annotate test-data/Identification_Parameters_default_modifications.par @ 55:bb0130ff73ce draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"

{
  "marshallableParameterType": "identification_parameters",
  "version": "5.0.1",
  "name": "IdentificationParametersOutput",
  "description": "Fixed: Carbamidomethylation of C.\nVariable: Oxidation of M.\nFragment Tolerance: 0.5 Da.\n",
  "defaultDescription": true,
  "searchParameters": {
    "version": "5.0.1",
    "precursorAccuracyType": "PPM",
    "fragmentAccuracyType": "DA",
    "precursorTolerance": 10.0,
    "fragmentIonMZTolerance": 0.5,
    "modificationParameters": {
      "fixedModifications": [
        "Carbamidomethylation of C"
      ],
      "variableModifications": [
        "Oxidation of M"
      ],
      "refinementVariableModifications": [],
      "refinementFixedModifications": [],
      "colors": {},
      "backUp": {
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          "modificationType": "modaa",
          "name": "Carbamidomethylation of C",
          "shortName": "cmm",
          "neutralLosses": [],
          "reporterIons": [],
          "pattern": {
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            "residueTargeted": {
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                "C"
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            },
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          },
          "atomChainAdded": {
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              },
              {
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                "id": 0
              },
              {
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              },
              {
                "atomSymbol": "H",
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                "id": 0
              },
              {
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                "id": 0
              },
              {
                "atomSymbol": "N",
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                "id": 0
              },
              {
                "atomSymbol": "O",
                "isotope": 0,
                "id": 0
              }
            ],
            "mass": -1.0,
            "id": 0
          },
          "atomChainRemoved": {
            "atomChain": [],
            "mass": -1.0,
            "id": 0
          },
          "unimodCvTerm": {
            "ontology": "UNIMOD",
            "accession": "UNIMOD:4",
            "name": "Carbamidomethyl",
            "id": 0
          },
          "psiModCvTerm": {
            "ontology": "MOD",
            "accession": "MOD:01060",
            "name": "S-carboxamidomethyl-L-cysteine",
            "id": 0
          },
          "category": "Common",
          "id": 0
        },
        "Oxidation of M": {
          "modificationType": "modaa",
          "name": "Oxidation of M",
          "shortName": "ox",
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            {
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                  {
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                    "id": 0
                  },
                  {
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                    "id": 0
                  },
                  {
                    "atomSymbol": "H",
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                    "id": 0
                  },
                  {
                    "atomSymbol": "H",
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                  },
                  {
                    "atomSymbol": "H",
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                  },
                  {
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                    "id": 0
                  },
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                    "atomSymbol": "S",
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                    "id": 0
                  }
                ],
                "mass": -1.0,
                "id": 0
              },
              "name": "CH4OS",
              "fixed": false,
              "id": 0
            }
          ],
          "reporterIons": [],
          "pattern": {
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            "residueTargeted": {
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              ]
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          },
          "atomChainAdded": {
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          },
          "unimodCvTerm": {
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            "accession": "UNIMOD:35",
            "name": "Oxidation",
            "id": 0
          },
          "psiModCvTerm": {
            "ontology": "MOD",
            "accession": "MOD:00719",
            "name": "L-methionine sulfoxide",
            "id": 0
          },
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          "id": 0
        }
      },
      "id": 0
    },
    "digestionParameters": {
      "cleavageParameter": "enzyme",
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          "name": "Trypsin",
          "aminoAcidBefore": [
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            "K"
          ],
          "aminoAcidAfter": [],
          "restrictionBefore": [],
          "restrictionAfter": [
            "P"
          ],
          "cvTerm": {
            "ontology": "PSI-MS",
            "accession": "MS:1001251",
            "name": "Trypsin",
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          },
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        }
      ],
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      },
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        "Trypsin": "specific"
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      "id": 0
    },
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    "rewindIons": [
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    ],
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    "maxChargeSearched": 4,
    "minIsotopicCorrection": 0,
    "maxIsotopicCorrection": 1,
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    "algorithmParameters": {
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        "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,
          "iterativeSpectrumEvalue": 0.01,
          "noProlineRuleSeries": [],
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          "id": 0
        }
      },
      "33": {
        "type": "com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters",
        "data": {
