Mercurial > repos > jjohnson > peptideshaker

comparison test-data/Identification_Parameters_specific.par @ 0:8b99cb00e1c4 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
author jjohnson
date Tue, 15 May 2018 14:50:35 -0400
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-1:000000000000 0:8b99cb00e1c4
1 {
2 "marshallableParameterType": "identification_parameters",
3 "name": "SEARCHGUI_IdentificationParameters",
4 "description": "Fixed: Carbamidomethylation of C.\nVariable: Oxidation of M.\nPrecursor Tolerance: 100.0 ppm.\nCharge: 1-3.\nDB: dataset_118.dat.\n",
5 "defaultDescription": true,
6 "searchParameters": {
7 "precursorAccuracyType": "PPM",
8 "fragmentAccuracyType": "DA",
9 "precursorTolerance": 100.0,
10 "precursorToleranceDalton": 0.5,
11 "fragmentIonMZTolerance": 0.5,
12 "ptmSettings": {
13 "fixedModifications": [
14 "Carbamidomethylation of C"
15 ],
16 "variableModifications": [
17 "Oxidation of M"
18 ],
19 "refinementVariableModifications": [],
20 "refinementFixedModifications": [],
21 "colors": {},
22 "backUp": {
23 "Oxidation of M": {
24 "type": 0,
25 "name": "Oxidation of M",
26 "shortName": "ox",
27 "neutralLosses": [
28 {
29 "composition": {
30 "atomChain": [
31 {
32 "atomSymbol": "C",
33 "isotope": 0
34 },
35 {
36 "atomSymbol": "H",
37 "isotope": 0
38 },
39 {
40 "atomSymbol": "H",
41 "isotope": 0
42 },
43 {
44 "atomSymbol": "H",
45 "isotope": 0
46 },
47 {
48 "atomSymbol": "H",
49 "isotope": 0
50 },
51 {
52 "atomSymbol": "O",
53 "isotope": 0
54 },
55 {
56 "atomSymbol": "S",
57 "isotope": 0
58 }
59 ],
60 "mass1": -1.0
61 },
62 "name": "CH4OS",
63 "fixed": false
64 }
65 ],
66 "reporterIons": [],
67 "pattern": {
68 "length": 0,
69 "residueTargeted": {
70 "0": [
71 "M"
72 ]
73 }
74 },
75 "atomChainAdded": {
76 "atomChain": [
77 {
78 "atomSymbol": "O",
79 "isotope": 0
80 }
81 ],
82 "mass1": -1.0
83 },
84 "cvTerm": {
85 "ontology": "UNIMOD",
86 "accession": "UNIMOD:35",
87 "name": "Oxidation"
88 }
89 },
90 "Carbamidomethylation of C": {
91 "type": 0,
92 "name": "Carbamidomethylation of C",
93 "shortName": "cmm",
94 "neutralLosses": [],
95 "reporterIons": [],
96 "pattern": {
97 "length": 0,
98 "residueTargeted": {
99 "0": [
100 "C"
101 ]
102 }
103 },
104 "atomChainAdded": {
105 "atomChain": [
106 {
107 "atomSymbol": "C",
108 "isotope": 0
109 },
110 {
111 "atomSymbol": "C",
112 "isotope": 0
113 },
114 {
115 "atomSymbol": "H",
116 "isotope": 0
117 },
118 {
119 "atomSymbol": "H",
120 "isotope": 0
121 },
122 {
123 "atomSymbol": "H",
124 "isotope": 0
125 },
126 {
127 "atomSymbol": "N",
128 "isotope": 0
129 },
130 {
131 "atomSymbol": "O",
132 "isotope": 0
133 }
134 ],
135 "mass1": -1.0
136 },
137 "cvTerm": {
138 "ontology": "UNIMOD",
139 "accession": "UNIMOD:4",
140 "name": "Carbamidomethyl"
141 }
142 }
143 }
144 },
145 "nMissedCleavages": 2,
146 "digestionPreferences": {
147 "cleavagePreference": "enzyme",
148 "enzymes": [
149 {
150 "id": 0,
151 "name": "Trypsin",
152 "aminoAcidBefore": [],
153 "aminoAcidAfter": [],
154 "restrictionBefore": [],
155 "restrictionAfter": [],
156 "aminoAcidBeforeSet": [
157 "R",
158 "K"
159 ],
160 "aminoAcidAfterSet": [],
161 "restrictionBeforeSet": [],
162 "restrictionAfterSet": [
163 "P"
164 ],
165 "isSemiSpecific": false,
