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comparison maxquant.xml @ 6:2133b0be850a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
author galaxyp
date Wed, 06 May 2020 13:35:51 -0400
parents 7f432d87c82c
children d253b379322b
comparison
equal deleted inserted replaced
5:7f432d87c82c 6:2133b0be850a
1 <tool id="maxquant" name="MaxQuant" version="@VERSION@"> 1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy1">
2 <macros> 2 <macros>
3 <xml name="output" token_format="tabular" token_label="default description" token_name="default"> 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@"> 4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
5 <filter>'@NAME@' in output_opts['output']</filter> 5 <filter>'@NAME@' in output_opts['output']</filter>
6 </data> 6 </data>
79 minPepLen: ${search_opts.min_peptide_len} 79 minPepLen: ${search_opts.min_peptide_len}
80 maxPeptideMass: ${search_opts.max_peptide_mass} 80 maxPeptideMass: ${search_opts.max_peptide_mass}
81 calcPeakProperties: ${search_opts.calc_peak_properties} 81 calcPeakProperties: ${search_opts.calc_peak_properties}
82 #set writeMzTab = "mzTab" in $output_opts.output 82 #set writeMzTab = "mzTab" in $output_opts.output
83 writeMzTab: $writeMzTab 83 writeMzTab: $writeMzTab
84 #if $lfq_opts.do_ibaq.ibaq == 'True': 84 #if $protein_quant.lfq_opts.do_ibaq.ibaq == 'True':
85 ibaq: ${lfq_opts.do_ibaq.ibaq} 85 ibaq: ${protein_quant.lfq_opts.do_ibaq.ibaq}
86 ibaqLogFit: ${lfq_opts.do_ibaq.ibaqLogFit} 86 ibaqLogFit: ${protein_quant.lfq_opts.do_ibaq.ibaqLogFit}
87 #end if 87 #end if
88 separateLfq: ${lfq_opts.separateLfq} 88 separateLfq: ${protein_quant.lfq_opts.separateLfq}
89 lfqStabilizeLargeRatios: ${lfq_opts.lfqStabilizeLargeRatios} 89 lfqStabilizeLargeRatios: ${protein_quant.lfq_opts.lfqStabilizeLargeRatios}
90 lfqRequireMsms: ${lfq_opts.lfqRequireMsms} 90 lfqRequireMsms: ${protein_quant.lfq_opts.lfqRequireMsms}
91 advancedSiteIntensities: ${lfq_opts.advancedSiteIntensities} 91 advancedSiteIntensities: ${protein_quant.lfq_opts.advancedSiteIntensities}
92 matchBetweenRuns: ${search_opts.match_between_runs} 92 matchBetweenRuns: ${search_opts.match_between_runs}
93 includeContaminants: ${search_opts.incl_contaminants}
94 quantMode: ${protein_quant.peptides_for_quantification}
95 restrictProteinQuantification: ${protein_quant.only_unmod_prot.unmod_prot}
96 #if $protein_quant.only_unmod_prot.unmod_prot == 'True':
97 #if $protein_quant.only_unmod_prot.mods_used_prot_quant:
98 restrictMods: [${protein_quant.only_unmod_prot.mods_used_prot_quant}]
99 #else:
100 restrictMods: []
101 #end if
102 useCounterparts: $protein_quant.only_unmod_prot.discard_unmod_cpart_peptides
103 #end if
93 paramGroups: 104 paramGroups:
94 #for $pg in $paramGroups: 105 #for $pg in $paramGroups:
95 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $pg.files] 106 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $pg.files]
96 #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names] 107 #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names]
97 - files: $names_with_ext 108 - files: $names_with_ext
109 #if $pg.enzymes: 120 #if $pg.enzymes:
110 enzymes: [${pg.enzymes}] 121 enzymes: [${pg.enzymes}]
111 #else: 122 #else:
112 enzymes: [] 123 enzymes: []
113 #end if 124 #end if
125 enzymeMode: ${pg.digestion_mode}
114 #if $pg.quant_method.select_quant_method == 'silac': 126 #if $pg.quant_method.select_quant_method == 'silac':
115 labelMods: 127 labelMods:
116 #if $pg.quant_method.light_labels: 128 #if $pg.quant_method.light_labels:
117 - [${pg.quant_method.light_labels}] 129 - [${pg.quant_method.light_labels}]
118 #else: 130 #else:
137 lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount} 149 lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount}
138 #end if 150 #end if
139 #if $pg.quant_method.select_quant_method == 'reporter_ion_ms2': 151 #if $pg.quant_method.select_quant_method == 'reporter_ion_ms2':
140 lcmsRunType: 'Reporter ion MS2' 152 lcmsRunType: 'Reporter ion MS2'
141 reporterMassTolerance: 0.003 153 reporterMassTolerance: 0.003
142 reporterPif: 0 154 reporterPif: ${pg.quant_method.reporter_pif}
