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comparison maxquant_mqpar.xml @ 3:2d67fb758956 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
author galaxyp
date Sat, 11 Apr 2020 11:50:09 -0400
parents 3fc2116ac6d9
children 9cb7dcc07dae
comparison
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2:3fc2116ac6d9 3:2d67fb758956
1 <tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@"> 1 <tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@">
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 ${on_string}" name="@NAME@">
10 <filter>'@NAME@' in output</filter>
11 </data>
12 </xml>
3 <import>macros.xml</import> 13 <import>macros.xml</import>
4 </macros> 14 </macros>
5 <requirements> 15 <expand macro="requirements"/>
6 <requirement type="package" version="@VERSION@">maxquant</requirement>
7 <requirement type="package" version="3.7">python</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 16 <command detect_errors="exit_code"><![CDATA[
17 ## link galaxy datasets to filenames accepted by maxquant
10 #import re 18 #import re
19 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $input.infiles]
20 #set names_with_ext = [($name if ($name).lower().endswith(str($input.ftype)) else $name + str($input.ftype)) for $name in $names]
21 #for $target, $link in zip($infiles, $names_with_ext)
22 ln -s '$target' '$link' &&
23 #end for
11 24
12 python3 '$__tool_directory__/mqwrapper.py' 25 python3 '$__tool_directory__/modify_mqpar.py'
26 #set inf = ','.join($names_with_ext)
27 --infiles='$inf'
28 --version=@VERSION@
13 --num_threads=\${GALAXY_SLOTS:-1} 29 --num_threads=\${GALAXY_SLOTS:-1}
14 --substitution_rx='@SUBSTITUTION_RX@' 30 --substitution_rx='@SUBSTITUTION_RX@'
15 #if $infile.select == "mzxml_files" 31 --fasta_files='$fasta_files'
16 --mzxml_files='$infile.mzxml_files' 32 --description_parse_rule='$description_parse_rule'
17 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $infile.mzxml_files]) 33 --identifier_parse_rule='$identifier_parse_rule'
18 #else 34 '$mqpar'
19 --raw_files='$infile.raw_files' 35
20 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $infile.raw_files]) 36 &&
37 maxquant mqpar.xml
38 #if 'log' in $output:
39 >> '$log'
21 #end if 40 #end if
22 --infile_names='$names' 41 && mv '$mqpar' combined/txt/mqpar.xml
23 --version='@VERSION@' 42 #if 'output_all' in $output:
24 --fasta_files='$fasta_files' 43 &&
25 --identifier_parse_rule='$identifier_parse_rule' 44 tar -zcf '$output_all' ./combined/txt
26 --description_parse_rule='$description_parse_rule' 45 #end if
27 --mqpar_in='$mqpar_in' 46
47 #if $qc.do_it:
48 &&
49 Rscript '$qr' '$qr_yaml'
50 #if 'log' in $output:
51 >> '$log' 2>&1
52 #end if
53 &&
54 cp ./combined/txt/report_v0.92.6_combined.pdf '$ptxqc_report'
55 #end if
56 ]]></command>
28 57
29 --evidence='$evidence' 58 <configfiles>
30 --msms='$msms' 59 <expand macro="ptxqc"/>
31 --parameters='$parameters' 60 </configfiles>
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 61
47 > '$log'
48 ]]></command>
49 <inputs> 62 <inputs>
50 <conditional name="infile"> 63 <conditional name="input">
51 <param name="select" type="select" label="choose the type of your input files"> 64 <param name="ftype" type="select" label="choose the type of your input files">
52 <option value="raw_files">Thermo.raw</option> 65 <option value=".thermo.raw">thermo.raw</option>
53 <option value="mzxml_files">mzXML</option> 66 <option value=".mzxml">mzXML</option>
67 <option value=".mzml">mzML</option>
54 </param> 68 </param>
55 <when value="raw_files"> 69 <when value=".thermo.raw">
56 <param multiple="true" name="raw_files" type="data" 70 <param multiple="true" name="infiles" type="data"
57 format="thermo.raw" label="RAW Files" 71 format="thermo.raw" label="RAW Files"
58 help="Specify one or more Thermo RAW files" /> 72 help="Specify one or more Thermo RAW files" />
59 </when> 73 </when>
60 <when value="mzxml_files"> 74 <when value=".mzxml">
61 <param multiple="true" name="mzxml_files" type="data" 75 <param multiple="true" name="infiles" type="data"
62 format="mzxml" label="mzXML Files" 76 format="mzXML" label="mzXML Files"
63 help="Specify one or more mzXML files" /> 77 help="Specify one or more mzXML files" />