166 "isWholeProtein": false,
167 "cvTerm": {
168 "ontology": "PSI-MS",
169 "accession": "MS:1001251",
170 "name": "Trypsin"
171 }
172 }
173 ],
174 "nMissedCleavages": {
175 "Trypsin": 2
176 },
177 "specificity": {
178 "Trypsin": "specific"
179 }
180 },
181 "fastaFile": {
182 "path": "./searchgui_tinydb1_concatenated_target_decoy.fasta"
183 },
184 "parametersFile": {},
185 "forwardIons": [
186 1
187 ],
188 "rewindIons": [
189 4
190 ],
191 "minChargeSearched": {
192 "sign": 1,
193 "value": 1
194 },
195 "maxChargeSearched": {
196 "sign": 1,
197 "value": 3
198 },
199 "minIsotopicCorrection": 0,
200 "maxIsotopicCorrection": 1,
201 "refMass": 2000.0,
202 "algorithmParameters": {
203 "1": {
204 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters",
205 "data": {
206 "maxEValue": 100.0,
207 "hitListLength": 10,
208 "minimalChargeForMultipleChargedFragments": {
209 "sign": 1,
210 "value": 3
211 },
212 "minPeptideLength": 8,
213 "maxPeptideLength": 30,
214 "removePrecursor": false,
215 "scalePrecursor": true,
216 "estimateCharge": true,
217 "selectedOutput": "OMX",
218 "memoryMappedSequenceLibraries": false,
219 "numberOfItotopicPeaks": 0,
220 "neutronThreshold": 1446.94,
221 "lowIntensityCutOff": 0.0,
222 "highIntensityCutOff": 0.2,
223 "intensityCutOffIncrement": 5.0E-4,
224 "singleChargeWindow": 27,
225 "doubleChargeWindow": 14,
226 "nPeaksInSingleChargeWindow": 2,
227 "nPeaksInDoubleChargeWindow": 2,
228 "maxHitsPerSpectrumPerCharge": 30,
229 "nAnnotatedMostIntensePeaks": 6,
230 "minAnnotatedPeaks": 2,
231 "minPeaks": 4,
232 "cleaveNtermMethionine": true,
233 "maxMzLadders": 128,
234 "maxFragmentCharge": 2,
235 "fractionOfPeaksForChargeEstimation": 0.95,
236 "determineChargePlusOneAlgorithmically": true,
237 "searchPositiveIons": true,
238 "minPrecPerSpectrum": 1,
239 "searchForwardFragmentFirst": false,
240 "searchRewindFragments": true,
241 "maxFragmentPerSeries": 100,
242 "useCorrelationCorrectionScore": true,
243 "consecutiveIonProbability": 0.5,
244 "iterativeSequenceEvalue": 0.0,
245 "iterativeReplaceEvalue": 0.0,
246 "iterativeSpectrumEvalue": 0.01,
247 "noProlineRuleSeries": [],
248 "ptmIndexes": {}
249 }
250 },
251 "2": {
252 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters",
253 "data": {
254 "maxEValue": 0.01,
255 "outputResults": "0",
256 "dynamicRange": 100.0,
257 "nPeaks": 50,
258 "minPrecursorMass": 200.0,
259 "minFragmentMz": 200.0,
260 "minPeaksPerSpectrum": 15,
261 "proteinQuickAcetyl": true,
262 "quickPyrolidone": true,
263 "refine": true,
264 "refineSemi": false,
265 "refinePointMutations": false,
266 "refineSpectrumSynthesis": true,
267 "refineUnanticipatedCleavages": true,
268 "refineSnaps": true,
269 "maximumExpectationValueRefinement": 0.01,
270 "potentialModificationsForFullRefinment": false,
271 "skylinePath": "",
272 "outputProteins": true,
273 "outputSequences": false,
274 "outputSpectra": true,
275 "outputHistograms": false,
276 "stpBias": false,
277 "useNoiseSuppression": true,
278 "proteinPtmComplexity": 6.0
279 }
280 },
281 "3": {
282 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters",
283 "data": {
284 "hitListLength": 10,
285 "estimateCharge": true,
286 "correctPrecursorMass": false,
287 "discardLowQualitySpectra": true,
