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comparison maxquant.xml @ 5:7f432d87c82c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
author galaxyp
date Wed, 15 Apr 2020 11:17:42 -0400
parents dcd39bcc7481
children 2133b0be850a
comparison
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4:dcd39bcc7481 5:7f432d87c82c
225 </valid> 225 </valid>
226 </sanitizer> 226 </sanitizer>
227 </param> 227 </param>
228 <param name="description_parse_rule" type="text" 228 <param name="description_parse_rule" type="text"
229 label="description parse rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" 229 label="description parse rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$"
230 help="Modify parse rules if needed"> 230 help="Modify parse rules if needed.">
231 <sanitizer> 231 <sanitizer>
232 <valid initial="string.printable"> 232 <valid initial="string.printable">
233 <remove value="&apos;"/> 233 <remove value="&apos;"/>
234 </valid> 234 </valid>
235 </sanitizer> 235 </sanitizer>
239 <section name="search_opts" title="Search Options" expanded="true"> 239 <section name="search_opts" title="Search Options" expanded="true">
240 <param format="tabular" name="template" type="data" optional="true" 240 <param format="tabular" name="template" type="data" optional="true"
241 label="Specify an experimental design template (if needed). For detailed 241 label="Specify an experimental design template (if needed). For detailed
242 instructions see the help text." /> 242 instructions see the help text." />
243 <param type="integer" name="min_peptide_len" 243 <param type="integer" name="min_peptide_len"
244 label="minimum peptide length" value="7"/> 244 label="minimum peptide length" value="7"
245 help="Peptides shorter than this value will not be reported nor be considered during protein identification and quantification
246 short peptides are usually not unique in the protein database and therefore not statistically informative."/>
245 <param type="integer" name="max_peptide_mass" 247 <param type="integer" name="max_peptide_mass"
246 label="maximum peptide mass" value="4600"/> 248 label="maximum peptide mass [Da]" value="4600"
249 help="Peptides that are heavier than this mass will be discarded in the Andromeda search."/>
247 <param type="integer" name="min_unique_pep" 250 <param type="integer" name="min_unique_pep"
248 label="minimum unique peptides" value="0" /> 251 label="minimum unique peptides" value="0"
252 help="The minimum number of unique peptides a protein group should have to be considered as identified and reported in the final table." />
249 <param name="calc_peak_properties" type="boolean" checked="false" 253 <param name="calc_peak_properties" type="boolean" checked="false"
250 label="Calculate peak properties?" 254 label="Calculate peak properties"
251 truevalue="True" falsevalue="False" /> 255 truevalue="True" falsevalue="False"
256 help="If checked, several quantities characterizing peaks and isotopes patterns are calculated. This may lead to a substantial increase in computation time."/>
252 <param name="match_between_runs" type="boolean" checked="false" 257 <param name="match_between_runs" type="boolean" checked="false"
253 label="Match between runs?" 258 label="Match between runs"
254 truevalue="True" falsevalue="False" /> 259 truevalue="True" falsevalue="False"
260 help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs."/>
255 </section> 261 </section>
256 262
257 <repeat name="paramGroups" title="Parameter Group" min="1" default="1"> 263 <repeat name="paramGroups" title="Parameter Group" min="1" default="1">
258 <param type="data" format="thermo.raw,mzXML,mzML" name="files" label="Infiles" multiple="true" 264 <param type="data" format="thermo.raw,mzXML,mzML" name="files" label="Infiles" multiple="true"
259 help="Only select infiles matching the filetype specified in the input options."/> 265 help="Only select infiles matching the filetype specified in the input options."/>
260 <param type="integer" name="maxMissedCleavages" 266 <param type="integer" name="maxMissedCleavages"
261 label="missed cleavages" value="2"/> 267 label="missed cleavages" value="2"
268 help="The number of missed cleavages that are maximally tolerated in the in-silico digestion of the protien sequences."/>
262 <param name="fixedModifications" type="select" label="fixed modifications" 269 <param name="fixedModifications" type="select" label="fixed modifications"
263 multiple="true" help="select zero or more fixed modifications"> 270 multiple="true" help="Select zero or more fixed modifications. They will always be attached to any occurence of the respective amino acid.">
264 <expand macro="modification"/> 271 <expand macro="modification"/>
265 <expand macro="default_mod_option" value="Carbamidomethyl (C)"/> 272 <expand macro="default_mod_option" value="Carbamidomethyl (C)"/>
266 </param> 273 </param>
