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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
author galaxyp
date Fri, 19 Jul 2019 19:13:15 -0400
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1 <tool id="maxquant" name="MaxQuant" 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 $input_opts.infile.select == "mzxml_files"
16 --mzxml_files='$input_opts.infile.mzxml_files'
17 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $input_opts.infile.mzxml_files])
18 #else
19 --raw_files='$input_opts.infile.raw_files'
20 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $input_opts.infile.raw_files])
21 #end if
22 --infile_names='$names'
23 --version='@VERSION@'
24 --fasta_files='$input_opts.fasta_files'
25 --identifier_parse_rule='$input_opts.identifier_parse_rule'
26 --description_parse_rule='$input_opts.description_parse_rule'
27
28 --exp_design='$search_opts.template'
29 --missed_cleavages=$search_opts.missed_cleavages
30 --min_peptide_len=$search_opts.min_peptide_len
31 --max_peptide_mass=$search_opts.max_peptide_mass
32 --min_unique_pep=$search_opts.min_unique_pep
33 $search_opts.calc_peak_properties
34 $search_opts.match_between_runs
35 #if $search_opts.fixed_mods
36 --fixed_mods='$search_opts.fixed_mods'
37 #end if
38 #if $search_opts.var_mods
39 --var_mods='$search_opts.var_mods'
40 #end if
41 #if $search_opts.proteases
42 --proteases='$search_opts.proteases'
43 #end if
44 #if $search_opts.silac.light_mods
45 --light_mods='$search_opts.silac.light_mods'
46 #end if
47 #if $search_opts.silac.medium_mods
48 --medium_mods='$search_opts.silac.medium_mods'
49 #end if
50 #if $search_opts.silac.heavy_mods
51 --heavy_mods='$search_opts.silac.heavy_mods'
52 #end if
53 #if $search_opts.lfq.do_lfq == "--lfq_mode=1"
54 $search_opts.lfq.do_lfq.lfq_mode
55 --lfq_min_ratio_count=$search_opts.lfq.do_lfq.lfq_min_ratio_count
56 --lfq_min_edges_per_node=$search_opts.lfq.do_lfq.lfq_min_edges_per_node
57 --lfq_avg_edges_per_node=$search_opts.lfq.do_lfq.lfq_avg_edges_per_node
58 $search_opts.lfq.do_lfq.lfq_skip_norm
59 $search_opts.lfq.do_lfq.separate_lfq
60 $search_opts.lfq.do_lfq.lfq_stabilize_large_ratios
61 $search_opts.lfq.do_lfq.lfq_require_msms
62 #if $search_opts.lfq.do_lfq.do_ibaq == "--ibaq"
63 $search_opts.lfq.do_lfq.do_ibaq.ibaq
64 $search_opts.lfq.do_lfq.do_ibaq.ibaq_log_fit
65 #end if
66 $search_opts.lfq.do_lfq.advanced_site_intensities
67 #end if
68
69 $output_opts.write_mztab
70 --evidence='$evidence'
71 --msms='$msms'
72 --parameters='$parameters'
73 --peptides='$peptides'
74 --proteinGroups='$proteinGroups'
75 --allPeptides='$allPeptides'
76 --libraryMatch='$libraryMatch'
77 --matchedFeatures='$matchedFeatures'
78 --modificationSpecificPeptides='$modificationSpecificPeptides'
79 --ms3Scans='$ms3Scans'
80 --msmsScans='$msmsScans'
81 --mzRange='$mzRange'
82 --peptideSection='$peptideSection'
83 --summary='$summary'
84 --mzTab='$mzTab'
85 --mqpar_out='$mqpar_out'
86
87 #if 'log' in $output_opts.output
88 > '$log'
89 #end if
90 #if 'output_all' in $output_opts.output
91 && tar -zcf '$output_all' ./combined/txt
92 #end if
93 ]]></command>
94 <inputs>
95 <section name="input_opts" title="Input Options" expanded="True">
96 <conditional name="infile">
97 <param name="select" type="select" label="choose the type of your input files">
98 <option value="raw_files">Thermo.raw</option>
99 <option value="mzxml_files">mzXML</option>
100 </param>
101 <when value="raw_files">
102 <param multiple="true" name="raw_files" type="data"
103 format="thermo.raw" label="RAW Files"
104 help="Specify one or more Thermo RAW files" />
105 </when>
106 <when value="mzxml_files">
107 <param multiple="true" name="mzxml_files" type="data"
108 format="mzxml" label="mzXML Files"
109 help="Specify one or more mzXML files" />
