output> 146 </output>