Mercurial > repos > galaxyp > peptideshaker

comparison test-data/Identification_Parameters_default.par @ 48:b72821cab1d7 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
author galaxyp
date Fri, 15 Jan 2021 14:05:46 +0000
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47:5da80a2c0ef9 48:b72821cab1d7
1 {
2 "marshallableParameterType": "identification_parameters",
3 "version": "5.0.1",
4 "name": "IdentificationParametersOutput",
5 "description": "Fragment Tolerance: 0.5 Da.\n",
6 "defaultDescription": true,
7 "searchParameters": {
8 "version": "5.0.1",
9 "precursorAccuracyType": "PPM",
10 "fragmentAccuracyType": "DA",
11 "precursorTolerance": 10.0,
12 "fragmentIonMZTolerance": 0.5,
13 "modificationParameters": {
14 "fixedModifications": [],
15 "variableModifications": [],
16 "refinementVariableModifications": [],
17 "refinementFixedModifications": [],
18 "colors": {},
19 "backUp": {},
20 "id": 0
21 },
22 "digestionParameters": {
23 "cleavageParameter": "enzyme",
24 "enzymes": [
25 {
26 "name": "Trypsin",
27 "aminoAcidBefore": [
28 "R",
29 "K"
30 ],
31 "aminoAcidAfter": [],
32 "restrictionBefore": [],
33 "restrictionAfter": [
34 "P"
35 ],
36 "cvTerm": {
37 "ontology": "PSI-MS",
38 "accession": "MS:1001251",
39 "name": "Trypsin",
40 "id": 0
41 },
42 "id": 0
43 }
44 ],
45 "nMissedCleavages": {
46 "Trypsin": 2
47 },
48 "specificity": {
49 "Trypsin": "specific"
50 },
51 "id": 0
52 },
53 "forwardIons": [
54 1
55 ],
56 "rewindIons": [
57 4
58 ],
59 "minChargeSearched": 2,
60 "maxChargeSearched": 4,
61 "minIsotopicCorrection": 0,
62 "maxIsotopicCorrection": 1,
63 "refMass": 2000.0,
64 "algorithmParameters": {
65 "1": {
66 "type": "com.compomics.util.parameters.identification.tool_specific.OmssaParameters",
67 "data": {
68 "maxEValue": 100.0,
69 "hitListLength": 10,
70 "minimalChargeForMultipleChargedFragments": 3,
71 "minPeptideLength": 8,
72 "maxPeptideLength": 30,
73 "removePrecursor": false,
74 "scalePrecursor": true,
75 "estimateCharge": true,
76 "selectedOutput": "OMX",
77 "memoryMappedSequenceLibraries": false,
78 "neutronThreshold": 1446.94,
79 "lowIntensityCutOff": 0.0,
80 "highIntensityCutOff": 0.2,
81 "intensityCutOffIncrement": 5.0E-4,
82 "singleChargeWindow": 27,
83 "doubleChargeWindow": 14,
84 "nPeaksInSingleChargeWindow": 2,
85 "nPeaksIndoubleChargeWindow": 2,
86 "maxHitsPerSpectrumPerCharge": 30,
87 "nAnnotatedMostIntensePeaks": 6,
88 "minAnnotatedPeaks": 2,
89 "minPeaks": 4,
90 "cleaveNtermMethionine": true,
91 "maxMzLadders": 128,
92 "maxFragmentCharge": 2,
93 "fractionOfPeaksForChargeEstimation": 0.95,
94 "determineChargePlusOneAlgorithmically": true,
95 "searchPositiveIons": true,
96 "minPrecPerSpectrum": 1,
97 "searchForwardFragmentFirst": false,
98 "searchRewindFragments": true,
99 "maxFragmentPerSeries": 100,
100 "useCorrelationCorrectionScore": true,
101 "consecutiveIonProbability": 0.5,
102 "iterativeSequenceEvalue": 0.0,
103 "iterativeReplaceEvalue": 0.0,
104 "iterativeSpectrumEvalue": 0.01,
105 "noProlineRuleSeries": [],
106 "ptmIndexes": {},
107 "id": 0
108 }
109 },
110 "33": {
111 "type": "com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters",
112 "data": {
113 "minPeptideLength": 8,
114 "maxPeptideLength": 30,
