Mercurial > repos > galaxyp > maxquant_mqpar

annotate maxquant_mqpar.xml @ 2:b95d333b4a3f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
author galaxyp
date Thu, 15 Aug 2019 08:08:23 -0400
parents a52165553917
children f9c1f29d9711
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
1 <tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@">
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
2 <macros>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
3 <import>macros.xml</import>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
4 </macros>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
5 <requirements>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
6 <requirement type="package" version="@VERSION@">maxquant</requirement>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
7 <requirement type="package" version="3.7">python</requirement>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
8 </requirements>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
10 #import re
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
11
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
12 python3 '$__tool_directory__/mqwrapper.py'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
13 --num_threads=\${GALAXY_SLOTS:-1}
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
14 --substitution_rx='@SUBSTITUTION_RX@'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
15 #if $infile.select == "mzxml_files"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
16 --mzxml_files='$infile.mzxml_files'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
17 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $infile.mzxml_files])
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
18 #else
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
19 --raw_files='$infile.raw_files'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
20 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $infile.raw_files])
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
21 #end if
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
22 --infile_names='$names'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
23 --version='@VERSION@'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
24 --fasta_files='$fasta_files'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
25 --identifier_parse_rule='$identifier_parse_rule'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
26 --description_parse_rule='$description_parse_rule'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
27 --mqpar_in='$mqpar_in'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
28
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
29 --evidence='$evidence'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
30 --msms='$msms'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
31 --parameters='$parameters'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
32 --peptides='$peptides'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
33 --proteinGroups='$proteinGroups'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
34 --allPeptides='$allPeptides'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
35 --libraryMatch='$libraryMatch'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
36 --matchedFeatures='$matchedFeatures'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
37 --modificationSpecificPeptides='$modificationSpecificPeptides'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
38 --ms3Scans='$ms3Scans'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
39 --msmsScans='$msmsScans'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
40 --mzRange='$mzRange'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
41 --peptideSection='$peptideSection'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
42 --summary='$summary'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
43 --mzTab='$mzTab'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
44 --output_all='$output_all'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
45 --mqpar_out='$mqpar_out'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
46
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
47 > '$log'
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
48 ]]></command>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
49 <inputs>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
50 <conditional name="infile">
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
51 <param name="select" type="select" label="choose the type of your input files">
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
52 <option value="raw_files">Thermo.raw</option>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
53 <option value="mzxml_files">mzXML</option>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
54 </param>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
55 <when value="raw_files">
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
56 <param multiple="true" name="raw_files" type="data"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
57 format="thermo.raw" label="RAW Files"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
58 help="Specify one or more Thermo RAW files" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
59 </when>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
60 <when value="mzxml_files">
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
61 <param multiple="true" name="mzxml_files" type="data"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
62 format="mzxml" label="mzXML Files"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
63 help="Specify one or more mzXML files" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
64 </when>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
65 </conditional>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
66 <param format="fasta" multiple="true" name="fasta_files"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
67 type="data" label="FASTA files"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
68 help="Specify one or more FASTA databases." />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
69 <param name="identifier_parse_rule" type="text"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
70 label="identifier parse rule" value="^&gt;.*\|(.*)\|.*$">
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
71 <sanitizer>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
72 <valid initial="string.printable">
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
73 <remove value="&apos;"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
74 </valid>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
75 </sanitizer>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
76 </param>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
77 <param name="description_parse_rule" type="text"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
78 label="description parse rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
79 help="Modify parse rules if needed">
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
80 <sanitizer>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
81 <valid initial="string.printable">
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
82 <remove value="&apos;"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
83 </valid>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
84 </sanitizer>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
85 </param>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
86 <param type="data" name="mqpar_in" format="xml"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
87 label="mqpar.xml file with your search parameters. RAW file names
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
88 must match the names displayed in galaxy. Their paths
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
89 from the local machine are ignored. E.g. a file named
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
90 'test01.raw' in galaxy can either be named 'test01.raw' or
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
91 'D:\path\to\test01.raw' in the mqpar.xml."/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
92
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
93 <param type="select" name="output" label="Select the desired outputs."