110 </when>
111 </conditional>
112 <param format="fasta" multiple="true" name="fasta_files"
113 type="data" label="FASTA files"
114 help="Specify one or more FASTA databases." />
115 <param name="identifier_parse_rule" type="text"
116 label="identifier parse rule" value="^&gt;.*\|(.*)\|.*$">
117 <sanitizer>
118 <valid initial="string.printable">
119 <remove value="&apos;"/>
120 </valid>
121 </sanitizer>
122 </param>
123 <param name="description_parse_rule" type="text"
124 label="description parse rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$"
125 help="Modify parse rules if needed">
126 <sanitizer>
127 <valid initial="string.printable">
128 <remove value="&apos;"/>
129 </valid>
130 </sanitizer>
131 </param>
132 </section>
133
134 <section name="search_opts" title="Search Options" expanded="true">
135 <param format="tabular" name="template" type="data" optional="true"
136 label="Specify an experimental design template (if needed). For detailed
137 instructions see the help text." />
138 <param type="integer" name="missed_cleavages"
139 label="missed cleavages" value="1"/>
140 <param type="integer" name="min_peptide_len"
141 label="minimum peptide length" value="7"/>
142 <param type="integer" name="max_peptide_mass"
143 label="maximum peptide mass" value="4600"/>
144 <param type="integer" name="min_unique_pep"
145 label="minimum unique peptides" value="1" />
146 <param name="calc_peak_properties" type="boolean" checked="false"
147 label="Calculate peak properties?"
148 truevalue="--calc_peak_properties" falsevalue="" />
149 <param name="match_between_runs" type="boolean" checked="false"
150 label="Match between runs?"
151 truevalue="--match_between_runs" falsevalue="" />
152 <param name="fixed_mods" type="select" label="fixed modifications"
153 multiple="true" help="select zero or more fixed modifications">
154 <expand macro="modification"/>
155 </param>
156 <param name="var_mods" type="select" label="variable modifications"
157 multiple="true" help="select zero or more variable modifications">
158 <expand macro="modification"/>
159 </param>
160 <param name="proteases" type="select" label="proteases"
161 multiple="true" help="select zero or more proteases">
162 <expand macro="proteases"/>
163 </param>
164 <section title="label based quantitation" name="silac" expanded="false">
165 <param name="light_mods" type="select" label="light labels"
166 multiple="true" help="select zero or more light modifications">
167 <expand macro="label"/>
168 </param>
169 <param name="medium_mods" type="select" label="medium labels"
170 multiple="true" help="select zero or more medium modifications">
171 <expand macro="label"/>
172 </param>
173 <param name="heavy_mods" type="select" label="heavy labels"
174 multiple="true" help="select zero or more heavy modifications">
175 <expand macro="label"/>
176 </param>
177 </section>
178 <section title="label free quantification" name="lfq" expanded="false">
179 <conditional name="do_lfq">
180 <param name="lfq_mode" type="select" label="Perform LFQ?">
181 <option value="">No</option>
182 <option value="--lfq_mode=1">Yes</option>
183 </param>
184 <when value="--lfq_mode=1">
185 <param type="integer" name="lfq_min_ratio_count"
186 label="LFQ minimum ratio count" value="2"/>
187 <param type="integer" name="lfq_min_edges_per_node"
188 label="LFQ minimum number of neighbours" value="3"/>
189 <param type="integer" name="lfq_avg_edges_per_node"
190 label="LFQ average number of neighbours" value="6"/>
191 <param name="lfq_skip_norm" type="boolean" checked="false"
192 label="Skip normalization?"
193 truevalue="--lfq_skip_norm" falsevalue="" />
194 <param name="separate_lfq" type="boolean" checked="false"
195 label="Separate LFQ in parameter Groups?"