115 "searchType": "Classic",
116 "totalPartitions": 1,
117 "dissociationType": "HCD",
118 "maxModsForPeptide": 2,
119 "initiatorMethionineBehavior": "Variable",
120 "scoreCutoff": 5.0,
121 "useDeltaScore": false,
122 "fragmentationTerminus": "Both",
123 "maxFragmentSize": 30000.0,
124 "massDiffAcceptorType": "OneMM",
125 "writeMzId": true,
126 "writePepXml": false,
127 "useProvidedPrecursorInfo": true,
128 "doPrecursorDeconvolution": true,
129 "deconvolutionIntensityRatio": 3.0,
130 "deconvolutionMassTolerance": 4.0,
131 "deconvolutionMassToleranceType": "PPM",
132 "trimMs1Peaks": false,
133 "trimMsMsPeaks": true,
134 "numberOfPeaksToKeepPerWindow": 200,
135 "minAllowedIntensityRatioToBasePeak": 0.01,
136 "normalizePeaksAcrossAllWindows": false,
137 "modPeptidesAreDifferent": false,
138 "noOneHitWonders": false,
139 "searchTarget": true,
140 "decoyType": "None",
141 "maxModificationIsoforms": 1024,
142 "minVariantDepth": 1,
143 "maxHeterozygousVariants": 4,
144 "runGptm": false,
145 "gPtmCategories": [
146 "Common_Biological",
147 "Common_Artifact",
148 "Metal"
149 ],
150 "id": 0
151 }
152 },
153 "2": {
154 "type": "com.compomics.util.parameters.identification.tool_specific.XtandemParameters",
155 "data": {
156 "maxEValue": 0.01,
157 "outputResults": "all",
158 "dynamicRange": 100.0,
159 "nPeaks": 50,
160 "minPrecursorMass": 500.0,
161 "minFragmentMz": 200.0,
162 "minPeaksPerSpectrum": 5,
163 "proteinQuickAcetyl": true,
164 "quickPyrolidone": true,
165 "refine": true,
166 "refineSemi": false,
167 "refinePointMutations": false,
168 "refineSpectrumSynthesis": true,
169 "refineUnanticipatedCleavages": true,
170 "refineSnaps": true,
171 "maximumExpectationValueRefinement": 0.01,
172 "potentialModificationsForFullRefinment": false,
173 "skylinePath": "",
174 "outputProteins": true,
175 "outputSequences": false,
176 "outputSpectra": true,
177 "outputHistograms": false,
178 "stpBias": false,
179 "useNoiseSuppression": false,
180 "proteinPtmComplexity": 6.0,
181 "parentMonoisotopicMassIsotopeError": true,
182 "id": 0
183 }
184 },
185 "3": {
186 "type": "com.compomics.util.parameters.identification.tool_specific.PepnovoParameters",
187 "data": {
188 "hitListLength": 10,
189 "estimateCharge": true,
190 "correctPrecursorMass": false,
191 "discardLowQualitySpectra": true,
192 "fragmentationModel": "CID_IT_TRYP",
193 "generateQuery": false,
194 "id": 0
195 }
196 },
197 "4": {
198 "type": "com.compomics.util.parameters.identification.tool_specific.AndromedaParameters",
199 "data": {
200 "maxPeptideMass": 4600.0,
201 "maxCombinations": 250,
202 "topPeaks": 8,
203 "topPeaksWindow": 100,
204 "includeWater": true,
205 "includeAmmonia": true,
206 "dependentLosses": true,
207 "fragmentAll": false,
208 "empiricalCorrection": true,
209 "higherCharge": true,
210 "fragmentationMethod": "CID",
211 "maxNumberOfModifications": 5,
212 "minPeptideLengthNoEnzyme": 8,
213 "maxPeptideLengthNoEnzyme": 30,
214 "equalIL": false,
215 "numberOfCandidates": 10,
216 "ptmIndexes": {},
217 "decoyMode": "none",
218 "id": 0
219 }
220 },
221 "5": {
222 "type": "com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters",
223 "data": {
224 "generateDecoy": false,
225 "reportBothBestHitsForTD": true,