143 reporterFraction: 0 155 reporterFraction: 0
144 reporterBasePeakRatio: 0 156 reporterBasePeakRatio: 0
157 filterPif: ${pg.quant_method.filter_pif}
145 isobaricLabels: 158 isobaricLabels:
146 #if $pg.quant_method.iso_labels.labeling == 'custom': 159 #if $pg.quant_method.iso_labels.labeling == 'custom':
147 #for $l in $pg.quant_method.iso_labels.iso_label: 160 #for $l in $pg.quant_method.iso_labels.iso_label:
148 - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike] 161 - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike]
149 #end for 162 #end for
214 <option value=".mzxml">mzxml</option> 227 <option value=".mzxml">mzxml</option>
215 <option value=".mzml">mzml</option> 228 <option value=".mzml">mzml</option>
216 </param> 229 </param>
217 <param format="fasta" multiple="true" name="fasta_files" 230 <param format="fasta" multiple="true" name="fasta_files"
218 type="data" label="FASTA files" 231 type="data" label="FASTA files"
219 help="Specify one or more FASTA databases." /> 232 help="Specify one or more FASTA databases."/>
220 <param name="identifier_parse_rule" type="text" 233 <param name="identifier_parse_rule" type="text"
221 label="identifier parse rule" value="^&gt;.*\|(.*)\|.*$"> 234 label="identifier parse rule" value="^&gt;.*\|(.*)\|.*$">
222 <sanitizer> 235 <sanitizer>
223 <valid initial="string.printable"> 236 <valid initial="string.printable">
224 <remove value="&apos;"/> 237 <remove value="&apos;"/>
237 </section> 250 </section>
238 251
239 <section name="search_opts" title="Search Options" expanded="true"> 252 <section name="search_opts" title="Search Options" expanded="true">
240 <param format="tabular" name="template" type="data" optional="true" 253 <param format="tabular" name="template" type="data" optional="true"
241 label="Specify an experimental design template (if needed). For detailed 254 label="Specify an experimental design template (if needed). For detailed
242 instructions see the help text." /> 255 instructions see the help text."/>
243 <param type="integer" name="min_peptide_len" 256 <param type="integer" name="min_peptide_len"
244 label="minimum peptide length" value="7" 257 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 258 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."/> 259 short peptides are usually not unique in the protein database and therefore not statistically informative."/>
247 <param type="integer" name="max_peptide_mass" 260 <param type="integer" name="max_peptide_mass"
248 label="maximum peptide mass [Da]" value="4600" 261 label="maximum peptide mass [Da]" value="4600"
249 help="Peptides that are heavier than this mass will be discarded in the Andromeda search."/> 262 help="Peptides that are heavier than this mass will be discarded in the Andromeda search."/>
250 <param type="integer" name="min_unique_pep" 263 <param type="integer" name="min_unique_pep"
251 label="minimum unique peptides" value="0" 264 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." /> 265 help="The minimum number of unique peptides a protein group should have to be considered as identified and reported in the final table."/>
253 <param name="calc_peak_properties" type="boolean" checked="false" 266 <param name="calc_peak_properties" type="boolean" checked="false"
254 label="Calculate peak properties" 267 label="Calculate peak properties"
255 truevalue="True" falsevalue="False" 268 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."/> 269 help="If checked, several quantities characterizing peaks and isotopes patterns are calculated. This may lead to a substantial increase in computation time."/>
257 <param name="match_between_runs" type="boolean" checked="false" 270 <param name="match_between_runs" type="boolean" checked="false"
258 label="Match between runs" 271 label="Match between runs"
259 truevalue="True" falsevalue="False" 272 truevalue="True" falsevalue="False"
260 help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs."/> 273 help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs."/>
274 <param name="incl_contaminants" type="boolean" checked="true"
275 label="Include contaminants"
276 truevalue="True" falsevalue="False"