267 <param name="variableModifications" type="select" label="variable modifications" 274 <param name="variableModifications" type="select" label="variable modifications"
268 multiple="true" help="select zero or more variable modifications"> 275 multiple="true" help="Select zero or more variable modifications. Do not specify label modifications here, neither ms1 level labels, like SILAC, nor isobaric labels.">
269 <expand macro="default_mod_option" value="Oxidation (M)"/> 276 <expand macro="default_mod_option" value="Oxidation (M)"/>
270 <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/> 277 <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/>
271 <expand macro="modification"/> 278 <expand macro="modification"/>
272 </param> 279 </param>
273 <param name="enzymes" type="select" label="proteases" 280 <param name="enzymes" type="select" label="enzyme"
274 multiple="true" help="select zero or more proteases"> 281 multiple="true" help="Select zero or more enzymes. The enzymes used for generating the in silico peptides for the Andromeda search.">
275 <expand macro="default_mod_option" value="Trypsin/P"/> 282 <expand macro="default_mod_option" value="Trypsin/P"/>
276 <expand macro="proteases"/> 283 <expand macro="proteases"/>
277 </param> 284 </param>
278 <conditional name="quant_method"> 285 <conditional name="quant_method">
279 <param name="select_quant_method" type="select" label="Quantitation Methods" 286 <param name="select_quant_method" type="select" label="Quantitation Methods"
280 help="Select a method if needed."> 287 help="Select a method if needed.">
281 <option value="">None</option> 288 <option value="">None</option>
282 <option value="lfq">label free quantification</option> 289 <option value="lfq">label free quantification</option>
283 <option value="silac">label based quantification (SILAC)</option> 290 <option value="silac">label based quantification</option>
284 <option value="reporter_ion_ms2">reporter ion MS2</option> 291 <option value="reporter_ion_ms2">reporter ion MS2</option>
285 </param> 292 </param>
286 <when value=""/> 293 <when value=""/>
287 <when value="silac"> 294 <when value="silac">
288 <param name="light_labels" type="select" label="light labels" 295 <param name="light_labels" type="select" label="light labels"
289 multiple="true" help="select zero or more light modifications"> 296 multiple="true" help="Select zero or more light modifications.">
290 <expand macro="label"/> 297 <expand macro="label"/>
291 </param> 298 </param>
292 <param name="medium_labels" type="select" label="medium labels" 299 <param name="medium_labels" type="select" label="medium labels"
293 multiple="true" help="select zero or more medium modifications"> 300 multiple="true" help="Select zero modifications if you have two labels. Select a medium modification if you have three labels.">
294 <expand macro="label"/> 301 <expand macro="label"/>
295 </param> 302 </param>
296 <param name="heavy_labels" type="select" label="heavy labels" 303 <param name="heavy_labels" type="select" label="heavy labels"
297 multiple="true" help="select zero or more heavy modifications"> 304 multiple="true" help="Select zero or more heavy modifications.">
298 <expand macro="label"/> 305 <expand macro="label"/>
299 </param> 306 </param>
300 </when> 307 </when>
301 <when value="lfq"> 308 <when value="lfq">
302 <param type="integer" name="lfqMinRatioCount" 309 <param type="integer" name="lfqMinRatioCount"
303 label="LFQ minimum ratio count" value="2"/> 310 label="LFQ minimum ratio count" value="2"
311 help="Minimum number of peptides that has to be available in pair-wise comparisons between two samples for a protein."/>
304 <param type="integer" name="lfqMinEdgesPerNode" 312 <param type="integer" name="lfqMinEdgesPerNode"
305 label="LFQ minimum number of neighbours" value="3"/> 313 label="LFQ minimum number of neighbours" value="3"
314 help="Defines the network to normalize the samples in the fast LFQ mode."/>
306 <param type="integer" name="lfqAvEdgesPerNode" 315 <param type="integer" name="lfqAvEdgesPerNode"
307 label="LFQ average number of neighbours" value="6"/> 316 label="LFQ average number of neighbours" value="6"
317 help="Defines the network to normalize the samples in the fast LFQ mode."/>
308 <param type="boolean" name="lfqSkipNorm" checked="true" 318 <param type="boolean" name="lfqSkipNorm" checked="true"
309 label="Skip normalization?" 319 label="Skip normalization"
310 truevalue="True" falsevalue="False" /> 320 truevalue="True" falsevalue="False"
321 help="If checked the high-speed version of MaxLFQ is used. This is recommended for large numbers of samples (Experiments). For less than 10 samples the original MaxLFQ normalization algorithm is used."/>
311 </when> 322 </when>
312 <when value="reporter_ion_ms2"> 323 <when value="reporter_ion_ms2">
313 <conditional name="iso_labels"> 324 <conditional name="iso_labels">
314 <param name="labeling" type="select" label="isobaric labeling" 325 <param name="labeling" type="select" label="isobaric labeling"