226 "instrumentID": "b, y",
227 "maxRank": 10,
228 "monoisotopic": true,
229 "lowMemoryMode": true,
230 "performDeisotoping": true,
231 "maxModifications": 3,
232 "maxVariableModifications": 4,
233 "maxModificationSites": 6,
234 "maxNeutralLosses": 1,
235 "maxNeutralLossesPerModification": 2,
236 "minPeptideLength": 8,
237 "maxPeptideLength": 30,
238 "maxLoadedProteins": 100000,
239 "maxLoadedSpectra": 2000,
240 "outputFormat": "csv",
241 "id": 0
242 }
243 },
244 "7": {
245 "type": "com.compomics.util.parameters.identification.tool_specific.MsgfParameters",
246 "data": {
247 "searchDecoyDatabase": false,
248 "instrumentID": 3,
249 "fragmentationType": 3,
250 "protocol": 0,
251 "minPeptideLength": 8,
252 "maxPeptideLength": 30,
253 "numberOfSpectrumMarches": 10,
254 "additionalOutput": false,
255 "numberTolerableTermini": 2,
256 "numberOfModificationsPerPeptide": 2,
257 "id": 0
258 }
259 },
260 "8": {
261 "type": "com.compomics.util.parameters.identification.tool_specific.DirecTagParameters",
262 "data": {
263 "ticCutoffPercentage": 100.0,
264 "maxPeakCount": 100,
265 "numIntensityClasses": 3,
266 "adjustPrecursorMass": false,
267 "minPrecursorAdjustment": -0.5,
268 "maxPrecursorAdjustment": 1.5,
269 "precursorAdjustmentStep": 0.1,
270 "numChargeStates": 3,
271 "outputSuffix": "",
272 "useChargeStateFromMS": true,
273 "duplicateSpectra": true,
274 "deisotopingMode": 0,
275 "isotopeMzTolerance": 0.25,
276 "complementMzTolerance": 0.1,
277 "tagLength": 4,
278 "maxDynamicMods": 2,
279 "maxTagCount": 10,
280 "intensityScoreWeight": 1.0,
281 "mzFidelityScoreWeight": 1.0,
282 "complementScoreWeight": 1.0,
283 "variableModifications": [],
284 "id": 0
285 }
286 },
287 "10": {
288 "type": "com.compomics.util.parameters.identification.tool_specific.CometParameters",
289 "data": {
290 "numberOfSpectrumMatches": 10,
291 "maxVariableMods": 10,
292 "requireVariableMods": false,
293 "minPeaks": 10,
294 "minPeakIntensity": 0.0,
295 "removePrecursor": 0,
296 "removePrecursorTolerance": 1.5,
297 "lowerClearMzRange": 0.0,
298 "upperClearMzRange": 0.0,
299 "enzymeType": 2,
300 "isotopeCorrection": 3,
301 "minPrecursorMass": 600.0,
302 "maxPrecursorMass": 5000.0,
303 "maxFragmentCharge": 3,
304 "removeMethionine": false,
305 "batchSize": 0,
306 "theoreticalFragmentIonsSumOnly": false,
307 "fragmentBinOffset": 0.0,
308 "useSparseMatrix": true,
309 "selectedOutputFormat": "PepXML",
310 "printExpectScore": true,
311 "minPeptideLength": 8,
312 "maxPeptideLength": 30,
313 "id": 0
314 }
315 },
316 "13": {
317 "type": "com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters",
318 "data": {
319 "minPeptideLength": 8,
320 "maxPeptideLength": 30,
321 "numberOfSpectrumMatches": 10,
322 "ticCutoffPercentage": 0.98,
323 "maxDynamicMods": 2,
324 "minTerminiCleavages": 2,
325 "minPrecursorMass": 600.0,
326 "maxPrecursorMass": 5000.0,
327 "useSmartPlusThreeModel": false,
328 "computeXCorr": false,
329 "numIntensityClasses": 3,
330 "classSizeMultiplier": 2,
331 "numberOfBatches": 50,
332 "lowerIsotopeCorrection": -1,
333 "upperIsotopeCorrection": 2,
334 "fragmentationRule": "CID",
335 "maxPeakCount": 300,
336 "outputFormat": "mzIdentML",
337 "id": 0
338 }
339 },
340 "27": {
