annotate test-data/Identification_Parameters_default.par @ 61:3ec27b4cee7c draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"

{
  "marshallableParameterType": "identification_parameters",
  "version": "5.0.1",
  "name": "IdentificationParametersOutput",
  "description": "Fragment Tolerance: 0.5 Da.\n",
  "defaultDescription": true,
  "searchParameters": {
    "version": "5.0.1",
    "precursorAccuracyType": "PPM",
    "fragmentAccuracyType": "DA",
    "precursorTolerance": 10.0,
    "fragmentIonMZTolerance": 0.5,
    "modificationParameters": {
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      "variableModifications": [],
      "refinementVariableModifications": [],
      "refinementFixedModifications": [],
      "colors": {},
      "backUp": {},
      "id": 0
    },
    "digestionParameters": {
      "cleavageParameter": "enzyme",
      "enzymes": [
        {
          "name": "Trypsin",
          "aminoAcidBefore": [
            "R",
            "K"
          ],
          "aminoAcidAfter": [],
          "restrictionBefore": [],
          "restrictionAfter": [
            "P"
          ],
          "cvTerm": {
            "ontology": "PSI-MS",
            "accession": "MS:1001251",
            "name": "Trypsin",
            "id": 0
          },
          "id": 0
        }
      ],
      "nMissedCleavages": {
        "Trypsin": 2
      },
      "specificity": {
        "Trypsin": "specific"
      },
      "id": 0
    },
    "forwardIons": [
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    ],
    "rewindIons": [
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    "minChargeSearched": 2,
    "maxChargeSearched": 4,
    "minIsotopicCorrection": 0,
    "maxIsotopicCorrection": 1,
    "refMass": 2000.0,
    "algorithmParameters": {
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        "type": "com.compomics.util.parameters.identification.tool_specific.OmssaParameters",
        "data": {
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          "hitListLength": 10,
          "minimalChargeForMultipleChargedFragments": 3,
          "minPeptideLength": 8,
          "maxPeptideLength": 30,
          "removePrecursor": false,
          "scalePrecursor": true,
          "estimateCharge": true,
          "selectedOutput": "OMX",
          "memoryMappedSequenceLibraries": false,
          "neutronThreshold": 1446.94,
          "lowIntensityCutOff": 0.0,
          "highIntensityCutOff": 0.2,
          "intensityCutOffIncrement": 5.0E-4,
          "singleChargeWindow": 27,
          "doubleChargeWindow": 14,
          "nPeaksInSingleChargeWindow": 2,
          "nPeaksIndoubleChargeWindow": 2,
          "maxHitsPerSpectrumPerCharge": 30,
          "nAnnotatedMostIntensePeaks": 6,
          "minAnnotatedPeaks": 2,
          "minPeaks": 4,
          "cleaveNtermMethionine": true,
          "maxMzLadders": 128,
          "maxFragmentCharge": 2,
          "fractionOfPeaksForChargeEstimation": 0.95,
          "determineChargePlusOneAlgorithmically": true,
          "searchPositiveIons": true,
          "minPrecPerSpectrum": 1,
          "searchForwardFragmentFirst": false,
          "searchRewindFragments": true,
          "maxFragmentPerSeries": 100,
          "useCorrelationCorrectionScore": true,
          "consecutiveIonProbability": 0.5,
          "iterativeSequenceEvalue": 0.0,
          "iterativeReplaceEvalue": 0.0,
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        }
      },
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        "type": "com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters",
        "data": {
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          "searchType": "Classic",
          "totalPartitions": 1,
          "dissociationType": "HCD",
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          "initiatorMethionineBehavior": "Variable",
          "scoreCutoff": 5.0,
          "useDeltaScore": false,
          "fragmentationTerminus": "Both",
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          "massDiffAcceptorType": "OneMM",
          "writeMzId": true,
          "writePepXml": false,
          "useProvidedPrecursorInfo": true,
          "doPrecursorDeconvolution": true,
          "deconvolutionIntensityRatio": 3.0,
          "deconvolutionMassTolerance": 4.0,
          "deconvolutionMassToleranceType": "PPM",
          "trimMs1Peaks": false,
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          "minAllowedIntensityRatioToBasePeak": 0.01,
          "normalizePeaksAcrossAllWindows": false,
          "modPeptidesAreDifferent": false,
          "noOneHitWonders": false,
          "searchTarget": true,
          "decoyType": "None",
          "maxModificationIsoforms": 1024,
          "minVariantDepth": 1,
          "maxHeterozygousVariants": 4,
          "runGptm": false,
          "gPtmCategories": [
