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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
author galaxyp
date Sat, 20 Jul 2019 04:53:23 -0400
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1 <tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <requirements>
6 <requirement type="package" version="@VERSION@">maxquant</requirement>
7 <requirement type="package" version="3.7">python</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 #import re
11
12 python3 '$__tool_directory__/mqwrapper.py'
13 --num_threads=\${GALAXY_SLOTS:-1}
14 --substitution_rx='@SUBSTITUTION_RX@'
15 #if $infile.select == "mzxml_files"
16 --mzxml_files='$infile.mzxml_files'
17 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $infile.mzxml_files])
18 #else
19 --raw_files='$infile.raw_files'
20 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $infile.raw_files])
21 #end if
22 --infile_names='$names'
23 --version='@VERSION@'
24 --fasta_files='$fasta_files'
25 --identifier_parse_rule='$identifier_parse_rule'
26 --description_parse_rule='$description_parse_rule'
27 --mqpar_in='$mqpar_in'
28
29 --evidence='$evidence'
30 --msms='$msms'
31 --parameters='$parameters'
32 --peptides='$peptides'
33 --proteinGroups='$proteinGroups'
34 --allPeptides='$allPeptides'
35 --libraryMatch='$libraryMatch'
36 --matchedFeatures='$matchedFeatures'
37 --modificationSpecificPeptides='$modificationSpecificPeptides'
38 --ms3Scans='$ms3Scans'
39 --msmsScans='$msmsScans'
40 --mzRange='$mzRange'
41 --peptideSection='$peptideSection'
42 --summary='$summary'
43 --mzTab='$mzTab'
44 --output_all='$output_all'
45 --mqpar_out='$mqpar_out'
46
47 > '$log'
48 ]]></command>
49 <inputs>
50 <conditional name="infile">
51 <param name="select" type="select" label="choose the type of your input files">
52 <option value="raw_files">Thermo.raw</option>
53 <option value="mzxml_files">mzXML</option>
54 </param>
55 <when value="raw_files">
56 <param multiple="true" name="raw_files" type="data"
57 format="thermo.raw" label="RAW Files"
58 help="Specify one or more Thermo RAW files" />
59 </when>
60 <when value="mzxml_files">
61 <param multiple="true" name="mzxml_files" type="data"
62 format="mzxml" label="mzXML Files"
63 help="Specify one or more mzXML files" />
64 </when>
65 </conditional>
66 <param format="fasta" multiple="true" name="fasta_files"
67 type="data" label="FASTA files"
68 help="Specify one or more FASTA databases." />
69 <param name="identifier_parse_rule" type="text"
70 label="identifier parse rule" value="^&gt;.*\|(.*)\|.*$">
71 <sanitizer>
72 <valid initial="string.printable">
73 <remove value="&apos;"/>
74 </valid>
75 </sanitizer>
76 </param>
77 <param name="description_parse_rule" type="text"
78 label="description parse rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$"
79 help="Modify parse rules if needed">
80 <sanitizer>
81 <valid initial="string.printable">
82 <remove value="&apos;"/>
83 </valid>
84 </sanitizer>
85 </param>
86 <param type="data" name="mqpar_in" format="xml"
87 label="mqpar.xml file with your search parameters. RAW file names
88 must match the names displayed in galaxy. Their paths
89 from the local machine are ignored. E.g. a file named
90 'test01.raw' in galaxy can either be named 'test01.raw' or
91 'D:\path\to\test01.raw' in the mqpar.xml."/>
92
93 <param type="select" name="output" label="Select the desired outputs."