277 help="‘Yes’ means that proteins from a contaminant list are automatically added to the list of proteins for in silico digestion (in the fasta file)"/>
278
261 </section> 279 </section>
262 280
281 <section name="protein_quant" title="Protein quantification" expanded="true">
282
283 <param name="peptides_for_quantification" type="select" label="Peptides for quantification"
284 help="Specify how the protein ratios will be calculated. When ‘All’ is selected the quantification is done on all peptides. With ‘Unique’, only the peptides unique for that specific protein group are used for quantification. The ‘unique + razor’ mode calculates protein ratios from the unique and razor peptides. Razor peptides are non-unique peptides assigned to the protein group with the most other peptides (Occam’s razor principle).">
285 <option value="0">All</option>
286 <option value="1" selected="true">Unique + razor</option>
287 <option value="2">Unique</option>
288 </param>
289
290 <conditional name="only_unmod_prot">
291 <param name="unmod_prot" type="select"
292 label="Use only unmodified peptides"
293 help="Indicate here which kind of peptides should be used for protein quantification. If ‘No’, all peptides are used irrespective of their modification state. If ‘Yes’, all unmodified peptides are used plus those peptides that have only the modifications specified in the field below.">
294 <option value="False">No</option>
295 <option value="True" selected="true">Yes</option>
296 </param>
297 <when value="True">
298 <param name="mods_used_prot_quant" type="select" multiple="true"
299 label="Modifications used in protein quantification"
300 help="Peptides containing only these modifications will be used for the quantification of proteins in addition to unmodified peptides. This includes ratio and intensity calculations including iBAQ">
301 <expand macro="modification"/>
302 </param>
303 <!-- note: the following default is different to the mquant default -->
304 <param name="discard_unmod_cpart_peptides" type="boolean" label="Discard unmodified counterpart peptides" checked="true"
305 truevalue="True" falsevalue="False"
306 help="If selected, also unmodified peptides will be discarded for which a modified counterpart has been identified with a modification that is not specified in the field above."/>
307 </when>
308 <when value="False">
309 </when>
310 </conditional>
311
312 <section name="lfq_opts" title="LFQ Options" expanded="false">
313 <param name="separateLfq" type="boolean" checked="false"
314 label="Separate LFQ in parameter Groups"
315 truevalue="True" falsevalue="False"
316 help="The MaxLFQ algorithm will be applied independently to samples in different parameter groups."/>
317 <param name="lfqStabilizeLargeRatios" type="boolean" checked="true"
318 label="Stabilize large LFQ ratios"
319 truevalue="True" falsevalue="False"
320 help="Large protein ratios will get an admixture of the total protein intensity ratio as described in the MaxLFQ paper"/>
321 <param name="lfqRequireMsms" type="boolean" checked="true"
322 label="Require MS/MS for LFQ comparisons"
323 truevalue="True" falsevalue="False"
324 help="Requires for each pari-wise peptide intensity comparison that at least one of two peptides has been identified by MS/MS"/>
325 <conditional name="do_ibaq">
326 <param name="ibaq" type="select"
327 label="iBAQ (calculates absolute protein abundances by normalizing to copy number and not protein mass)">
328 <option value="False">No</option>
329 <option value="True">Yes</option>
330 </param>
331 <when value="True">
332 <param name="ibaqLogFit" type="boolean" checked="true"
333 label="Logarithmic fit"
334 truevalue="True" falsevalue="False"/>
335 </when>
336 <when value="False">
337 </when>
338 </conditional>
339 <param name="advancedSiteIntensities" type="boolean" checked="true"
340 label="Advanced site intensities"
341 truevalue="True" falsevalue="False"/>
342 </section>
343
344 </section>
345
346
263 <repeat name="paramGroups" title="Parameter Group" min="1" default="1"> 347 <repeat name="paramGroups" title="Parameter Group" min="1" default="1">