            "Common_Biological",
            "Common_Artifact",
            "Metal"
          ],
          "id": 0
        }
      },
      "2": {
        "type": "com.compomics.util.parameters.identification.tool_specific.XtandemParameters",
        "data": {
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          "outputResults": "all",
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          "minPrecursorMass": 500.0,
          "minFragmentMz": 200.0,
          "minPeaksPerSpectrum": 5,
          "proteinQuickAcetyl": true,
          "quickPyrolidone": true,
          "refine": true,
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          "refinePointMutations": false,
          "refineSpectrumSynthesis": true,
          "refineUnanticipatedCleavages": true,
          "refineSnaps": true,
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          "potentialModificationsForFullRefinment": false,
          "skylinePath": "",
          "outputProteins": true,
          "outputSequences": false,
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          "outputHistograms": false,
          "stpBias": false,
          "useNoiseSuppression": false,
          "proteinPtmComplexity": 6.0,
          "parentMonoisotopicMassIsotopeError": true,
          "id": 0
        }
      },
      "3": {
        "type": "com.compomics.util.parameters.identification.tool_specific.PepnovoParameters",
        "data": {
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          "correctPrecursorMass": false,
          "discardLowQualitySpectra": true,
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          "id": 0
        }
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      "4": {
        "type": "com.compomics.util.parameters.identification.tool_specific.AndromedaParameters",
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          "topPeaks": 8,
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          "dependentLosses": true,
          "fragmentAll": false,
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          "minPeptideLengthNoEnzyme": 8,
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          "ptmIndexes": {},
          "decoyMode": "none",
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      },
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        "type": "com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters",
        "data": {
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          "maxRank": 10,
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          "maxLoadedSpectra": 2000,
          "outputFormat": "csv",
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        }
      },
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        "type": "com.compomics.util.parameters.identification.tool_specific.MsgfParameters",
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          "protocol": 0,
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          "additionalOutput": false,
          "numberTolerableTermini": 2,
          "numberOfModificationsPerPeptide": 2,
          "id": 0
        }
      },
      "8": {
        "type": "com.compomics.util.parameters.identification.tool_specific.DirecTagParameters",
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          "numIntensityClasses": 3,
          "adjustPrecursorMass": false,
          "minPrecursorAdjustment": -0.5,
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          "numChargeStates": 3,
          "outputSuffix": "",
          "useChargeStateFromMS": true,
          "duplicateSpectra": true,
          "deisotopingMode": 0,
          "isotopeMzTolerance": 0.25,
          "complementMzTolerance": 0.1,
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          "intensityScoreWeight": 1.0,
          "mzFidelityScoreWeight": 1.0,
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          "variableModifications": [],
          "id": 0
        }
      },
      "10": {
        "type": "com.compomics.util.parameters.identification.tool_specific.CometParameters",
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          "minPeaks": 10,
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          "id": 0
        }
      },
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          "acticationType": "HCD",
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      },
      "28": {
        "type": "com.compomics.util.parameters.identification.tool_specific.TideParameters",
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          "maxVariableModificationsPerTypePerPeptide": 2,
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          "minPrecursorMass": 200.0,
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          "decoyFormat": "none",
          "keepTerminalAminoAcids": "NC",