288 "fragmentationModel": "CID_IT_TRYP",
289 "generateQuery": false
290 }
291 },
292 "4": {
293 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters",
294 "data": {
295 "maxPeptideMass": 4600.0,
296 "maxCombinations": 250,
297 "topPeaks": 8,
298 "topPeaksWindow": 100,
299 "includeWater": true,
300 "includeAmmonia": true,
301 "dependentLosses": true,
302 "fragmentAll": false,
303 "empiricalCorrection": true,
304 "higherCharge": true,
305 "fragmentationMethod": "CID",
306 "maxNumberOfModifications": 5,
307 "minPeptideLengthNoEnzyme": 8,
308 "maxPeptideLengthNoEnzyme": 25,
309 "equalIL": false,
310 "numberOfCandidates": 10,
311 "ptmIndexes": {},
312 "decoyMode": "none"
313 }
314 },
315 "5": {
316 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters",
317 "data": {
318 "generateDecoy": false,
319 "instrumentID": "b, y",
320 "maxRank": 10,
321 "monoisotopic": true,
322 "lowMemoryMode": true
323 }
324 },
325 "7": {
326 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters",
327 "data": {
328 "searchDecoyDatabase": false,
329 "instrumentID": 3,
330 "fragmentationType": 3,
331 "protocol": 0,
332 "minPeptideLength": 8,
333 "maxPeptideLength": 30,
334 "numberOfSpectrumMarches": 10,
335 "additionalOutput": false,
336 "lowerIsotopeErrorRange": -1,
337 "upperIsotopeErrorRange": 2,
338 "numberTolerableTermini": 2,
339 "numberOfPtmsPerPeptide": 2
340 }
341 },
342 "8": {
343 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters",
344 "data": {
345 "ticCutoffPercentage": 100.0,
346 "maxPeakCount": 100,
347 "numIntensityClasses": 3,
348 "adjustPrecursorMass": false,
349 "minPrecursorAdjustment": -0.5,
350 "maxPrecursorAdjustment": 1.5,
351 "precursorAdjustmentStep": 0.1,
352 "numChargeStates": 3,
353 "outputSuffix": "",
354 "useChargeStateFromMS": true,
355 "duplicateSpectra": true,
356 "deisotopingMode": 0,
357 "isotopeMzTolerance": 0.25,
358 "complementMzTolerance": 0.1,
359 "tagLength": 4,
360 "maxDynamicMods": 2,
361 "maxTagCount": 10,
362 "intensityScoreWeight": 1.0,
363 "mzFidelityScoreWeight": 1.0,
364 "complementScoreWeight": 1.0,
365 "variablePtms": []
366 }
367 },
368 "10": {
369 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters",
370 "data": {
371 "numberOfSpectrumMatches": 10,
372 "maxVariableMods": 10,
373 "requireVariableMods": false,
374 "minPeaks": 10,
375 "minPeakIntensity": 0.0,
376 "removePrecursor": 0,
377 "removePrecursorTolerance": 1.5,
378 "lowerClearMzRange": 0.0,
379 "upperClearMzRange": 0.0,
380 "enzymeType": 2,
381 "isotopeCorrection": 1,
382 "minPrecursorMass": 600.0,
383 "maxPrecursorMass": 5000.0,
384 "maxFragmentCharge": 3,
385 "removeMethionine": false,
386 "batchSize": 0,
387 "theoreticalFragmentIonsSumOnly": false,
388 "fragmentBinOffset": 0.0,
389 "useSparseMatrix": true,
390 "selectedOutputFormat": "PepXML",
391 "printExpectScore": true
392 }
393 },
394 "27": {
395 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters",
396 "data": {
397 "numberOfPeptides": 10,
398 "lowerPrecursorMass": 300,
399 "upperPrecursorMass": 5000,
400 "acticationType": "HCD"
401 }
402 },
403 "28": {
404 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters",
405 "data": {
406 "fastIndexFolderName": "fasta-index",