78 </when>
79 <when value=".mzml">
80 <param multiple="true" name="infiles" type="data"
81 format="mzML" label="mzML Files"
82 help="Specify one or more mzML files" />
64 </when> 83 </when>
65 </conditional> 84 </conditional>
66 <param format="fasta" multiple="true" name="fasta_files" 85 <param format="fasta" multiple="true" name="fasta_files"
67 type="data" label="FASTA files" 86 type="data" label="FASTA files"
68 help="Specify one or more FASTA databases." /> 87 help="Specify one or more FASTA databases." />
81 <valid initial="string.printable"> 100 <valid initial="string.printable">
82 <remove value="&apos;"/> 101 <remove value="&apos;"/>
83 </valid> 102 </valid>
84 </sanitizer> 103 </sanitizer>
85 </param> 104 </param>
86 <param type="data" name="mqpar_in" format="xml" 105 <param type="data" name="mqpar" format="xml"
87 label="mqpar.xml file with your search parameters. RAW file names 106 label="mqpar.xml file with your search parameters. RAW file names
88 must match the names displayed in galaxy. Their paths 107 must match the names displayed in galaxy. Their paths
89 from the local machine are ignored. E.g. a file named 108 from the local machine are ignored. E.g. a file named
90 'test01.raw' in galaxy can either be named 'test01.raw' or 109 'test01.raw' in galaxy can either be named 'test01.raw' or
91 'D:\path\to\test01.raw' in the mqpar.xml."/> 110 'D:\path\to\test01.raw' in the mqpar.xml."/>
92 111 <expand macro="ptxqc-opts"/>
93 <param type="select" name="output" label="Select the desired outputs." 112 <param type="select" name="output" label="Select the desired outputs."
94 multiple="true" optional="false"> 113 multiple="true" optional="false">
95 <expand macro="output_option" name="proteinGroups" label="Protein Groups"/> 114 <option value="proteinGroups">Protein Groups</option>
96 <expand macro="output_option" name="mqpar_out" label="mqpar.xml"/> 115 <option value="mqpar">mqpar.xml</option>
97 <expand macro="output_option" name="peptides" label="Peptides"/> 116 <option value="peptides">Peptides</option>
98 <expand macro="output_option" name="evidence" label="Evidence"/> 117 <option value="evidence">Evidence</option>
99 <expand macro="output_option" name="parameters" label="Tabular Paramters"/> 118 <option value="parameters">Tabular Paramters</option>
100 <expand macro="output_option" name="msms" label="MSMS"/> 119 <option value="msms">MSMS</option>
101 <expand macro="output_option" name="mzTab" label="mzTab"/> 120 <option value="mzTab">mzTab</option>
102 <expand macro="output_option" name="allPeptides" label="all peptides"/> 121 <option value="allPeptides">all peptides</option>
103 <expand macro="output_option" name="libraryMatch" label="library match"/> 122 <option value="libraryMatch">library match</option>
104 <expand macro="output_option" name="matchedFeatures" 123 <option value="matchedFeatures">matched features</option>
105 label="matched features"/> 124 <option value="modificationSpecificPeptides">modification specific peptides</option>
106 <expand macro="output_option" name="modificationSpecificPeptides" 125 <option value="ms3Scans">ms3 scans</option>
107 label="modification specific peptides"/> 126 <option value="msmsScans">msms scans</option>
108 <expand macro="output_option" name="ms3Scans" label="ms3 scans"/> 127 <option value="mzRange">mz range</option>
109 <expand macro="output_option" name="msmsScans" label="msms scans"/> 128 <option value="peptideSection">peptide section</option>
110 <expand macro="output_option" name="mzRange" label="mz range"/> 129 <option value="summary">summary</option>
111 <expand macro="output_option" name="peptideSection" label="peptide section"/> 130 <option value="output_all">complete 'combined/txt/' directory (compressed)</option>
112 <expand macro="output_option" name="summary" label="summary"/> 131 <option value="log">MaxQuant and PTXQC log</option>
113 <expand macro="output_option" name="output_all"
114 label="complete 'combined/txt/' directory (compressed)"/>
115 </param> 132 </param>
116 </inputs> 133 </inputs>
117 134
118 <outputs> 135 <expand macro="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>
145 136
146 <tests> 137 <tests>
147 <test> 138 <test>
