annotate test-data/05/config.yml @ 10:f522c08e900c draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"

            fastaFiles: [/tmp/tmp0wswhy4o/files/4/7/7/dataset_4770959a-66d4-405f-a5b5-48d25389063a.dat]
            parseRules:
              identifierParseRule: '^>.*\|(.*)\|.*$'
              descriptionParseRule: '^>.*\|.*\|[^ ]+ (.*) OS.*$'
            minUniquePeptides: 1
            minPepLen: 7
            maxPeptideMass: 4600
            calcPeakProperties: False
            writeMzTab: False
            ibaq: True
            ibaqLogFit: False
            separateLfq: False
            lfqStabilizeLargeRatios: True
            lfqRequireMsms: True
            advancedSiteIntensities: True
            matchBetweenRuns: True
            matchingTimeWindow: 0.7
            matchingIonMobilityWindow: 0.05
            alignmentTimeWindow: 20
            alignmentIonMobilityWindow: 1
            matchUnidentifiedFeatures: False
            includeContaminants: True
            minPeptideLengthForUnspecificSearch: 8
            maxPeptideLengthForUnspecificSearch: 25
            decoyMode: revert
            peptideFdr: 0.01
            proteinFdr: 0.01
            quantMode: 1
            restrictProteinQuantification: True
            restrictMods: [Oxidation (M),Acetyl (Protein N-term)]
            useCounterparts: True
            paramGroups:
              - files: ['BSA_min_22.mzxml']
                maxMissedCleavages: 1
                fixedModifications: [Carbamidomethyl (C)]
                variableModifications: [Oxidation (M)]
                enzymes: [Trypsin/P]
                enzymeMode: 0
                lfqMode: 1
                lfqSkipNorm: True
                lfqMinEdgesPerNode: 3
                lfqAvEdgesPerNode: 6
                lfqMinRatioCount: 2