Mercurial > repos > jjohnson > peptideshaker

comparison test-data/Identification_Parameters_default.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": "DB: dataset_118.dat.\n",
5 "defaultDescription": true,
6 "searchParameters": {
7 "precursorAccuracyType": "PPM",
8 "fragmentAccuracyType": "DA",
9 "precursorTolerance": 10.0,
10 "precursorToleranceDalton": 0.5,
11 "fragmentIonMZTolerance": 0.5,
12 "ptmSettings": {
13 "fixedModifications": [],
14 "variableModifications": [],
15 "refinementVariableModifications": [],
16 "refinementFixedModifications": [],
17 "colors": {},
18 "backUp": {}
19 },
20 "nMissedCleavages": 2,
21 "digestionPreferences": {
22 "cleavagePreference": "enzyme",
23 "enzymes": [
24 {
25 "id": 0,
26 "name": "Trypsin",
27 "aminoAcidBefore": [],
28 "aminoAcidAfter": [],
29 "restrictionBefore": [],
30 "restrictionAfter": [],
31 "aminoAcidBeforeSet": [
32 "R",
33 "K"
34 ],
35 "aminoAcidAfterSet": [],
36 "restrictionBeforeSet": [],
37 "restrictionAfterSet": [
38 "P"
39 ],
40 "isSemiSpecific": false,
41 "isWholeProtein": false,
42 "cvTerm": {
43 "ontology": "PSI-MS",
44 "accession": "MS:1001251",
45 "name": "Trypsin"
46 }
47 }
48 ],
49 "nMissedCleavages": {
50 "Trypsin": 2
51 },
52 "specificity": {
53 "Trypsin": "specific"
54 }
55 },
56 "fastaFile": {
57 "path": "./searchgui_tinydb1_concatenated_target_decoy.fasta"
58 },
59 "parametersFile": {},
60 "forwardIons": [
61 1
62 ],
63 "rewindIons": [
64 4
65 ],
66 "minChargeSearched": {
67 "sign": 1,
68 "value": 2
69 },
70 "maxChargeSearched": {
71 "sign": 1,
72 "value": 4
73 },
74 "minIsotopicCorrection": 0,
75 "maxIsotopicCorrection": 1,
76 "refMass": 2000.0,
77 "algorithmParameters": {
78 "1": {
79 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters",
80 "data": {
81 "maxEValue": 100.0,
82 "hitListLength": 10,
83 "minimalChargeForMultipleChargedFragments": {
84 "sign": 1,
85 "value": 3
86 },
87 "minPeptideLength": 8,
88 "maxPeptideLength": 30,
89 "removePrecursor": false,
90 "scalePrecursor": true,
91 "estimateCharge": true,
92 "selectedOutput": "OMX",
93 "memoryMappedSequenceLibraries": false,
94 "numberOfItotopicPeaks": 0,
95 "neutronThreshold": 1446.94,
96 "lowIntensityCutOff": 0.0,
97 "highIntensityCutOff": 0.2,
98 "intensityCutOffIncrement": 5.0E-4,
99 "singleChargeWindow": 27,
100 "doubleChargeWindow": 14,
101 "nPeaksInSingleChargeWindow": 2,
102 "nPeaksInDoubleChargeWindow": 2,
103 "maxHitsPerSpectrumPerCharge": 30,
104 "nAnnotatedMostIntensePeaks": 6,
105 "minAnnotatedPeaks": 2,
106 "minPeaks": 4,
107 "cleaveNtermMethionine": true,
108 "maxMzLadders": 128,
109 "maxFragmentCharge": 2,
110 "fractionOfPeaksForChargeEstimation": 0.95,
111 "determineChargePlusOneAlgorithmically": true,
112 "searchPositiveIons": true,
113 "minPrecPerSpectrum": 1,
114 "searchForwardFragmentFirst": false,
115 "searchRewindFragments": true,
116 "maxFragmentPerSeries": 100,
117 "useCorrelationCorrectionScore": true,
118 "consecutiveIonProbability": 0.5,
119 "iterativeSequenceEvalue": 0.0,
120 "iterativeReplaceEvalue": 0.0,
121 "iterativeSpectrumEvalue": 0.01,
122 "noProlineRuleSeries": [],
123 "ptmIndexes": {}
124 }
125 },
126 "2": {
127 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters",
128 "data": {
129 "maxEValue": 0.01,
130 "outputResults": "all",
131 "dynamicRange": 100.0,
132 "nPeaks": 50,
133 "minPrecursorMass": 500.0,
134 "minFragmentMz": 200.0,
