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comparison maxquant_mqpar.xml @ 15:97a7f34fcb6a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
author galaxyp
date Wed, 11 Aug 2021 09:24:23 +0000
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children 1f39c833f65f
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14:e42225f8a659 15:97a7f34fcb6a
1 <tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@">
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 ${on_string}" name="@NAME@">
10 <filter>'@NAME@' in output</filter>
11 </data>
12 </xml>
13 <import>macros.xml</import>
14 </macros>
15 <expand macro="requirements"/>
16 <command detect_errors="exit_code"><![CDATA[
17 ## link galaxy datasets to filenames accepted by maxquant
18 #import re
19 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $input_opts.infiles]
20 #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names]
21 #for $target, $link in zip($infiles, $names_with_ext)
22 #if str($input_opts.ftype) == '.thermo.raw':
23 cp '$target' '$link' &&
24 #else:
25 ln -s '$target' '$link' &&
26 #end if
27 #end for
28
29 python3 '$__tool_directory__/modify_mqpar.py'
30 #set inf = ','.join($names_with_ext)
31 --infiles='$inf'
32 --version=@VERSION@
33 --num_threads=\${GALAXY_SLOTS:-1}
34 --substitution_rx='@SUBSTITUTION_RX@'
35 --fasta_files='$fasta_files'
36 --description_parse_rule='$description_parse_rule'
37 --identifier_parse_rule='$identifier_parse_rule'
38 '$mqpar_input'
39
40 &&
41 maxquant mqpar.xml
42 #if 'log' in $output:
43 >> '$log'
44 #end if
45 && mv mqpar.xml combined/txt/mqpar.xml
46 #if 'output_all' in $output:
47 &&
48 tar -zcf '$output_all' ./combined/txt
49 #end if
50
51 #if $qc.do_it:
52 &&
53 Rscript '$qr' '$qr_yaml'
54 #if 'log' in $output:
55 >> '$log' 2>&1
56 #end if
57 &&
58 cp ./combined/txt/report_v@VERSION_PTXQC@_combined.pdf '$ptxqc_report'
59 #end if
60 ]]></command>
61
62 <configfiles>
63 <expand macro="ptxqc"/>
64 </configfiles>
65
66 <inputs>
67 <conditional name="input_opts">
68 <param name="ftype" type="select" label="choose the type of your input files">
69 <option value=".thermo.raw">thermo.raw</option>
70 <option value=".mzxml">mzXML</option>
71 <option value=".mzml">mzML</option>
72 </param>
73 <when value=".thermo.raw">
74 <param multiple="true" name="infiles" type="data"
75 format="thermo.raw" label="RAW Files"
76 help="Specify one or more Thermo RAW files" />
77 </when>
78 <when value=".mzxml">
79 <param multiple="true" name="infiles" type="data"
80 format="mzXML" label="mzXML Files"
81 help="Specify one or more mzXML files" />
82 </when>
83 <when value=".mzml">
84 <param multiple="true" name="infiles" type="data"
85 format="mzML" label="mzML Files"
86 help="Specify one or more mzML files" />
87 </when>
88 </conditional>
89 <param format="fasta" multiple="true" name="fasta_files"
90 type="data" label="FASTA files"
91 help="Specify one or more FASTA databases." />
92 <param name="identifier_parse_rule" type="text"
93 label="identifier parse rule" value="^&gt;.*\|(.*)\|.*$">
94 <sanitizer>
95 <valid initial="string.printable">
96 <remove value="&apos;"/>
97 </valid>
98 </sanitizer>
99 </param>
100 <param name="description_parse_rule" type="text"
101 label="description parse rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$"
102 help="Modify parse rules if needed">
103 <sanitizer>
104 <valid initial="string.printable">
105 <remove value="&apos;"/>
106 </valid>
107 </sanitizer>
108 </param>
109 <param type="data" name="mqpar_input" format="xml"
110 label="mqpar.xml file with your search parameters. RAW file names
111 must match the names displayed in galaxy. Their paths
112 from the local machine are ignored. E.g. a file named
113 'test01.raw' in galaxy can either be named 'test01.raw' or
114 'D:\path\to\test01.raw' in the mqpar.xml."/>
115 <expand macro="ptxqc-opts"/>
116 <param type="select" name="output" label="Select the desired outputs."
117 multiple="true" optional="false">
118 <option value="proteinGroups">Protein Groups</option>
119 <option value="mqpar">mqpar.xml</option>
120 <option value="peptides">Peptides</option>
121 <option value="evidence">Evidence</option>
122 <option value="parameters">Tabular Paramters</option>
123 <option value="msms">MSMS</option>
124 <option value="mzTab">mzTab</option>
125 <option value="allPeptides">all peptides</option>
126 <option value="libraryMatch">library match</option>
127 <option value="matchedFeatures">matched features</option>
128 <option value="modificationSpecificPeptides">modification specific peptides</option>
129 <option value="ms3Scans">ms3 scans</option>
130 <option value="msmsScans">msms scans</option>
131 <option value="mzRange">mz range</option>
132 <option value="peptideSection">peptide section</option>
133 <option value="summary">summary</option>
134 <option value="output_all">complete 'combined/txt/' directory (compressed)</option>
135 <option value="log">MaxQuant and PTXQC log</option>
136 </param>
137 </inputs>
138
139 <expand macro="outputs"/>
140
141 <tests>
142 <test>
143 <param name="ftype" value=".mzxml" />
144 <param name="infiles" value="BSA_min_22,BSA_min_21.mzXML" />
145 <param name="fasta_files" value="bsa.fasta" />
146 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
147 <param name="description_parse_rule" value="&gt;(.*)" />
148 <param name="mqpar_input" value="mqpar/mqpar.xml" />
149 <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" />
150 <output name="evidence">
151 <assert_contents>
152 <has_text text="AEFVEVTK" />
153 </assert_contents>
154 </output>
155 <output name="msms">
156 <assert_contents>
157 <has_text text="ECCHGDLLECADDR" />
158 </assert_contents>
159 </output>
160 <output name="allPeptides" file="mqpar/txt/allPeptides.txt" lines_diff="32" />
161 <output name="msmsScans">
162 <assert_contents>
163 <has_text text="LLEEQVFMANGVSLQLQR" />
164 </assert_contents>
165 </output>
166 <output name="mzRange" file="mqpar/txt/mzRange.txt" />
167 <output name="parameters" file="mqpar/txt/parameters.txt" lines_diff="8"/>
168 <output name="peptides">
169 <assert_contents>
170 <has_text text="VEVTKLVTDLTKVHKECCHGDLLECADDRA" />
171 </assert_contents>
172 </output>
173 <output name="proteinGroups">
174 <assert_contents>
175 <has_text text="ENSBTAP00000007350" />
176 </assert_contents>
177 </output>
178 <output name="summary" file="mqpar/txt/summary.txt" />
179 <output name="modificationSpecificPeptides">
180 <assert_contents>
181 <has_text text="ECCHGDLLECADDR" />
182 </assert_contents>
183 </output>
184 <output name="mqpar" file="mqpar/txt/mqpar.xml" lines_diff="8" />
185 </test>
186 </tests>
187 <help><![CDATA[
188 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
189
190 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.
191
192 **Input files**
193
194 - Thermo raw file or mzXML file
195 - 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)
196 - mqpar.xml:
197 - 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.
198
199 **Output files**
200
201 Different output file options are available, most of them are part of the MaxQuant txt folder. An additional mztab output option is implemented.
202 ]]></help>
203 <expand macro="citations"/>
204 </tool>