metamorpheus: macros.xml annotate

annotate macros.xml @ 0:e8d7b7dc55fc draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"

author	galaxyp
date	Wed, 26 May 2021 15:42:20 +0000
parents
children	975f857ad9b8

rev	line source
0 e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	1 <macros>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	2 <token name="@PROFILE@">21.01</token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	3 <token name="@TOOL_VERSION@">0.0.316</token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	4 <token name="@VERSION_SUFFIX@">0</token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	5 <xml name="requirements">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	6 <requirements>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	7 <requirement type="package" version="@TOOL_VERSION@">metamorpheus</requirement>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	8 <yield/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	9 </requirements>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	10 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	11
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	12 <token name="@DEFAULT_COMMON_TOML@">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	13 [CommonParameters]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	14 # MaxThreadsToUsePerFile = 11
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	15 ListOfModsFixed = "Common Fixed\tCarbamidomethyl on C\t\tCommon Fixed\tCarbamidomethyl on U"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	16 ListOfModsVariable = "Common Variable\tOxidation on M"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	17 DoPrecursorDeconvolution = true # Calibration false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	18 UseProvidedPrecursorInfo = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	19 DeconvolutionIntensityRatio = 3.0
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	20 DeconvolutionMaxAssumedChargeState = 12
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	21 DeconvolutionMassTolerance = "±4.0000 PPM"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	22 TotalPartitions = 1
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	23 ProductMassTolerance = "±20.0000 PPM" # Calibration 25.0000
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	24 PrecursorMassTolerance = "±5.0000 PPM" # Calibration 15.0000
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	25 AddCompIons = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	26 ScoreCutoff = 5.0
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	27 ReportAllAmbiguity = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	28 NumberOfPeaksToKeepPerWindow = 200
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	29 MinimumAllowedIntensityRatioToBasePeak = 0.01
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	30 NormalizePeaksAccrossAllWindows = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	31 TrimMs1Peaks = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	32 TrimMsMsPeaks = true # Calibration false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	33 UseDeltaScore = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	34 QValueOutputFilter = 1.0
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	35 CustomIons = []
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	36 AssumeOrphanPeaksAreZ1Fragments = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	37 MaxHeterozygousVariants = 4
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	38 MinVariantDepth = 1
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	39 DissociationType = "HCD"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	40 SeparationType = "HPLC"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	41 MS2ChildScanDissociationType = "Unknown"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	42 MS3ChildScanDissociationType = "Unknown"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	43 </token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	44
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	45 <token name="@DEFAULT_DIGESTION_TOML@">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	46 [CommonParameters.DigestionParams]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	47 MaxMissedCleavages = 2
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	48 InitiatorMethionineBehavior = "Variable"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	49 MinPeptideLength = 7
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	50 MaxPeptideLength = 2147483647
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	51 MaxModificationIsoforms = 1024
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	52 MaxModsForPeptide = 2
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	53 Protease = "trypsin"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	54 SearchModeType = "Full"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	55 FragmentationTerminus = "Both"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	56 SpecificProtease = "trypsin"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	57 GeneratehUnlabeledProteinsForSilac = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	58 </token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	59
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	60 <token name="@DEFAULT_CALIBRATION_TOML@"><![CDATA[
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	61 TaskType = "Calibrate"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	62
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	63 [CalibrationParameters]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	64 WriteIntermediateFiles = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	65 WriteIndexedMzml = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	66 MinMS1IsotopicPeaksNeededForConfirmedIdentification = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	67 MinMS2IsotopicPeaksNeededForConfirmedIdentification = 2
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	68 NumFragmentsNeededForEveryIdentification = 10
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	69
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	70 [CommonParameters]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	71 MaxThreadsToUsePerFile = 11
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	72 ListOfModsFixed = "Common Fixed\tCarbamidomethyl on C\t\tCommon Fixed\tCarbamidomethyl on U"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	73 ListOfModsVariable = "Common Variable\tOxidation on M"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	74 DoPrecursorDeconvolution = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	75 UseProvidedPrecursorInfo = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	76 DeconvolutionIntensityRatio = 3.0
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	77 DeconvolutionMaxAssumedChargeState = 12
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	78 DeconvolutionMassTolerance = "±4.0000 PPM"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	79 TotalPartitions = 1
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	80 ProductMassTolerance = "±25.0000 PPM"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	81 PrecursorMassTolerance = "±15.0000 PPM"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	82 AddCompIons = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	83 ScoreCutoff = 5.0
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	84 ReportAllAmbiguity = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	85 NumberOfPeaksToKeepPerWindow = 200
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	86 MinimumAllowedIntensityRatioToBasePeak = 0.01
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	87 NormalizePeaksAccrossAllWindows = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	88 TrimMs1Peaks = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	89 TrimMsMsPeaks = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	90 UseDeltaScore = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	91 QValueOutputFilter = 1.0