196 truevalue="--separate_lfq" falsevalue="" />
197 <param name="lfq_stabilize_large_ratios" type="boolean" checked="true"
198 label="Stabilize large LFQ ratios?"
199 truevalue="--lfq_stabilize_large_ratios" falsevalue="" />
200 <param name="lfq_require_msms" type="boolean" checked="true"
201 label="Require MS/MS for LFQ comparisons?"
202 truevalue="--lfq_require_msms" falsevalue="" />
203 <conditional name="do_ibaq">
204 <param name="ibaq" type="select" label="iBAQ?">
205 <option value="">No</option>
206 <option value="--ibaq">Yes</option>
207 </param>
208 <when value="--ibaq">
209 <param name="ibaq_log_fit" type="boolean" checked="true"
210 label="Logarithmic fit?"
211 truevalue="--ibaq_log_fit" falsevalue="" />
212 </when>
213 <when value="">
214 </when>
215 </conditional>
216 <param name="advanced_site_intensities" type="boolean" checked="true"
217 label="Advanced site intensities?"
218 truevalue="--advanced_site_intensities" falsevalue="" />
219 </when>
220 <when value="">
221 </when>
222 </conditional>
223 </section>
224 </section>
225
226 <section title="Output Options" name="output_opts" expanded="true">
227 <param name="write_mztab" type="boolean" checked="false"
228 label="Write mztab file?"
229 truevalue="--write_mztab" falsevalue="" />
230 <param type="select" name="output" label="Select the desired outputs."
231 multiple="true" optional="false">
232 <expand macro="output_option" name="proteinGroups" label="Protein Groups"/>
233 <expand macro="output_option" name="mqpar_out" label="mqpar.xml"/>
234 <expand macro="output_option" name="peptides" label="Peptides"/>
235 <expand macro="output_option" name="evidence" label="Evidence"/>
236 <expand macro="output_option" name="parameters" label="Tabular Paramters"/>
237 <expand macro="output_option" name="msms" label="MSMS"/>
238 <expand macro="output_option" name="mzTab" label="mzTab"/>
239 <expand macro="output_option" name="allPeptides" label="all peptides"/>
240 <expand macro="output_option" name="libraryMatch" label="library match"/>
241 <expand macro="output_option" name="matchedFeatures" label="matched features"/>
242 <expand macro="output_option" name="modificationSpecificPeptides" label="modification specific peptides"/>
243 <expand macro="output_option" name="ms3Scans" label="ms3 scans"/>
244 <expand macro="output_option" name="msmsScans" label="msms scans"/>
245 <expand macro="output_option" name="mzRange" label="mz range"/>
246 <expand macro="output_option" name="peptideSection" label="peptide section"/>
247 <expand macro="output_option" name="summary" label="summary"/>
248 <expand macro="output_option" name="output_all" label="complete 'combined/txt/' directory (compressed)"/>
249 <expand macro="output_option" name="log" label="MaxQuant log"/>
250 </param>
251 </section>
252 </inputs>
253
254 <outputs>
255 <expand macro="output" name="proteinGroups" label="MaxQuant Protein Groups"/>
256 <expand macro="output" name="mqpar_out" label="mqpar.xml" format="xml"/>
257 <expand macro="output" name="peptides" label="MaxQuant Peptides"/>
258 <expand macro="output" name="evidence" label="MaxQuant Evidence"/>
259 <expand macro="output" name="parameters" label="MaxQuant Tabular Parameters"/>
260 <expand macro="output" name="msms" label="MaxQuant MSMS"/>
261 <expand macro="output" name="mzTab" label="mzTab"/>
262 <expand macro="output" name="allPeptides" label="all peptides"/>
263 <expand macro="output" name="libraryMatch" label="library match"/>
264 <expand macro="output" name="matchedFeatures" label="matched features"/>
265 <expand macro="output" name="modificationSpecificPeptides" label="modification specific peptides"/>
266 <expand macro="output" name="ms3Scans" label="ms3 scans"/>
267 <expand macro="output" name="msmsScans" label="msms Scans"/>
268 <expand macro="output" name="mzRange" label="mz range"/>
269 <expand macro="output" name="peptideSection" label="peptide section"/>
270 <expand macro="output" name="summary" label="MaxQuant summary"/>