135 "minPeaksPerSpectrum": 5,
136 "proteinQuickAcetyl": true,
137 "quickPyrolidone": true,
138 "refine": true,
139 "refineSemi": false,
140 "refinePointMutations": false,
141 "refineSpectrumSynthesis": true,
142 "refineUnanticipatedCleavages": true,
143 "refineSnaps": true,
144 "maximumExpectationValueRefinement": 0.01,
145 "potentialModificationsForFullRefinment": false,
146 "skylinePath": "",
147 "outputProteins": true,
148 "outputSequences": false,
149 "outputSpectra": true,
150 "outputHistograms": false,
151 "stpBias": false,
152 "useNoiseSuppression": false,
153 "proteinPtmComplexity": 6.0
154 }
155 },
156 "3": {
157 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters",
158 "data": {
159 "hitListLength": 10,
160 "estimateCharge": true,
161 "correctPrecursorMass": false,
162 "discardLowQualitySpectra": true,
163 "fragmentationModel": "CID_IT_TRYP",
164 "generateQuery": false
165 }
166 },
167 "4": {
168 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters",
169 "data": {
170 "maxPeptideMass": 4600.0,
171 "maxCombinations": 250,
172 "topPeaks": 8,
173 "topPeaksWindow": 100,
174 "includeWater": true,
175 "includeAmmonia": true,
176 "dependentLosses": true,
177 "fragmentAll": false,
178 "empiricalCorrection": true,
179 "higherCharge": true,
180 "fragmentationMethod": "CID",
181 "maxNumberOfModifications": 5,
182 "minPeptideLengthNoEnzyme": 8,
183 "maxPeptideLengthNoEnzyme": 25,
184 "equalIL": false,
185 "numberOfCandidates": 10,
186 "ptmIndexes": {},
187 "decoyMode": "none"
188 }
189 },
190 "5": {
191 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters",
192 "data": {
193 "generateDecoy": false,
194 "instrumentID": "b, y",
195 "maxRank": 10,
196 "monoisotopic": true,
197 "lowMemoryMode": true
198 }
199 },
200 "7": {
201 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters",
202 "data": {
203 "searchDecoyDatabase": false,
204 "instrumentID": 3,
205 "fragmentationType": 3,
206 "protocol": 0,
207 "minPeptideLength": 8,
208 "maxPeptideLength": 30,
209 "numberOfSpectrumMarches": 10,
210 "additionalOutput": false,
211 "lowerIsotopeErrorRange": -1,
212 "upperIsotopeErrorRange": 2,
213 "numberTolerableTermini": 2,
214 "numberOfPtmsPerPeptide": 2
215 }
216 },
217 "8": {
218 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters",
219 "data": {
220 "ticCutoffPercentage": 100.0,
221 "maxPeakCount": 100,
222 "numIntensityClasses": 3,
223 "adjustPrecursorMass": false,
224 "minPrecursorAdjustment": -0.5,
225 "maxPrecursorAdjustment": 1.5,
226 "precursorAdjustmentStep": 0.1,
227 "numChargeStates": 3,
228 "outputSuffix": "",
229 "useChargeStateFromMS": true,
230 "duplicateSpectra": true,
231 "deisotopingMode": 0,
232 "isotopeMzTolerance": 0.25,
233 "complementMzTolerance": 0.1,
234 "tagLength": 4,
235 "maxDynamicMods": 2,
236 "maxTagCount": 10,
237 "intensityScoreWeight": 1.0,
238 "mzFidelityScoreWeight": 1.0,
239 "complementScoreWeight": 1.0,
240 "variablePtms": []
241 }
242 },
243 "10": {
244 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters",
245 "data": {
246 "numberOfSpectrumMatches": 10,
247 "maxVariableMods": 10,
248 "requireVariableMods": false,
249 "minPeaks": 10,
250 "minPeakIntensity": 0.0,
251 "removePrecursor": 0,
252 "removePrecursorTolerance": 1.5,
253 "lowerClearMzRange": 0.0,
254 "upperClearMzRange": 0.0,
255 "enzymeType": 2,
256 "isotopeCorrection": 1,
257 "minPrecursorMass": 600.0,
258 "maxPrecursorMass": 5000.0,