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
94 multiple="true" optional="false">
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
95 <expand macro="output_option" name="proteinGroups" label="Protein Groups"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
96 <expand macro="output_option" name="mqpar_out" label="mqpar.xml"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
97 <expand macro="output_option" name="peptides" label="Peptides"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
98 <expand macro="output_option" name="evidence" label="Evidence"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
99 <expand macro="output_option" name="parameters" label="Tabular Paramters"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
100 <expand macro="output_option" name="msms" label="MSMS"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
101 <expand macro="output_option" name="mzTab" label="mzTab"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
102 <expand macro="output_option" name="allPeptides" label="all peptides"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
103 <expand macro="output_option" name="libraryMatch" label="library match"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
104 <expand macro="output_option" name="matchedFeatures"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
105 label="matched features"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
106 <expand macro="output_option" name="modificationSpecificPeptides"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
107 label="modification specific peptides"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
108 <expand macro="output_option" name="ms3Scans" label="ms3 scans"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
109 <expand macro="output_option" name="msmsScans" label="msms scans"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
110 <expand macro="output_option" name="mzRange" label="mz range"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
111 <expand macro="output_option" name="peptideSection" label="peptide section"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
112 <expand macro="output_option" name="summary" label="summary"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
113 <expand macro="output_option" name="output_all"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
114 label="complete 'combined/txt/' directory (compressed)"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
115 </param>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
116 </inputs>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
117
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
118 <outputs>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
119 <expand macro="output" name="mqpar_out" label="mqpar.xml" format="xml"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
120 <expand macro="output" name="proteinGroups" label="MaxQuant Protein Groups"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
121 <expand macro="output" name="peptides" label="MaxQuant Peptides"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
122 <expand macro="output" name="evidence" label="MaxQuant Evidence"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
123 <expand macro="output" name="parameters" label="MaxQuant Tabular Parameters"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
124 <expand macro="output" name="msms" label="MaxQuant MSMS"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
125 <expand macro="output" name="mzTab" label="mzTab"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
126 <expand macro="output" name="allPeptides" label="all peptides"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
127 <expand macro="output" name="libraryMatch" label="library match"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
128 <expand macro="output" name="matchedFeatures" label="matched features"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
129 <expand macro="output" name="modificationSpecificPeptides"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
130 label="modification specific peptides"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
131 <expand macro="output" name="ms3Scans" label="ms3 scans"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
132 <expand macro="output" name="msmsScans"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
133 label="msms Scans"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
134 <expand macro="output" name="mzRange"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
135 label="mz range"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
136 <expand macro="output" name="peptideSection"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
137 label="peptide section"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
138 <expand macro="output" name="summary"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
139 label="MaxQuant summary"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
140 <expand macro="output" format="tar" name="output_all"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
141 label="'combined/txt/' directory"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
142 <data name="log" format="txt"
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
143 label="log"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
144 </outputs>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
145
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
146 <tests>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
147 <test>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
148 <param name="select" value="mzxml_files" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
149 <param name="mzxml_files" value="BSA_min_22,BSA_min_21.mzXML" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
150 <param name="fasta_files" value="bsa.fasta" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
151 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
152 <param name="description_parse_rule" value="&gt;(.*)" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
153 <param name="mqpar_in" value="two/mqpar.xml" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
154 <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
155 <output name="evidence" file="two/combined/txt/evidence.txt" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
156 <output name="msms" file="two/combined/txt/msms.txt" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
157 <output name="mzTab" file="two/combined/txt/mzTab.mzTab" lines_diff="4"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
158 <output name="allPeptides" file="two/combined/txt/allPeptides.txt" lines_diff="14"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
159 <output name="msmsScans" file="two/combined/txt/msmsScans.txt" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
160 <output name="mzRange" file="two/combined/txt/mzRange.txt" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
161 <output name="parameters" file="two/combined/txt/parameters.txt" lines_diff="8"/>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
162 <output name="peptides" file="two/combined/txt/peptides.txt" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
163 <output name="peptideSection" file="two/combined/txt/peptideSection.txt" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
164 <output name="proteinGroups" file="two/combined/txt/proteinGroups.txt" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
165 <output name="summary" file="two/combined/txt/summary.txt" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
166 <output name="modificationSpecificPeptides" file="two/combined/txt/modificationSpecificPeptides.txt" />
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
167 </test>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
168 </tests>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
169 <help><![CDATA[
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
170 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
171
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
172 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.
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
173
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
174 **Input files**
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
175
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
176 - Thermo raw file or mzXML file
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
177 - 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)
2
b95d333b4a3f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 0
diff changeset
178 - mqpar.xml:
b95d333b4a3f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 0
diff changeset
179 - 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.
0
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
180
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
181 **Output files**
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
182
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
183 Different output file options are available, most of them are part of the MaxQuant txt folder. An additional mztab output option is implemented.
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
184 ]]></help>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
185 <citations>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
186 <citation type="bibtex">
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
187 @article{cox2008maxquant,
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
188 title={MaxQuant enables high peptide identification rates, individualized
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
189 ppb-range mass accuracies and proteome-wide protein quantification},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
190 author={Cox, J{\"u}rgen and Mann, Matthias},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
191 journal={Nature biotechnology},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
192 volume={26},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
193 number={12},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
194 pages={1367},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
195 year={2008},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
196 publisher={Nature Publishing Group}
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
197 }
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
198 </citation>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
199 <citation type="bibtex">
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
200 @article{tyanova2016maxquant,
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
201 title={The MaxQuant computational platform for mass
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
202 spectrometry-based shotgun proteomics},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
203 author={Tyanova, Stefka and Temu, Tikira and Cox, J{\"u}rgen},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
204 journal={Nature protocols},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
205 volume={11},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
206 number={12},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
207 pages={2301},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
208 year={2016},
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
209 publisher={Nature Publishing Group}
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
210 }
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
211 </citation>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
212 </citations>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
213 </tool>