271 <expand macro="output" format="tar" name="output_all" label="'combined/txt/' directory"/>
272 <expand macro="output" name="log" format="txt" label="log"/>
273 </outputs>
274
275 <tests>
276 <test>
277 <param name="select" value="mzxml_files" />
278 <param name="mzxml_files" value="BSA_min_23.mzXML" />
279 <param name="fasta_files" value="bsa.fasta" />
280 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
281 <param name="description_parse_rule" value="&gt;(.*)" />
282 <param name="min_unique_pep" value="0" />
283 <param name="fixed_mods" value="Carbamidomethyl (C)" />
284 <param name="var_mods" value="Oxidation (M)" />
285 <param name="proteases" value="Trypsin/P" />
286 <param name="write_mztab" value="true" />
287 <param name="output" value="evidence,msms,allPeptides,msmsScans,mzTab,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides" />
288 <output name="evidence" file="single/combined/txt/evidence.txt" />
289 <output name="msms" file="single/combined/txt/msms.txt" />
290 <output name="mzTab" file="single/combined/txt/mzTab.mzTab" lines_diff="4"/>
291 <output name="allPeptides" file="single/combined/txt/allPeptides.txt" />
292 <output name="msmsScans" file="single/combined/txt/msmsScans.txt" />
293 <output name="mzRange" file="single/combined/txt/mzRange.txt" />
294 <output name="parameters" file="single/combined/txt/parameters.txt" lines_diff="10"/>
295 <output name="peptides" file="single/combined/txt/peptides.txt" />
296 <output name="peptideSection" file="single/combined/txt/peptideSection.txt" />
297 <output name="proteinGroups" file="single/combined/txt/proteinGroups.txt" />
298 <output name="summary" file="single/combined/txt/summary.txt" />
299 <output name="modificationSpecificPeptides" file="single/combined/txt/modificationSpecificPeptides.txt" />
300 </test>
301 </tests>
302
303 <help><![CDATA[
304 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
305
306 This tool is a wrapper for MaxQuant v@VERSION@. The current version of the wrapper only supports a very reduced set of search parameters, but another version of the tool that gets its parameters directly from a mqpar.xml file is available, too. If possible, this tool should be preferred.
307
308 **Input files**
309
310 - Thermo raw file or mzXML file
311 - 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)
312 - Optional files:
313 - Tabular file with experimental design template:
314 - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Fraction are abitrary strings, Experiment is an integer, PTM is either True or False.
315
316 ::
317
318 Name Fraction Experiment PTM
319 File1 1 E1 False
320 File2 2 E1 False
321 File3 3 E1 False
322 ...
323 ...
324
325 **Parameter Options**
326
327 - Quantification options
328 - label based:
329 - for two channels: choose options from light and heavy sections, for three channels choose options from light, medium and heavy sections
330 - label-free
331
332 **Output files**
333
334 Different output file options are available, most of them are part of the MaxQuant txt directory.
335 ]]></help>
336 <citations>
337 <citation type="bibtex">
338 @article{cox2008maxquant,
339 title={MaxQuant enables high peptide identification rates, individualized
340 ppb-range mass accuracies and proteome-wide protein quantification},
341 author={Cox, J{\"u}rgen and Mann, Matthias},
342 journal={Nature biotechnology},
343 volume={26},
344 number={12},
345 pages={1367},
346 year={2008},
347 publisher={Nature Publishing Group}
348 }
349 </citation>
350 <citation type="bibtex">
351 @article{tyanova2016maxquant,
352 title={The MaxQuant computational platform for mass
353 spectrometry-based shotgun proteomics},
354 author={Tyanova, Stefka and Temu, Tikira and Cox, J{\"u}rgen},
355 journal={Nature protocols},
356 volume={11},
357 number={12},
358 pages={2301},
359 year={2016},
360 publisher={Nature Publishing Group}
361 }
362 </citation>
363 </citations>
364 </tool>