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	92 CustomIons = []
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	93 AssumeOrphanPeaksAreZ1Fragments = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	94 MaxHeterozygousVariants = 4
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	95 MinVariantDepth = 1
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	96 DissociationType = "HCD"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	97 SeparationType = "HPLC"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	98 MS2ChildScanDissociationType = "Unknown"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	99 MS3ChildScanDissociationType = "Unknown"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	100
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	101 @DEFAULT_DIGESTION_TOML@
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	102 ]]></token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	103
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	104 <token name="@DEFAULT_GPTMD_TOML@"><![CDATA[
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	105 TaskType = "Gptmd"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	106
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	107 [GptmdParameters]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	108 ListOfModsGptmd = "Common Biological\tAcetylation on K\t\tCommon Biological\tAcetylation on X\t\tCommon Biological\tADP-ribosylation on S\t\tCommon Artifact\tAmmonia loss on C\t\tCommon Artifact\tAmmonia loss on N\t\tCommon Biological\tButyrylation on K\t\tMetal\tCalcium on D\t\tMetal\tCalcium on E\t\tCommon Artifact\tCarbamyl on C\t\tCommon Artifact\tCarbamyl on K\t\tCommon Artifact\tCarbamyl on M\t\tCommon Artifact\tCarbamyl on R\t\tCommon Artifact\tCarbamyl on X\t\tCommon Biological\tCarboxylation on D\t\tCommon Biological\tCarboxylation on E\t\tCommon Biological\tCarboxylation on K\t\tCommon Biological\tCitrullination on R\t\tCommon Biological\tCrotonylation on K\t\tMetal\tCu[I] on D\t\tMetal\tCu[I] on E\t\tCommon Artifact\tDeamidation on N\t\tCommon Artifact\tDeamidation on Q\t\tCommon Biological\tDimethylation on K\t\tCommon Biological\tDimethylation on R\t\tMetal\tFe[II] on D\t\tMetal\tFe[II] on E\t\tMetal\tFe[III] on D\t\tMetal\tFe[III] on E\t\tCommon Biological\tFormylation on K\t\tCommon Biological\tGlu to PyroGlu on Q\t\tCommon Biological\tGlutarylation on K\t\tCommon Biological\tHexNAc on Nxs\t\tCommon Biological\tHexNAc on Nxt\t\tCommon Biological\tHexNAc on S\t\tCommon Biological\tHexNAc on T\t\tCommon Biological\tHydroxybutyrylation on K\t\tCommon Biological\tHydroxylation on K\t\tCommon Biological\tHydroxylation on N\t\tCommon Biological\tHydroxylation on P\t\tMetal\tMagnesium on D\t\tMetal\tMagnesium on E\t\tCommon Biological\tMalonylation on K\t\tCommon Biological\tMethylation on K\t\tCommon Biological\tMethylation on R\t\tCommon Biological\tNitrosylation on C\t\tCommon Biological\tNitrosylation on Y\t\tCommon Biological\tPhosphorylation on S\t\tCommon Biological\tPhosphorylation on T\t\tCommon Biological\tPhosphorylation on Y\t\tMetal\tPotassium on D\t\tMetal\tPotassium on E\t\tCommon Biological\tPyridoxal phosphate on K\t\tMetal\tSodium on D\t\tMetal\tSodium on E\t\tCommon Biological\tSuccinylation on K\t\tCommon Biological\tSulfonation on Y\t\tCommon Biological\tTrimethylation on K\t\tCommon Artifact\tWater Loss on E\t\tMetal\tZinc on D\t\tMetal\tZinc on E"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	109
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	110 @DEFAULT_COMMON_TOML@
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	111
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	112 @DEFAULT_DIGESTION_TOML@
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	113 ]]></token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	114
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	115 <token name="@DEFAULT_SEARCH_TOML@"><![CDATA[
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	116 TaskType = "Search"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	117
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	118 [SearchParameters]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	119 DisposeOfFileWhenDone = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	120 DoParsimony = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	121 ModPeptidesAreDifferent = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	122 NoOneHitWonders = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	123 MatchBetweenRuns = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	124 Normalize = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	125 QuantifyPpmTol = 5.0
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	126 DoHistogramAnalysis = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	127 SearchTarget = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	128 DecoyType = "Reverse"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	129 MassDiffAcceptorType = "OneMM"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	130 WritePrunedDatabase = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	131 KeepAllUniprotMods = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	132 DoLocalizationAnalysis = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	133 DoQuantification = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	134 SearchType = "Classic"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	135 LocalFdrCategories = ["FullySpecific"]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	136 MaxFragmentSize = 30000.0
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	137 HistogramBinTolInDaltons = 0.003
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	138 MaximumMassThatFragmentIonScoreIsDoubled = 0.0
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	139 WriteMzId = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	140 WritePepXml = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	141 WriteDecoys = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	142 WriteContaminants = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	143 WriteIndividualFiles = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	144 CompressIndividualFiles = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	145 TCAmbiguity = "RemoveContaminant"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	146
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	147 [SearchParameters.ModsToWriteSelection]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	148 'N-linked glycosylation' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	149 'O-linked glycosylation' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	150 'Other glycosylation' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	151 'Common Biological' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	152 'Less Common' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	153 Metal = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	154 '2+ nucleotide substitution' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	155 '1 nucleotide substitution' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	156 UniProt = 2
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	157
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	158 @DEFAULT_COMMON_TOML@
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	159
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	160 @DEFAULT_DIGESTION_TOML@
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	161 ]]></token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	162