315 help="Select one of the standard labelings (correction factors are zero) or create a custom labeling."> 326 help="Select one of the standard labelings (correction factors are zero) or create a custom labeling.">
331 <when value="itraq4plex"></when> 342 <when value="itraq4plex"></when>
332 <when value="itraq8plex"></when> 343 <when value="itraq8plex"></when>
333 <when value="iodotmt6plex"></when> 344 <when value="iodotmt6plex"></when>
334 <when value="custom"> 345 <when value="custom">
335 <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> 346 <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
336 <param name="internallabel" type="select" label="internal label"> 347 <param name="internallabel" type="select" label="internal label" help="contains Lys">
337 <expand macro="iso_labels"/> 348 <expand macro="iso_labels"/>
338 </param> 349 </param>
339 <param name="terminallabel" type="select" label="terminal label"> 350 <param name="terminallabel" type="select" label="terminal label" help="contains Nter">
340 <option value="">None</option> 351 <option value="">None</option>
341 <expand macro="iso_labels"/> 352 <expand macro="iso_labels"/>
342 </param> 353 </param>
343 <param name="cm2" type="float" label="correction factor -2%" value="0.0"/> 354 <param name="cm2" type="float" label="correction factor -2%" value="0.0"/>
344 <param name="cm1" type="float" label="correction factor -1%" value="0.0"/> 355 <param name="cm1" type="float" label="correction factor -1%" value="0.0"/>
354 </conditional> 365 </conditional>
355 </repeat> 366 </repeat>
356 367
357 <section title="LFQ Options" name="lfq_opts" expanded="false"> 368 <section title="LFQ Options" name="lfq_opts" expanded="false">
358 <param name="separateLfq" type="boolean" checked="false" 369 <param name="separateLfq" type="boolean" checked="false"
359 label="Separate LFQ in parameter Groups?" 370 label="Separate LFQ in parameter Groups"
360 truevalue="True" falsevalue="False" /> 371 truevalue="True" falsevalue="False"
372 help="The MaxLFQ algorithm will be applied independently to samples in different parameter groups."/>
361 <param name="lfqStabilizeLargeRatios" type="boolean" checked="true" 373 <param name="lfqStabilizeLargeRatios" type="boolean" checked="true"
362 label="Stabilize large LFQ ratios?" 374 label="Stabilize large LFQ ratios"
363 truevalue="True" falsevalue="False" /> 375 truevalue="True" falsevalue="False"
376 help="Large protein ratios will get an admixture of the total protein intensity ratio as described in the MaxLFQ paper"/>
364 <param name="lfqRequireMsms" type="boolean" checked="true" 377 <param name="lfqRequireMsms" type="boolean" checked="true"
365 label="Require MS/MS for LFQ comparisons?" 378 label="Require MS/MS for LFQ comparisons"
366 truevalue="True" falsevalue="False" /> 379 truevalue="True" falsevalue="False"
380 help="Requires for each pari-wise peptide intensity comparison that at least one of two peptides has been identified by MS/MS"/>
367 <conditional name="do_ibaq"> 381 <conditional name="do_ibaq">
368 <param name="ibaq" type="select" label="iBAQ?"> 382 <param name="ibaq" type="select" label="iBAQ (calculates absolute protein abundances by normalizing to copy number and not protein mass)">
369 <option value="False">No</option> 383 <option value="False">No</option>
370 <option value="True">Yes</option> 384 <option value="True">Yes</option>
371 </param> 385 </param>
372 <when value="True"> 386 <when value="True">
373 <param name="ibaqLogFit" type="boolean" checked="true" 387 <param name="ibaqLogFit" type="boolean" checked="true"
374 label="Logarithmic fit?" 388 label="Logarithmic fit"
375 truevalue="True" falsevalue="False" /> 389 truevalue="True" falsevalue="False" />
376 </when> 390 </when>
377 <when value="False"> 391 <when value="False">
378 </when> 392 </when>
379 </conditional> 393 </conditional>
380 <param name="advancedSiteIntensities" type="boolean" checked="true" 394 <param name="advancedSiteIntensities" type="boolean" checked="true"
381 label="Advanced site intensities?" 395 label="Advanced site intensities"
382 truevalue="True" falsevalue="False" /> 396 truevalue="True" falsevalue="False" />
383 </section> 397 </section>
384 398
385 <expand macro="ptxqc-opts"/> 399 <expand macro="ptxqc-opts"/>
386 <section title="Output Options" name="output_opts" expanded="true"> 400 <section title="Output Options" name="output_opts" expanded="true">
537 </tests> 551 </tests>
538 552
539 <help><![CDATA[ 553 <help><![CDATA[
540 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. 554 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
541 555
542 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. 556 This tool is a wrapper for MaxQuant v@VERSION@. The current version of the wrapper only supports a reduced set of parameters, but another version of the tool that gets its parameters directly from a mqpar.xml file is available, too.