407 "maxVariablePtmsPerTypePerPeptide": 2,
408 "minPeptideLength": 6,
409 "maxPeptideLength": 30,
410 "minPrecursorMass": 200.0,
411 "maxPrecursorMass": 7200.0,
412 "decoyFormat": "none",
413 "keepTerminalAminoAcids": "NC",
414 "decoySeed": 1,
415 "outputFolderName": "crux-output",
416 "printPeptides": false,
417 "verbosity": 30,
418 "monoisotopicPrecursor": true,
419 "clipNtermMethionine": false,
420 "digestionType": "full-digest",
421 "computeSpScore": false,
422 "numberOfSpectrumMatches": 10,
423 "computeExactPValues": false,
424 "minSpectrumMz": 0.0,
425 "minSpectrumPeaks": 20,
426 "spectrumCharges": "all",
427 "removePrecursor": false,
428 "removePrecursorTolerance": 1.5,
429 "printProgressIndicatorSize": 1000,
430 "useFlankingPeaks": false,
431 "useNeutralLossPeaks": false,
432 "mzBinWidth": 0.02,
433 "mzBinOffset": 0.0,
434 "concatenateTargetDecoy": false,
435 "textOutput": true,
436 "sqtOutput": false,
437 "pepXmlOutput": false,
438 "mzidOutput": false,
439 "pinOutput": false,
440 "removeTempFolders": true
441 }
442 },
443 "13": {
444 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters",
445 "data": {
446 "minPeptideLength": 8,
447 "maxPeptideLength": 30,
448 "numberOfSpectrumMatches": 10,
449 "ticCutoffPercentage": 0.98,
450 "maxDynamicMods": 2,
451 "minTerminiCleavages": 2,
452 "minPrecursorMass": 600.0,
453 "maxPrecursorMass": 5000.0,
454 "useSmartPlusThreeModel": true,
455 "computeXCorr": false,
456 "numIntensityClasses": 3,
457 "classSizeMultiplier": 2,
458 "numberOfBatches": 50,
459 "lowerIsotopeCorrection": -1,
460 "upperIsotopeCorrection": 2,
461 "fragmentationRule": "CID",
462 "maxPeakCount": 300,
463 "outputFormat": "mzIdentML"
464 }
465 },
466 "29": {
467 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters",
468 "data": {
469 "fragmentationMethod": "HCD",
470 "massAnalyzer": "FT"
471 }
472 }
473 }
474 },
475 "annotationSettings": {
476 "yAxisZoomExcludesBackgroundPeaks": true,
477 "showAllPeaks": false,
478 "intensityThresholdType": "percentile",
479 "intensityLimit": 0.75,
480 "automaticAnnotation": true,
481 "selectedIonsMap": {
482 "TAG_FRAGMENT_ION": [
483 4,
484 1
485 ],
486 "REPORTER_ION": [],
487 "RELATED_ION": [
488 0,
489 1,
490 2,
491 3,
492 4,
493 5,
494 6,
495 7,
496 8,
497 9,
498 10,
499 11,
500 12,
501 13,
502 14,
503 15,
504 16,
505 17,
506 18
507 ],
508 "PEPTIDE_FRAGMENT_ION": [
509 4,
510 1
511 ],
512 "PRECURSOR_ION": [
513 0
514 ],
515 "IMMONIUM_ION": [
516 0,
517 1,
518 2,
519 3,
520 4,
521 5,
522 6,
523 7,
524 8,
525 9,
526 10,
527 11,
528 12,
529 13,
530 14,
531 15,
532 16,
533 17,
534 18,
535 19,
536 20
537 ]
538 },
539 "neutralLossesList": [
540 {
541 "composition": {
542 "atomChain": [
543 {
544 "atomSymbol": "H",
545 "isotope": 0
546 },
547 {
548 "atomSymbol": "H",
549 "isotope": 0
550 },
551 {
552 "atomSymbol": "O",
553 "isotope": 0
554 }
555 ],
556 "mass1": -1.0,
557 "stringValue1": "H(2)O"
558 },
559 "name": "H2O",
560 "fixed": false,
561 "aminoAcids": [
562 "D",
563 "E",
564 "S",
565 "T"
566 ]
567 },
568 {
569 "composition": {
570 "atomChain": [
571 {
572 "atomSymbol": "N",
573 "isotope": 0
574 },
575 {
576 "atomSymbol": "H",
577 "isotope": 0
578 },
579 {
580 "atomSymbol": "H",
581 "isotope": 0
582 },
583 {
584 "atomSymbol": "H",