264 <param type="data" format="thermo.raw,mzXML,mzML" name="files" label="Infiles" multiple="true" 348 <param type="data" format="thermo.raw,mzXML,mzML" name="files" label="Infiles" multiple="true"
265 help="Only select infiles matching the filetype specified in the input options."/> 349 help="Only select infiles matching the filetype specified in the input options."/>
266 <param type="integer" name="maxMissedCleavages" 350 <param type="integer" name="maxMissedCleavages"
267 label="missed cleavages" value="2" 351 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."/> 352 help="The number of missed cleavages that are maximally tolerated in the in-silico digestion of the protien sequences."/>
269 <param name="fixedModifications" type="select" label="fixed modifications" 353 <param name="fixedModifications" type="select" label="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."> 354 multiple="true"
271 <expand macro="modification"/> 355 help="Select zero or more fixed modifications. They will always be attached to any occurence of the respective amino acid.">
356 <expand macro="modification"/>
272 <expand macro="default_mod_option" value="Carbamidomethyl (C)"/> 357 <expand macro="default_mod_option" value="Carbamidomethyl (C)"/>
273 </param> 358 </param>
274 <param name="variableModifications" type="select" label="variable modifications" 359 <param name="variableModifications" type="select" label="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."> 360 multiple="true"
361 help="Select zero or more variable modifications. Do not specify label modifications here, neither ms1 level labels, like SILAC, nor isobaric labels.">
276 <expand macro="default_mod_option" value="Oxidation (M)"/> 362 <expand macro="default_mod_option" value="Oxidation (M)"/>
277 <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/> 363 <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/>
278 <expand macro="modification"/> 364 <expand macro="modification"/>
279 </param> 365 </param>
280 <param name="enzymes" type="select" label="enzyme" 366 <param name="enzymes" type="select" label="enzyme"
281 multiple="true" help="Select zero or more enzymes. The enzymes used for generating the in silico peptides for the Andromeda search."> 367 multiple="true"
368 help="Select zero or more enzymes. The enzymes used for generating the in silico peptides for the Andromeda search.">
282 <expand macro="default_mod_option" value="Trypsin/P"/> 369 <expand macro="default_mod_option" value="Trypsin/P"/>
283 <expand macro="proteases"/> 370 <expand macro="proteases"/>
284 </param> 371 </param>
372 <param name="digestion_mode" type="select" label="Digestion mode"
373 help="'Unspecific means that no cleavage rule is applied but instead all peptides up to a maximal length are considered">
374 <option value="0" selected="true">Specific</option>
375 <option value="1">Semi-specific free N-terminus</option>
376 <option value="2">Semi-specific free C-terminus</option>
377 <option value="3">Semi-specific</option>
378 <option value="4">Unspecific</option>
379 <option value="5">No digestion</option>
380 </param>
381
285 <conditional name="quant_method"> 382 <conditional name="quant_method">
286 <param name="select_quant_method" type="select" label="Quantitation Methods" 383 <param name="select_quant_method" type="select" label="Quantitation Methods"
287 help="Select a method if needed."> 384 help="Select a method if needed.">
288 <option value="">None</option> 385 <option value="">None</option>
289 <option value="lfq">label free quantification</option> 386 <option value="lfq">label free quantification</option>
290 <option value="silac">label based quantification</option> 387 <option value="silac">label based quantification</option>
291 <option value="reporter_ion_ms2">reporter ion MS2</option> 388 <option value="reporter_ion_ms2">reporter ion MS2</option>
292 </param> 389 </param>
293 <when value=""/> 390 <when value=""/>
294 <when value="silac"> 391 <when value="silac">
295 <param name="light_labels" type="select" label="light labels" 392 <param name="light_labels" type="select" label="light labels"