543 557
544 **Input files** 558 **Input files**
545 559
546 - Thermo raw files or mzXML files (in parameter group section): 560 - Thermo raw, mzML, mzXMLfiles (in parameter group section)
547 - The datatype of all files has to be either 'thermo.raw' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes) 561
548 - Fasta files: specify parse rules accordingly, default rules are compatible with uniprot 562 - The datatype of all files has to be either 'thermo.raw', 'mzML' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
563 - Fasta file: specify parse rules accordingly, default rules are compatible with uniprot
549 - Optional files: 564 - Optional files:
565
550 - Tabular file with experimental design template: 566 - Tabular file with experimental design template:
567
551 - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Experiment are abitrary strings, Fraction is an integer or emtpy, PTM is either 'True', 'False' or empty. Consider you uploaded files named File1.mzxml, ..., File5.mzxml. This is a (syntactically) correct experimental design template: 568 - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Experiment are abitrary strings, Fraction is an integer or emtpy, PTM is either 'True', 'False' or empty. Consider you uploaded files named File1.mzxml, ..., File5.mzxml. This is a (syntactically) correct experimental design template:
552 569
553 :: 570 ::
554 571
555 Name Fraction Experiment PTM 572 Name Fraction Experiment PTM
556 File1 1 E1 False 573 File1 1 E1 False
557 File2 2 E1 False 574 File2 2 E1 False
558 ghost 234 none 575 ghost 234 none
559 File3 3 E1 False 576 File3 3 E1 False
560 File4 E2 true 577 File4 E2 True
561 File5 E1 578 File5 E1
562 579
563 - This is the counter-example with one error per line: 580 - This is the counter-example with one error per line:
564 581
565 :: 582 ::
567 Name Fraction Experiment PTM 584 Name Fraction Experiment PTM
568 File1 1 E1 no (wrong PTM value) 585 File1 1 E1 no (wrong PTM value)
569 File2.mzxml 1 E2 (filename with extension) 586 File2.mzxml 1 E2 (filename with extension)
570 File3 f3 E1 (fraction not an integer) 587 File3 f3 E1 (fraction not an integer)
571 File4 1 (missing experiment) 588 File4 1 (missing experiment)
572 (File5 misssing) 589 (File5 missing)
573 590
574 **Parameter Options** 591 **Parameter Options**
575 592
576 - Quantification options 593 - Quantitation methods (in section parameter groups)
577 - label based: 594
578 - for two channels: choose options from light and heavy sections, for three channels choose options from light, medium and heavy sections 595 - label free (LFQ): Protein intensity will be reported as 'LFQ intensity' columns in the proteinGroups table
579 - label-free 596 - label based: quantifies MS1 labelled samples ('SILAC', 'Dimethyl', 'ICAT', 'ICPL', 'mTRAQ', '18 O')
580 - reporter ion ms2: either use the pre-defined labelings with correction factors set to 0 or specify a custom labeling 597
598 - for two channels: choose options from light and heavy sections
599 - for three channels: choose options from light, medium and heavy sections
600 - reporter ion ms2: quantifies conventional isobaric labelling samples. Either use the pre-defined labellings with correction factors set to 0 or specify a custom labelling
601 - PTXQC quality control: quality control software creates an automatic quality control pdf report
602
581 603
582 **Output files** 604 **Output files**
583 605
584 Different output file options are available, most of them are part of the MaxQuant txt directory. If ptxqc report ist selected, a quality control report will be created. 606 Different output file options are available, most of them are part of the MaxQuant txt directory.
585 ]]></help> 607 ]]></help>
586 <expand macro="citations"/> 608 <expand macro="citations"/>
587 </tool> 609 </tool>