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          "maxPeptideLength": 30,
          "searchType": "Classic",
          "totalPartitions": 1,
          "dissociationType": "HCD",
          "maxModsForPeptide": 2,
          "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,
          "trimMsMsPeaks": true,
          "numberOfPeaksToKeepPerWindow": 200,
          "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": {
          "maxEValue": 0.01,
          "outputResults": "all",
          "dynamicRange": 100.0,
          "nPeaks": 50,
          "minPrecursorMass": 500.0,
          "minFragmentMz": 200.0,
          "minPeaksPerSpectrum": 5,
          "proteinQuickAcetyl": true,
          "quickPyrolidone": true,
          "refine": true,
          "refineSemi": false,
          "refinePointMutations": false,
          "refineSpectrumSynthesis": true,
          "refineUnanticipatedCleavages": true,
          "refineSnaps": true,
          "maximumExpectationValueRefinement": 0.01,
          "potentialModificationsForFullRefinment": false,
          "skylinePath": "",
          "outputProteins": true,
          "outputSequences": false,
          "outputSpectra": true,
          "outputHistograms": false,
          "stpBias": false,
          "useNoiseSuppression": false,
          "proteinPtmComplexity": 6.0,
          "parentMonoisotopicMassIsotopeError": true,
          "id": 0
        }
      },
      "3": {
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          "discardLowQualitySpectra": true,
          "fragmentationModel": "CID_IT_TRYP",
          "generateQuery": false,
          "id": 0
        }
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          "maxCombinations": 250,
          "topPeaks": 8,
          "topPeaksWindow": 100,
          "includeWater": true,
          "includeAmmonia": true,
          "dependentLosses": true,
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          "empiricalCorrection": true,
          "higherCharge": true,
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          "minPeptideLengthNoEnzyme": 8,
          "maxPeptideLengthNoEnzyme": 30,
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          "reportBothBestHitsForTD": true,
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          "maxRank": 10,
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          "performDeisotoping": true,
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          "maxVariableModifications": 4,
          "maxModificationSites": 6,
          "maxNeutralLosses": 1,
          "maxNeutralLossesPerModification": 2,
          "minPeptideLength": 8,
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          "maxLoadedProteins": 100000,
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          "outputFormat": "csv",
          "id": 0
        }
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          "id": 0
        }
      },
      "8": {
        "type": "com.compomics.util.parameters.identification.tool_specific.DirecTagParameters",
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          "adjustPrecursorMass": false,
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          "numChargeStates": 3,
          "outputSuffix": "",
          "useChargeStateFromMS": true,
          "duplicateSpectra": true,
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      },
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          "acticationType": "HCD",
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        }
      },
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          "maxVariableModificationsPerTypePerPeptide": 2,
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          "minPrecursorMass": 200.0,
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          "decoyFormat": "none",
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          "monoisotopicPrecursor": true,
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          "spectrumCharges": "all",
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          "useFlankingPeaks": false,
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          "mzBinWidth": 0.02,
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          "concatenateTargetDecoy": false,
          "textOutput": true,
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          "removeTempFolders": true,
          "id": 0
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      },
      "29": {
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        "data": {
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        }
      }
    },
    "flanking": false,
    "id": 0
  },
  "annotationParameters": {
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    "showAllPeaks": false,
    "intensityThresholdType": "percentile",
    "intensityLimit": 0.75,
    "automaticAnnotation": true,
    "selectedIonsMap": {
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        1,
        2,
        3,
        4,
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      "PEPTIDE_FRAGMENT_ION": [
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      "PRECURSOR_ION": [
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      "TAG_FRAGMENT_ION": [
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      "REPORTER_ION": [],
      "RELATED_ION": [
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    "neutralLossesList": [
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    ],
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  },
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    "useGeneMapping": false,
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    "isPpm": true,
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  "modificationLocalizationParameters": {
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    },
    "alignNonConfidentModifications": true,
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  "proteinInferenceParameters": {
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    "simplifyProteinGroups": true,
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    "confidenceThreshold": 0.05,
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  },
  "idValidationParameters": {
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    "defaultPeptideFDR": 1.0,
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    "validationQCPreferences": {
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  "fractionParameters": {
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    "fractionMolecularWeightRanges": {},
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    "targetDecoyFileNameTag": "_concatenated_target_decoy",
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}