296 multiple="true" help="Select zero or more light modifications."> 393 multiple="true" help="Select zero or more light modifications.">
297 <expand macro="label"/> 394 <expand macro="label"/>
298 </param> 395 </param>
299 <param name="medium_labels" type="select" label="medium labels" 396 <param name="medium_labels" type="select" label="medium labels"
300 multiple="true" help="Select zero modifications if you have two labels. Select a medium modification if you have three labels."> 397 multiple="true"
301 <expand macro="label"/> 398 help="Select zero modifications if you have two labels. Select a medium modification if you have three labels.">
302 </param> 399 <expand macro="label"/>
303 <param name="heavy_labels" type="select" label="heavy labels" 400 </param>
304 multiple="true" help="Select zero or more heavy modifications."> 401 <param name="heavy_labels" type="select" label="heavy labels"
305 <expand macro="label"/> 402 multiple="true" help="Select zero or more heavy modifications.">
306 </param> 403 <expand macro="label"/>
404 </param>
307 </when> 405 </when>
308 <when value="lfq"> 406 <when value="lfq">
309 <param type="integer" name="lfqMinRatioCount" 407 <param type="integer" name="lfqMinRatioCount"
310 label="LFQ minimum ratio count" value="2" 408 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."/> 409 help="Minimum number of peptides that has to be available in pair-wise comparisons between two samples for a protein."/>
312 <param type="integer" name="lfqMinEdgesPerNode" 410 <param type="integer" name="lfqMinEdgesPerNode"
313 label="LFQ minimum number of neighbours" value="3" 411 label="LFQ minimum number of neighbours" value="3"
314 help="Defines the network to normalize the samples in the fast LFQ mode."/> 412 help="Defines the network to normalize the samples in the fast LFQ mode."/>
315 <param type="integer" name="lfqAvEdgesPerNode" 413 <param type="integer" name="lfqAvEdgesPerNode"
316 label="LFQ average number of neighbours" value="6" 414 label="LFQ average number of neighbours" value="6"
317 help="Defines the network to normalize the samples in the fast LFQ mode."/> 415 help="Defines the network to normalize the samples in the fast LFQ mode."/>
318 <param type="boolean" name="lfqSkipNorm" checked="true" 416 <param type="boolean" name="lfqSkipNorm" checked="true"
319 label="Skip normalization" 417 label="Skip normalization"
320 truevalue="True" falsevalue="False" 418 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."/> 419 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."/>
322 </when> 420 </when>
323 <when value="reporter_ion_ms2"> 421 <when value="reporter_ion_ms2">
324 <conditional name="iso_labels"> 422 <conditional name="iso_labels">
325 <param name="labeling" type="select" label="isobaric labeling" 423 <param name="labeling" type="select" label="isobaric labeling"
326 help="Select one of the standard labelings (correction factors are zero) or create a custom labeling."> 424 help="Select one of the standard labelings (correction factors are zero) or create a custom labeling.">
332 <option value="tmt11plex">TMT11plex</option> 430 <option value="tmt11plex">TMT11plex</option>
333 <option value="itraq4plex">iTRAQ4plex</option> 431 <option value="itraq4plex">iTRAQ4plex</option>
334 <option value="itraq8plex">iTRAQ8plex</option> 432 <option value="itraq8plex">iTRAQ8plex</option>
335 <option value="iodotmt6plex">iodoTMT6plex</option> 433 <option value="iodotmt6plex">iodoTMT6plex</option>
336 </param> 434 </param>
435
337 <when value="tmt2plex"></when> 436 <when value="tmt2plex"></when>
338 <when value="tmt6plex"></when> 437 <when value="tmt6plex"></when>
339 <when value="tmt8plex"></when> 438 <when value="tmt8plex"></when>
340 <when value="tmt10plex"></when> 439 <when value="tmt10plex"></when>
341 <when value="tmt11plex"></when> 440 <when value="tmt11plex"></when>
343 <when value="itraq8plex"></when> 442 <when value="itraq8plex"></when>
344 <when value="iodotmt6plex"></when> 443 <when value="iodotmt6plex"></when>
345 <when value="custom"> 444 <when value="custom">
346 <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> 445 <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