259 "maxFragmentCharge": 3,
260 "removeMethionine": false,
261 "batchSize": 0,
262 "theoreticalFragmentIonsSumOnly": false,
263 "fragmentBinOffset": 0.0,
264 "useSparseMatrix": true,
265 "selectedOutputFormat": "PepXML",
266 "printExpectScore": true
267 }
268 },
269 "27": {
270 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters",
271 "data": {
272 "numberOfPeptides": 10,
273 "lowerPrecursorMass": 300,
274 "upperPrecursorMass": 5000,
275 "acticationType": "HCD"
276 }
277 },
278 "28": {
279 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters",
280 "data": {
281 "fastIndexFolderName": "fasta-index",
282 "maxVariablePtmsPerTypePerPeptide": 2,
283 "minPeptideLength": 6,
284 "maxPeptideLength": 30,
285 "minPrecursorMass": 200.0,
286 "maxPrecursorMass": 7200.0,
287 "decoyFormat": "none",
288 "keepTerminalAminoAcids": "NC",
289 "decoySeed": 1,
290 "outputFolderName": "crux-output",
291 "printPeptides": false,
292 "verbosity": 30,
293 "monoisotopicPrecursor": true,
294 "clipNtermMethionine": false,
295 "digestionType": "full-digest",
296 "computeSpScore": false,
297 "numberOfSpectrumMatches": 10,
298 "computeExactPValues": false,
299 "minSpectrumMz": 0.0,
300 "minSpectrumPeaks": 20,
301 "spectrumCharges": "all",
302 "removePrecursor": false,
303 "removePrecursorTolerance": 1.5,
304 "printProgressIndicatorSize": 1000,
305 "useFlankingPeaks": false,
306 "useNeutralLossPeaks": false,
307 "mzBinWidth": 0.02,
308 "mzBinOffset": 0.0,
309 "concatenateTargetDecoy": false,
310 "textOutput": true,
311 "sqtOutput": false,
312 "pepXmlOutput": false,
313 "mzidOutput": false,
314 "pinOutput": false,
315 "removeTempFolders": true
316 }
317 },
318 "13": {
319 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters",
320 "data": {
321 "minPeptideLength": 8,
322 "maxPeptideLength": 30,
323 "numberOfSpectrumMatches": 10,
324 "ticCutoffPercentage": 0.98,
325 "maxDynamicMods": 2,
326 "minTerminiCleavages": 2,
327 "minPrecursorMass": 600.0,
328 "maxPrecursorMass": 5000.0,
329 "useSmartPlusThreeModel": true,
330 "computeXCorr": false,
331 "numIntensityClasses": 3,
332 "classSizeMultiplier": 2,
333 "numberOfBatches": 50,
334 "lowerIsotopeCorrection": -1,
335 "upperIsotopeCorrection": 2,
336 "fragmentationRule": "CID",
337 "maxPeakCount": 300,
338 "outputFormat": "mzIdentML"
339 }
340 },
341 "29": {
342 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters",
343 "data": {
344 "fragmentationMethod": "HCD",
345 "massAnalyzer": "FT"
346 }
347 }
348 }
349 },
350 "annotationSettings": {
351 "yAxisZoomExcludesBackgroundPeaks": true,
352 "showAllPeaks": false,
353 "intensityThresholdType": "percentile",
354 "intensityLimit": 0.75,
355 "automaticAnnotation": true,
356 "selectedIonsMap": {
357 "TAG_FRAGMENT_ION": [
358 4,
359 1
360 ],
361 "REPORTER_ION": [],
362 "RELATED_ION": [
363 0,
364 1,
365 2,
366 3,
367 4,
368 5,
369 6,
370 7,
371 8,
372 9,
373 10,
374 11,
375 12,
376 13,
377 14,
378 15,
379 16,
380 17,
381 18
382 ],
383 "PEPTIDE_FRAGMENT_ION": [
384 4,
385 1
386 ],
387 "PRECURSOR_ION": [
388 0
389 ],
390 "IMMONIUM_ION": [
391 0,
392 1,
393 2,
394 3,
395 4,
396 5,
397 6,
398 7,
399 8,
400 9,
401 10,
402 11,
403 12,
404 13,
405 14,
406 15,
407 16,
408 17,
409 18,
410 19,
411 20
412 ]
413 },
414 "neutralLossesList": [
415 {
416 "composition": {
417 "atomChain": [
418 {
419 "atomSymbol": "H",
420 "isotope": 0
421 },
422 {