585 "isotope": 0
586 }
587 ],
588 "mass1": -1.0,
589 "stringValue1": "H(3)N"
590 },
591 "name": "NH3",
592 "fixed": false,
593 "aminoAcids": [
594 "K",
595 "N",
596 "Q",
597 "R"
598 ]
599 },
600 {
601 "composition": {
602 "atomChain": [
603 {
604 "atomSymbol": "C",
605 "isotope": 0
606 },
607 {
608 "atomSymbol": "H",
609 "isotope": 0
610 },
611 {
612 "atomSymbol": "H",
613 "isotope": 0
614 },
615 {
616 "atomSymbol": "H",
617 "isotope": 0
618 },
619 {
620 "atomSymbol": "H",
621 "isotope": 0
622 },
623 {
624 "atomSymbol": "O",
625 "isotope": 0
626 },
627 {
628 "atomSymbol": "S",
629 "isotope": 0
630 }
631 ],
632 "mass1": -1.0
633 },
634 "name": "CH4OS",
635 "fixed": false
636 }
637 ],
638 "neutralLossesAuto": true,
639 "reporterIons": true,
640 "relatedIons": true,
641 "fragmentIonAccuracy": 0.5,
642 "fragmentIonPpm": false,
643 "showForwardIonDeNovoTags": false,
644 "showRewindIonDeNovoTags": false,
645 "deNovoCharge": 1,
646 "highResolutionAnnotation": true,
647 "tiesResolution": "mostAccurateMz"
648 },
649 "sequenceMatchingPreferences": {
650 "sequenceMatchingType": "indistiguishableAminoAcids",
651 "limitX": 0.25,
652 "peptideMapperType": "fm_index"
653 },
654 "peptideVariantsPreferences": {
655 "useSpecificCount": false,
656 "nVariants": 0,
657 "nAaDeletions": 0,
658 "nAaInsertions": 0,
659 "nAaSubstitutions": 0,
660 "nAaSwap": 0,
661 "aaSubstitutionMatrix": {
662 "name": "No Substitution",
663 "description": "No substitution",
664 "substitutions": {},
665 "reverseMap": {}
666 }
667 },
668 "genePreferences": {
669 "autoUpdate": false,
670 "useGeneMapping": false
671 },
672 "psmScoringPreferences": {
673 "spectrumMatchingScores": {
674 "8": [
675 1
676 ],
677 "3": [
678 1
679 ],
680 "27": [
681 1
682 ]
683 },
684 "defaultScores": [
685 -1
686 ],
687 "minDecoysInBin": 10
688 },
689 "peptideAssumptionFilter": {
690 "minPepLength": 8,
691 "maxPepLength": 30,
692 "maxMassDeviation": 10.0,
693 "isPpm": true,
694 "unknownPtm": true,
695 "minIsotopes": 0,
696 "maxIsotopes": 1
697 },
698 "ptmScoringPreferences": {
699 "flr": 1.0,
700 "probabilitsticScoreCalculation": true,
701 "selectedProbabilisticScore": "PhosphoRS",
702 "estimateFlr": false,
703 "probabilisticScoreThreshold": 95.0,
704 "probabilisticScoreNeutralLosses": false,
705 "sequenceMatchingPreferences": {
706 "sequenceMatchingType": "aminoAcid",
707 "limitX": 0.25,
708 "peptideMapperType": "fm_index"
709 },
710 "alignNonConfidentPTMs": true
711 },
712 "proteinInferencePreferences": {
713 "proteinSequenceDatabase": {
714 "path": "./searchgui_tinydb1_concatenated_target_decoy.fasta"
715 },
716 "simplifyProteinGroups": true,
717 "simplifyGroupsScore": true,
718 "simplifyGroupsEvidence": true,
719 "simplifyGroupsEnzymaticity": true,
720 "simplifyGroupsUncharacterized": true
721 },
722 "idValidationPreferences": {
723 "defaultProteinFDR": 1.0,
724 "defaultPeptideFDR": 1.0,
725 "defaultPsmFDR": 1.0,
726 "separatePeptides": true,
727 "separatePsms": true,
728 "mergeSmallSubgroups": true,
729 "validationQCPreferences": {
730 "dbSize": false,
731 "firstDecoy": true,
732 "confidenceMargin": 1.0
733 }
734 },
735 "fractionSettings": {
736 "proteinConfidenceMwPlots": 95.0,
737 "fractionMolecularWeightRanges": {}
738 }
739 }