341 "type": "com.compomics.util.parameters.identification.tool_specific.PNovoParameters",
342 "data": {
343 "numberOfPeptides": 10,
344 "lowerPrecursorMass": 300,
345 "upperPrecursorMass": 5000,
346 "acticationType": "HCD",
347 "id": 0
348 }
349 },
350 "28": {
351 "type": "com.compomics.util.parameters.identification.tool_specific.TideParameters",
352 "data": {
353 "fastIndexFolderName": "fasta-index",
354 "maxVariableModificationsPerPeptide": 255,
355 "maxVariableModificationsPerTypePerPeptide": 2,
356 "minPeptideLength": 6,
357 "maxPeptideLength": 30,
358 "minPrecursorMass": 200.0,
359 "maxPrecursorMass": 7200.0,
360 "decoyFormat": "none",
361 "keepTerminalAminoAcids": "NC",
362 "decoySeed": 1,
363 "outputFolderName": "crux-output",
364 "printPeptides": false,
365 "verbosity": 30,
366 "monoisotopicPrecursor": true,
367 "clipNtermMethionine": false,
368 "digestionType": "full-digest",
369 "computeSpScore": false,
370 "numberOfSpectrumMatches": 10,
371 "computeExactPValues": false,
372 "minSpectrumMz": 0.0,
373 "minSpectrumPeaks": 20,
374 "spectrumCharges": "all",
375 "removePrecursor": false,
376 "removePrecursorTolerance": 1.5,
377 "printProgressIndicatorSize": 1000,
378 "useFlankingPeaks": false,
379 "useNeutralLossPeaks": false,
380 "mzBinWidth": 0.02,
381 "mzBinOffset": 0.0,
382 "concatenateTargetDecoy": false,
383 "textOutput": true,
384 "sqtOutput": false,
385 "pepXmlOutput": false,
386 "mzidOutput": false,
387 "pinOutput": false,
388 "removeTempFolders": true,
389 "id": 0
390 }
391 },
392 "29": {
393 "type": "com.compomics.util.parameters.identification.tool_specific.NovorParameters",
394 "data": {
395 "fragmentationMethod": "HCD",
396 "massAnalyzer": "FT",
397 "id": 0
398 }
399 }
400 },
401 "flanking": false,
402 "id": 0
403 },
404 "annotationParameters": {
405 "yAxisZoomExcludesBackgroundPeaks": true,
406 "showAllPeaks": false,
407 "intensityThresholdType": "percentile",
408 "intensityLimit": 0.75,
409 "automaticAnnotation": true,
410 "selectedIonsMap": {
411 "PEPTIDE_FRAGMENT_ION": [
412 4,
413 1
414 ],
415 "REPORTER_ION": [],
416 "IMMONIUM_ION": [
417 0,
418 1,
419 2,
420 3,
421 4,
422 5,
423 6,
424 7,
425 8,
426 9,
427 10,
428 11,
429 12,
430 13,
431 14,
432 15,
433 16,
434 17,
435 18,
436 19,
437 20
438 ],
439 "RELATED_ION": [
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441 1,
442 2,
443 3,
444 4,
445 5,
446 6,
447 7,
448 8,
449 9,
450 10,
451 11,
452 12,
453 13,
454 14,
455 15,
456 16,
457 17,
458 18
459 ],
460 "TAG_FRAGMENT_ION": [
461 4,
462 1
463 ],
464 "PRECURSOR_ION": [
465 0
466 ]
467 },
468 "neutralLossesList": [
469 {
470 "composition": {
471 "atomChain": [
472 {
473 "atomSymbol": "H",
474 "isotope": 0,
475 "id": 0
476 },
477 {
478 "atomSymbol": "H",
479 "isotope": 0,
480 "id": 0
481 },
482 {
483 "atomSymbol": "O",
484 "isotope": 0,
485 "id": 0
486 }
487 ],
488 "mass": -1.0,
489 "id": 0
490 },
491 "name": "H2O",
492 "fixed": false,
493 "aminoAcids": [
494 "D",
495 "E",
496 "S",
497 "T"
498 ],
499 "id": 0
500 },
501 {
502 "composition": {
503 "atomChain": [
504 {
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506 "isotope": 0,
507 "id": 0
508 },
509 {
510 "atomSymbol": "H",
511 "isotope": 0,
512 "id": 0
513 },
514 {