423 "atomSymbol": "H",
424 "isotope": 0
425 },
426 {
427 "atomSymbol": "O",
428 "isotope": 0
429 }
430 ],
431 "mass1": -1.0,
432 "stringValue1": "H(2)O"
433 },
434 "name": "H2O",
435 "fixed": false,
436 "aminoAcids": [
437 "D",
438 "E",
439 "S",
440 "T"
441 ]
442 },
443 {
444 "composition": {
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448 "isotope": 0
449 },
450 {
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452 "isotope": 0
453 },
454 {
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456 "isotope": 0
457 },
458 {
459 "atomSymbol": "H",
460 "isotope": 0
461 }
462 ],
463 "mass1": -1.0,
464 "stringValue1": "H(3)N"
465 },
466 "name": "NH3",
467 "fixed": false,
468 "aminoAcids": [
469 "K",
470 "N",
471 "Q",
472 "R"
473 ]
474 }
475 ],
476 "neutralLossesAuto": true,
477 "reporterIons": true,
478 "relatedIons": true,
479 "fragmentIonAccuracy": 0.5,
480 "fragmentIonPpm": false,
481 "showForwardIonDeNovoTags": false,
482 "showRewindIonDeNovoTags": false,
483 "deNovoCharge": 1,
484 "highResolutionAnnotation": true,
485 "tiesResolution": "mostAccurateMz"
486 },
487 "sequenceMatchingPreferences": {
488 "sequenceMatchingType": "indistiguishableAminoAcids",
489 "limitX": 0.25,
490 "peptideMapperType": "fm_index"
491 },
492 "peptideVariantsPreferences": {
493 "useSpecificCount": false,
494 "nVariants": 0,
495 "nAaDeletions": 0,
496 "nAaInsertions": 0,
497 "nAaSubstitutions": 0,
498 "nAaSwap": 0,
499 "aaSubstitutionMatrix": {
500 "name": "No Substitution",
501 "description": "No substitution",
502 "substitutions": {},
503 "reverseMap": {}
504 }
505 },
506 "genePreferences": {
507 "autoUpdate": false,
508 "useGeneMapping": false
509 },
510 "psmScoringPreferences": {
511 "spectrumMatchingScores": {
512 "8": [
513 1
514 ],
515 "3": [
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517 ],
518 "27": [
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520 ]
521 },
522 "defaultScores": [
523 -1
524 ],
525 "minDecoysInBin": 10
526 },
527 "peptideAssumptionFilter": {
528 "minPepLength": 8,
529 "maxPepLength": 30,
530 "maxMassDeviation": 10.0,
531 "isPpm": true,
532 "unknownPtm": true,
533 "minIsotopes": 0,
534 "maxIsotopes": 1
535 },
536 "ptmScoringPreferences": {
537 "flr": 1.0,
538 "probabilitsticScoreCalculation": true,
539 "selectedProbabilisticScore": "PhosphoRS",
540 "estimateFlr": false,
541 "probabilisticScoreThreshold": 95.0,
542 "probabilisticScoreNeutralLosses": false,
543 "sequenceMatchingPreferences": {
544 "sequenceMatchingType": "aminoAcid",
545 "limitX": 0.25,
546 "peptideMapperType": "fm_index"
547 },
548 "alignNonConfidentPTMs": true
549 },
550 "proteinInferencePreferences": {
551 "proteinSequenceDatabase": {
552 "path": "./searchgui_tinydb1_concatenated_target_decoy.fasta"
553 },
554 "simplifyProteinGroups": true,
555 "simplifyGroupsScore": true,
556 "simplifyGroupsEvidence": true,
557 "simplifyGroupsEnzymaticity": true,
558 "simplifyGroupsUncharacterized": true
559 },
560 "idValidationPreferences": {
561 "defaultProteinFDR": 1.0,
562 "defaultPeptideFDR": 1.0,
563 "defaultPsmFDR": 1.0,
564 "separatePeptides": true,
565 "separatePsms": true,
566 "mergeSmallSubgroups": true,
567 "validationQCPreferences": {
568 "dbSize": false,
569 "firstDecoy": true,
570 "confidenceMargin": 1.0
571 }
572 },
573 "fractionSettings": {
574 "proteinConfidenceMwPlots": 95.0,
575 "fractionMolecularWeightRanges": {}
576 }
577 }