94 multiple="true" optional="false">
95 <expand macro="output_option" name="proteinGroups" label="Protein Groups"/>
96 <expand macro="output_option" name="mqpar_out" label="mqpar.xml"/>
97 <expand macro="output_option" name="peptides" label="Peptides"/>
98 <expand macro="output_option" name="evidence" label="Evidence"/>
99 <expand macro="output_option" name="parameters" label="Tabular Paramters"/>
100 <expand macro="output_option" name="msms" label="MSMS"/>
101 <expand macro="output_option" name="mzTab" label="mzTab"/>
102 <expand macro="output_option" name="allPeptides" label="all peptides"/>
103 <expand macro="output_option" name="libraryMatch" label="library match"/>
104 <expand macro="output_option" name="matchedFeatures"
105 label="matched features"/>
106 <expand macro="output_option" name="modificationSpecificPeptides"
107 label="modification specific peptides"/>
108 <expand macro="output_option" name="ms3Scans" label="ms3 scans"/>
109 <expand macro="output_option" name="msmsScans" label="msms scans"/>
110 <expand macro="output_option" name="mzRange" label="mz range"/>
111 <expand macro="output_option" name="peptideSection" label="peptide section"/>
112 <expand macro="output_option" name="summary" label="summary"/>
113 <expand macro="output_option" name="output_all"
114 label="complete 'combined/txt/' directory (compressed)"/>
115 </param>
116 </inputs>
117
118 <outputs>
119 <expand macro="output" name="mqpar_out" label="mqpar.xml" format="xml"/>
120 <expand macro="output" name="proteinGroups" label="MaxQuant Protein Groups"/>
121 <expand macro="output" name="peptides" label="MaxQuant Peptides"/>
122 <expand macro="output" name="evidence" label="MaxQuant Evidence"/>
123 <expand macro="output" name="parameters" label="MaxQuant Tabular Parameters"/>
124 <expand macro="output" name="msms" label="MaxQuant MSMS"/>
125 <expand macro="output" name="mzTab" label="mzTab"/>
126 <expand macro="output" name="allPeptides" label="all peptides"/>
127 <expand macro="output" name="libraryMatch" label="library match"/>
128 <expand macro="output" name="matchedFeatures" label="matched features"/>
129 <expand macro="output" name="modificationSpecificPeptides"
130 label="modification specific peptides"/>
131 <expand macro="output" name="ms3Scans" label="ms3 scans"/>
132 <expand macro="output" name="msmsScans"
133 label="msms Scans"/>
134 <expand macro="output" name="mzRange"
135 label="mz range"/>
136 <expand macro="output" name="peptideSection"
137 label="peptide section"/>
138 <expand macro="output" name="summary"
139 label="MaxQuant summary"/>
140 <expand macro="output" format="tar" name="output_all"
141 label="'combined/txt/' directory"/>
142 <data name="log" format="txt"
143 label="log"/>
144 </outputs>
145
146 <tests>
147 <test>
148 <param name="select" value="mzxml_files" />
149 <param name="mzxml_files" value="BSA_min_22,BSA_min_21.mzXML" />
150 <param name="fasta_files" value="bsa.fasta" />
151 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
152 <param name="description_parse_rule" value="&gt;(.*)" />
153 <param name="mqpar_in" value="two/mqpar.xml" />
154 <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides" />
155 <output name="evidence" file="two/combined/txt/evidence.txt" />
156 <output name="msms" file="two/combined/txt/msms.txt" />
157 <output name="mzTab" file="two/combined/txt/mzTab.mzTab" lines_diff="4"/>
158 <output name="allPeptides" file="two/combined/txt/allPeptides.txt" lines_diff="14"/>
159 <output name="msmsScans" file="two/combined/txt/msmsScans.txt" />
160 <output name="mzRange" file="two/combined/txt/mzRange.txt" />
161 <output name="parameters" file="two/combined/txt/parameters.txt" lines_diff="8"/>
162 <output name="peptides" file="two/combined/txt/peptides.txt" />
163 <output name="peptideSection" file="two/combined/txt/peptideSection.txt" />
164 <output name="proteinGroups" file="two/combined/txt/proteinGroups.txt" />
165 <output name="summary" file="two/combined/txt/summary.txt" />
166 <output name="modificationSpecificPeptides" file="two/combined/txt/modificationSpecificPeptides.txt" />
167 </test>
168 </tests>
169 <help><![CDATA[
170 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
171
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.
173
174 **Input files**
175
176 - Thermo raw file or mzXML file
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)
178 - Optional files:
179 - mqpar.xml:
180 - 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.
181
182 **Output files**
183
184 Different output file options are available, most of them are part of the MaxQuant txt folder. An additional mztab output option is implemented.
185 ]]></help>
186 <citations>
187 <citation type="bibtex">
188 @article{cox2008maxquant,
189 title={MaxQuant enables high peptide identification rates, individualized
190 ppb-range mass accuracies and proteome-wide protein quantification},
191 author={Cox, J{\"u}rgen and Mann, Matthias},
192 journal={Nature biotechnology},
193 volume={26},
194 number={12},
195 pages={1367},
196 year={2008},
197 publisher={Nature Publishing Group}
198 }
199 </citation>
200 <citation type="bibtex">
201 @article{tyanova2016maxquant,
202 title={The MaxQuant computational platform for mass
203 spectrometry-based shotgun proteomics},
204 author={Tyanova, Stefka and Temu, Tikira and Cox, J{\"u}rgen},
205 journal={Nature protocols},
206 volume={11},
207 number={12},
208 pages={2301},
209 year={2016},
210 publisher={Nature Publishing Group}
211 }
212 </citation>
213 </citations>
214 </tool>