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517 "id": 0
518 },
519 {
520 "atomSymbol": "H",
521 "isotope": 0,
522 "id": 0
523 }
524 ],
525 "mass": -1.0,
526 "id": 0
527 },
528 "name": "NH3",
529 "fixed": false,
530 "aminoAcids": [
531 "K",
532 "N",
533 "Q",
534 "R"
535 ],
536 "id": 0
537 }
538 ],
539 "neutralLossesAuto": true,
540 "reporterIons": true,
541 "relatedIons": true,
542 "fragmentIonAccuracy": 10.0,
543 "fragmentIonPpm": false,
544 "showForwardIonDeNovoTags": false,
545 "showRewindIonDeNovoTags": false,
546 "deNovoCharge": 1,
547 "tiesResolution": "mostAccurateMz",
548 "id": 0
549 },
550 "sequenceMatchingParameters": {
551 "sequenceMatchingType": "indistiguishableAminoAcids",
552 "limitX": 0.25,
553 "enzymaticTagsOnly": false,
554 "maxPtmsPerTagPeptide": 3,
555 "minAminoAcidScore": 30,
556 "minTagLength": 3,
557 "id": 0
558 },
559 "peptideVariantsParameters": {
560 "variantType": "NO_VARIANT",
561 "nVariants": 0,
562 "nAaDeletions": 0,
563 "nAaInsertions": 0,
564 "nAaSubstitutions": 0,
565 "nAaSwap": 0,
566 "aaSubstitutionMatrix": {
567 "name": "No Substitution",
568 "description": "No substitution",
569 "substitutions": {},
570 "reverseMap": {},
571 "id": 0
572 },
573 "fixedVariants": {},
574 "id": 0
575 },
576 "geneParameters": {
577 "autoUpdate": false,
578 "useGeneMapping": false,
579 "id": 0
580 },
581 "psmScoringParameters": {
582 "spectrumMatchingScores": {
583 "8": [
584 1
585 ],
586 "3": [
587 1
588 ],
589 "27": [
590 1
591 ]
592 },
593 "defaultScores": [
594 -1
595 ],
596 "minDecoysInBin": 10,
597 "id": 0
598 },
599 "peptideAssumptionFilter": {
600 "minPepLength": 8,
601 "maxPepLength": 30,
602 "maxMassDeviation": 10.0,
603 "isPpm": true,
604 "unknownModification": true,
605 "minIsotopes": 0,
606 "maxIsotopes": 1,
607 "id": 0
608 },
609 "modificationLocalizationParameters": {
610 "probabilisticScoreCalculation": true,
611 "selectedProbabilisticScore": "PhosphoRS",
612 "dScoreThreshold": 95.0,
613 "probabilisticScoreThreshold": 95.0,
614 "probabilisticScoreNeutralLosses": false,
615 "sequenceMatchingParameters": {
616 "sequenceMatchingType": "aminoAcid",
617 "limitX": 0.25,
618 "enzymaticTagsOnly": false,
619 "maxPtmsPerTagPeptide": 3,
620 "minAminoAcidScore": 30,
621 "minTagLength": 3,
622 "id": 0
623 },
624 "alignNonConfidentModifications": true,
625 "id": 0
626 },
627 "proteinInferenceParameters": {
628 "modificationRefinement": true,
629 "simplifyProteinGroups": true,
630 "simplifyGroupsEvidence": true,
631 "simplifyGroupsConfidence": true,
632 "simplifyGroupsEnzymaticity": true,
633 "simplifyGroupsVariants": true,
634 "confidenceThreshold": 0.05,
635 "id": 0
636 },
637 "idValidationParameters": {
638 "defaultProteinFDR": 1.0,
639 "defaultPeptideFDR": 1.0,
640 "defaultPsmFDR": 1.0,
641 "validationQCPreferences": {
642 "dbSize": false,
643 "firstDecoy": true,
644 "confidenceMargin": 1.0,
645 "id": 0
646 },
647 "id": 0
648 },
649 "fractionParameters": {
650 "proteinConfidenceMwPlots": 95.0,
651 "fractionMolecularWeightRanges": {},
652 "id": 0
653 },
654 "fastaParameters": {
655 "targetDecoy": true,
656 "decoyFlag": "-REVERSED",
657 "decoySuffix": true,
658 "targetDecoyFileNameTag": "_concatenated_target_decoy",
659 "id": 0
660 },
661 "id": 0
662 }