347 <param name="internallabel" type="select" label="internal label" help="contains Lys"> 446 <param name="internallabel" type="select" label="internal label" help="contains Lys">
348 <expand macro="iso_labels"/> 447 <expand macro="iso_labels"/>
349 </param> 448 </param>
350 <param name="terminallabel" type="select" label="terminal label" help="contains Nter"> 449 <param name="terminallabel" type="select" label="terminal label" help="contains Nter">
351 <option value="">None</option> 450 <option value="">None</option>
352 <expand macro="iso_labels"/> 451 <expand macro="iso_labels"/>
353 </param> 452 </param>
354 <param name="cm2" type="float" label="correction factor -2%" value="0.0"/> 453 <param name="cm2" type="float" label="correction factor -2%" value="0.0"/>
355 <param name="cm1" type="float" label="correction factor -1%" value="0.0"/> 454 <param name="cm1" type="float" label="correction factor -1%" value="0.0"/>
356 <param name="cp1" type="float" label="correction factor +1%" value="0.0"/> 455 <param name="cp1" type="float" label="correction factor +1%" value="0.0"/>
357 <param name="cp2" type="float" label="correction factor +2%" value="0.0"/> 456 <param name="cp2" type="float" label="correction factor +2%" value="0.0"/>
358 <param type="boolean" name="tmtlike" checked="false" 457 <param type="boolean" name="tmtlike" checked="false"
359 label="TMT-like" 458 label="TMT-like"
360 truevalue="True" falsevalue="False" /> 459 truevalue="True" falsevalue="False"/>
361 </repeat> 460 </repeat>
362 </when> 461 </when>
363 </conditional> 462 </conditional>
463 <param name="filter_pif" type="boolean" checked="false" label="Filter by PIF"
464 truevalue="True" falsevalue="False"
465 help="If checked, quantified PSMs will be filtered by their precursor intensity fraction to avoid using peptides that clearly suffer from co-fragmentation with other peptide species."/>
466 <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0" max="1"
467 help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>
364 </when> 468 </when>
365 </conditional> 469 </conditional>
366 </repeat> 470 </repeat>
367 471
368 <section title="LFQ Options" name="lfq_opts" expanded="false">
369 <param name="separateLfq" type="boolean" checked="false"
370 label="Separate LFQ in parameter Groups"
371 truevalue="True" falsevalue="False"
372 help="The MaxLFQ algorithm will be applied independently to samples in different parameter groups."/>
373 <param name="lfqStabilizeLargeRatios" type="boolean" checked="true"
374 label="Stabilize large LFQ ratios"
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"/>
377 <param name="lfqRequireMsms" type="boolean" checked="true"
378 label="Require MS/MS for LFQ comparisons"
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"/>
381 <conditional name="do_ibaq">
382 <param name="ibaq" type="select" label="iBAQ (calculates absolute protein abundances by normalizing to copy number and not protein mass)">
383 <option value="False">No</option>
384 <option value="True">Yes</option>
385 </param>
386 <when value="True">
387 <param name="ibaqLogFit" type="boolean" checked="true"
388 label="Logarithmic fit"
389 truevalue="True" falsevalue="False" />
390 </when>
391 <when value="False">
392 </when>
393 </conditional>
394 <param name="advancedSiteIntensities" type="boolean" checked="true"
395 label="Advanced site intensities"
396 truevalue="True" falsevalue="False" />
397 </section>
398
399 <expand macro="ptxqc-opts"/> 472 <expand macro="ptxqc-opts"/>
473
400 <section title="Output Options" name="output_opts" expanded="true"> 474 <section title="Output Options" name="output_opts" expanded="true">
401 <param name="dry_run" type="boolean" checked="false" 475 <param name="dry_run" type="boolean" checked="false"
402 label="Only create config files? (i.e. for testing)" 476 label="Only create config files? (i.e. for testing)"
403 truevalue="True" falsevalue="" /> 477 truevalue="True" falsevalue=""/>
404 <param type="select" name="output" label="Select the desired outputs." 478 <param type="select" name="output" label="Select the desired outputs."