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          "computeExactPValues": false,
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          "mzBinWidth": 0.02,
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          "concatenateTargetDecoy": false,
          "textOutput": true,
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          "pepXmlOutput": false,
          "mzidOutput": false,
          "pinOutput": false,
          "removeTempFolders": true,
          "id": 0
        }
      },
      "29": {
        "type": "com.compomics.util.parameters.identification.tool_specific.NovorParameters",
        "data": {
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          "massAnalyzer": "FT",
          "id": 0
        }
      }
    },
    "flanking": false,
    "id": 0
  },
  "annotationParameters": {
    "yAxisZoomExcludesBackgroundPeaks": true,
    "showAllPeaks": false,
    "intensityThresholdType": "percentile",
    "intensityLimit": 0.75,
    "automaticAnnotation": true,
    "selectedIonsMap": {
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      ],
      "REPORTER_ION": [],
      "IMMONIUM_ION": [
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      "RELATED_ION": [
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      ],
      "TAG_FRAGMENT_ION": [
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      ],
      "PRECURSOR_ION": [
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    },
    "neutralLossesList": [
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            },
            {
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            },
            {
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      {
        "composition": {
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    ],
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    "fragmentIonAccuracy": 10.0,
    "fragmentIonPpm": false,
    "showForwardIonDeNovoTags": false,
    "showRewindIonDeNovoTags": false,
    "deNovoCharge": 1,
    "tiesResolution": "mostAccurateMz",
    "id": 0
  },
  "sequenceMatchingParameters": {
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    "limitX": 0.25,
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    "maxPtmsPerTagPeptide": 3,
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    "minTagLength": 3,
    "id": 0
  },
  "peptideVariantsParameters": {
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    "nAaDeletions": 0,
    "nAaInsertions": 0,
    "nAaSubstitutions": 0,
    "nAaSwap": 0,
    "aaSubstitutionMatrix": {
      "name": "No Substitution",
      "description": "No substitution",
      "substitutions": {},
      "reverseMap": {},
      "id": 0
    },
    "fixedVariants": {},
    "id": 0
  },
  "geneParameters": {
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    "useGeneMapping": false,
    "id": 0
  },
  "psmScoringParameters": {
    "spectrumMatchingScores": {
      "8": [
        1
      ],
      "3": [
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      ],
      "27": [
        1
      ]
    },
    "defaultScores": [
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    ],
    "minDecoysInBin": 10,
    "id": 0
  },
  "peptideAssumptionFilter": {
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    "maxPepLength": 30,
    "maxMassDeviation": 10.0,
    "isPpm": true,
    "unknownModification": true,
    "minIsotopes": 0,
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  "modificationLocalizationParameters": {
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    "selectedProbabilisticScore": "PhosphoRS",
    "dScoreThreshold": 95.0,
    "probabilisticScoreThreshold": 95.0,
    "probabilisticScoreNeutralLosses": false,
    "sequenceMatchingParameters": {
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      "limitX": 0.25,
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    },
    "alignNonConfidentModifications": true,
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  },
  "proteinInferenceParameters": {
    "modificationRefinement": true,
    "simplifyProteinGroups": true,
    "simplifyGroupsEvidence": true,
    "simplifyGroupsConfidence": true,
    "simplifyGroupsEnzymaticity": true,
    "simplifyGroupsVariants": true,
    "confidenceThreshold": 0.05,
    "id": 0
  },
  "idValidationParameters": {
    "defaultProteinFDR": 1.0,
    "defaultPeptideFDR": 1.0,
    "defaultPsmFDR": 1.0,
    "validationQCPreferences": {
      "dbSize": false,
      "firstDecoy": true,
      "confidenceMargin": 1.0,
      "id": 0
    },
    "id": 0
  },
  "fractionParameters": {
    "proteinConfidenceMwPlots": 95.0,
    "fractionMolecularWeightRanges": {},
    "id": 0
  },
  "fastaParameters": {
    "targetDecoy": true,
    "decoyFlag": "-REVERSED",
    "decoySuffix": true,
    "targetDecoyFileNameTag": "_concatenated_target_decoy",
    "id": 0
  },
  "id": 0
}