148 <param name="select" value="mzxml_files" /> 139 <param name="ftype" value=".mzxml" />
149 <param name="mzxml_files" value="BSA_min_22,BSA_min_21.mzXML" /> 140 <param name="infiles" value="BSA_min_22,BSA_min_21.mzXML" />
150 <param name="fasta_files" value="bsa.fasta" /> 141 <param name="fasta_files" value="bsa.fasta" />
151 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 142 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
152 <param name="description_parse_rule" value="&gt;(.*)" /> 143 <param name="description_parse_rule" value="&gt;(.*)" />
153 <param name="mqpar_in" value="two/mqpar.xml" /> 144 <param name="mqpar" value="mqpar.xml" />
154 <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides" /> 145 <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,output_all" />
155 <output name="evidence" file="two/combined/txt/evidence.txt" /> 146 <output name="evidence" file="txt/evidence.txt" />
156 <output name="msms" file="two/combined/txt/msms.txt" /> 147 <output name="msms" file="txt/msms.txt" lines_diff="2" />
157 <output name="mzTab" file="two/combined/txt/mzTab.mzTab" lines_diff="4"/> 148 <output name="allPeptides" file="txt/allPeptides.txt" lines_diff="32" />
158 <output name="allPeptides" file="two/combined/txt/allPeptides.txt" lines_diff="14"/> 149 <output name="msmsScans" file="txt/msmsScans.txt" lines_diff="4"/>
159 <output name="msmsScans" file="two/combined/txt/msmsScans.txt" /> 150 <output name="mzRange" file="txt/mzRange.txt" />
160 <output name="mzRange" file="two/combined/txt/mzRange.txt" /> 151 <output name="parameters" file="txt/parameters.txt" lines_diff="8"/>
161 <output name="parameters" file="two/combined/txt/parameters.txt" lines_diff="8"/> 152 <output name="peptides" file="txt/peptides.txt" />
162 <output name="peptides" file="two/combined/txt/peptides.txt" /> 153 <output name="proteinGroups" file="txt/proteinGroups.txt" />
163 <output name="peptideSection" file="two/combined/txt/peptideSection.txt" /> 154 <output name="summary" file="txt/summary.txt" />
164 <output name="proteinGroups" file="two/combined/txt/proteinGroups.txt" /> 155 <output name="modificationSpecificPeptides" file="txt/modificationSpecificPeptides.txt" />
165 <output name="summary" file="two/combined/txt/summary.txt" />
166 <output name="modificationSpecificPeptides" file="two/combined/txt/modificationSpecificPeptides.txt" />
167 </test> 156 </test>
168 </tests> 157 </tests>
169 <help><![CDATA[ 158 <help><![CDATA[
170 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. 159 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
171 160
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. 161 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.
173 162
174 **Input files** 163 **Input files**
175 164
176 - Thermo raw file or mzXML file 165 - 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) 166 - 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)
180 169
181 **Output files** 170 **Output files**
182 171
183 Different output file options are available, most of them are part of the MaxQuant txt folder. An additional mztab output option is implemented. 172 Different output file options are available, most of them are part of the MaxQuant txt folder. An additional mztab output option is implemented.
184 ]]></help> 173 ]]></help>
185 <citations> 174 <expand macro="citations"/>
186 <citation type="bibtex">
187 @article{cox2008maxquant,
188 title={MaxQuant enables high peptide identification rates, individualized
189 ppb-range mass accuracies and proteome-wide protein quantification},
190 author={Cox, J{\"u}rgen and Mann, Matthias},
191 journal={Nature biotechnology},
192 volume={26},
193 number={12},
194 pages={1367},
195 year={2008},
196 publisher={Nature Publishing Group}
197 }
198 </citation>
199 <citation type="bibtex">
200 @article{tyanova2016maxquant,
201 title={The MaxQuant computational platform for mass
202 spectrometry-based shotgun proteomics},
203 author={Tyanova, Stefka and Temu, Tikira and Cox, J{\"u}rgen},
204 journal={Nature protocols},
205 volume={11},
206 number={12},
207 pages={2301},
208 year={2016},
209 publisher={Nature Publishing Group}
210 }
211 </citation>
212 </citations>
213 </tool> 175 </tool>