405 multiple="true" optional="false"> 479 multiple="true" optional="false">
406 <option value="proteinGroups">Protein Groups</option> 480 <option value="proteinGroups">Protein Groups</option>
407 <option value="mqpar">mqpar.xml</option> 481 <option value="mqpar">mqpar.xml</option>
408 <option value="peptides">Peptides</option> 482 <option value="peptides">Peptides</option>
428 502
429 <expand macro="outputs"/> 503 <expand macro="outputs"/>
430 504
431 <tests> 505 <tests>
432 <!-- functional test with small mzXML file, no quantitation methods --> 506 <!-- functional test with small mzXML file, no quantitation methods -->
507 <!-- Disable this test when initally testing as it takes avery long tome to run -->
433 <test expect_num_outputs="15"> 508 <test expect_num_outputs="15">
434 <param name="ftype" value=".mzxml" /> 509 <param name="ftype" value=".mzxml" />
435 <param name="fasta_files" value="bsa.fasta" /> 510 <param name="fasta_files" value="bsa.fasta" />
436 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 511 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
437 <param name="description_parse_rule" value="&gt;(.*)" /> 512 <param name="description_parse_rule" value="&gt;(.*)" />
462 <test expect_num_outputs="3"> 537 <test expect_num_outputs="3">
463 <param name="ftype" value=".mzxml" /> 538 <param name="ftype" value=".mzxml" />
464 <param name="fasta_files" value="bsa.fasta" /> 539 <param name="fasta_files" value="bsa.fasta" />
465 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 540 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
466 <param name="description_parse_rule" value="&gt;(.*)" /> 541 <param name="description_parse_rule" value="&gt;(.*)" />
542 <param name="incl_contaminants" value="False" /> <!-- non-default value -->
543 <section name="protein_quant">
544 <param name="peptides_for_quantification" value="0"/><!-- non-default value -->
545 <conditional name="only_unmod_prot">
546 <param name="unmod_prot" value="True"/>
547 <param name="mods_used_prot_quant" value="Pro5,Pro6"/>
548 </conditional>
549 </section>
467 <repeat name="paramGroups"> 550 <repeat name="paramGroups">
468 <param name="files" value="BSA_min_23.mzXML"/> 551 <param name="files" value="BSA_min_23.mzXML"/>
469 <param name="variableModifications" value="Oxidation (M)" /> 552 <param name="variableModifications" value="Oxidation (M)" />
470 <param name="fixedModifications" value="" /> 553 <param name="fixedModifications" value="" />
471 <conditional name="quant_method"> 554 <conditional name="quant_method">
483 <param name="internallabel" value="TMT2plex-Lys127" /> 566 <param name="internallabel" value="TMT2plex-Lys127" />
484 <param name="terminallabel" value="TMT2plex-Nter127" /> 567 <param name="terminallabel" value="TMT2plex-Nter127" />
485 <param name="tmtlike" value="True" /> 568 <param name="tmtlike" value="True" />
486 </repeat> 569 </repeat>
487 </conditional> 570 </conditional>
571 <param name="filter_pif" value="False" />
572 <param name="reporter_pif" value="0.6" />
488 </conditional> 573 </conditional>
489 </repeat> 574 </repeat>
490 <repeat name="paramGroups"> 575 <repeat name="paramGroups">
491 <param name="files" value="BSA_min_22"/> 576 <param name="files" value="BSA_min_22"/>
492 <param name="variableModifications" value="" /> 577 <param name="variableModifications" value="" />
495 <conditional name="quant_method"> 580 <conditional name="quant_method">
496 <param name="select_quant_method" value="reporter_ion_ms2" /> 581 <param name="select_quant_method" value="reporter_ion_ms2" />
497 <conditional name="iso_labels"> 582 <conditional name="iso_labels">
498 <param name="labeling" value="itraq4plex" /> 583 <param name="labeling" value="itraq4plex" />
499 </conditional> 584 </conditional>
585 <param name="filter_pif" value="True" />
586 <param name="reporter_pif" value="0.8" />
500 </conditional> 587 </conditional>
501 </repeat> 588 </repeat>
502 <param name="dry_run" value="True" /> 589 <param name="dry_run" value="True" />
503 <param name="output" value="config,mqpar,mzTab" /> 590 <param name="output" value="config,mqpar,mzTab" />
504 <output name="config" file="02/config.yml" lines_diff="2" /> 591 <output name="config" file="02/config.yml" lines_diff="2" />