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	163 <xml name="input_spectrums" token_multiple="false" token_filetype="Spectrum">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	164 <param name="spectrums" type="data" format="mzml" multiple="@MULTIPLE@" label="MS/MS @FILETYPE@ files"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	165 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	166 <xml name="calib_toml">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	167 <param name="calib_tomls" type="data" format="toml" multiple="true" optional="true" label="Calibrated Spectrum TOML files"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	168 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	169 <xml name="input_databases">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	170 <param name="databases" type="data" format="uniprotxml,fasta" multiple="true" label="Reference Protein Databases"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	171 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	172 <xml name="input_toml">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	173 <param name="input_toml" type="data" format="toml" optional="true" label="Optional Config toml from history"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	174 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	175 <token name="@CMD_IMPORTS@">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	176 #import re
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	177 #def identifier_or_name($input1)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	178 #if hasattr($input1, 'element_identifier')
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	179 #return $input1.element_identifier
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	180 #else
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	181 #return $input1.name
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	182 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	183 #end def
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	184 #def clean($name1)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	185 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa\|fasta\|xml\|imzml\|mzml\|raw\|mgf)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	186 #return $name_clean
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	187 #end def
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	188 #def ln_name($ds)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	189 #set $ext = ''
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	190 #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	191 #set $ext = ".mzML"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	192 #else if $ds.is_of_type('thermo.raw')
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	193 #set $ext = ".raw"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	194 #else if $ds.is_of_type('toml')
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	195 #set $ext = ".toml"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	196 #else if $ds.is_of_type('uniprotxml')
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	197 #set $ext = ".xml"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	198 #else if $ds.is_of_type('fasta')
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	199 #set $ext = ".fasta"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	200 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	201 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	202 #return $name
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	203 #end def
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	204 </token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	205
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	206 <token name="@PREPARE_INPUTS@"><![CDATA[
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	207 @CMD_IMPORTS@
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	208 #set $spectrum_names = []
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	209 #set $database_names = []
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	210 #set $inputs_dir = 'inputs'
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	211 mkdir -p $inputs_dir &&
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	212 #for $sf in $spectrums
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	213 #set $i_name = $ln_name($sf)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	214 $spectrum_names.append($i_name)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	215 ln -s '${sf}' '${inputs_dir}/${i_name}' &&
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	216 #end for
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	217 #for $db in $databases
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	218 #set $d_name = $ln_name($db)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	219 $database_names.append($d_name)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	220 ln -s '${db}' '${d_name}' &&
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	221 #end for
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	222 ]]></token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	223 <token name="@LN_CALIB_TOML@"><![CDATA[
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	224 #for $tf in $calib_tomls
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	225 #set $t_name = $ln_name($tf)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	226 ln -s '${tf}' '${inputs_dir}/${t_name}' &&
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	227 #end for
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	228 ]]></token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	229
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	230 <token name="@MERGE_TOMLS@"><![CDATA[
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	231 #def merge_tomls($tomls, $merged):
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	232 #import re
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	233 #set $config = dict()
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	234 #set $config['categories'] = []
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	235 #set $category = ' '
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	236 #for $toml in $tomls
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	237 #set $fh = open(toml,'r')
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	238 #for $line in $fh:
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	239 #set $entry = $line.rstrip()
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	240 #if $entry.strip() == '':
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	241 #continue
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	242 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	243 #set $m = $re.match('^((TaskType)\s=\s(.*))$', $entry)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	244 #if $m:
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	245 #if $m.groups()[0] not in $config:
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	246 #set $config['TaskType'] = $entry
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	247 #continue
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	248 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	249 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	250 #set $m = $re.match('^(\[.+\])$', $entry)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	251 #if $m:
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	252 #set $category = $m.groups()[0]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	253 #if $category not in $config['categories']:
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	254 $config['categories'].append($category)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	255 #set $config[$category] = []
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	256 #continue
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	257 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	258 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	259 #set $m = $re.match('^(\S+)\s=\s(.*)$',$entry)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	260 #if $m:
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	261 #set $pname = $m.groups()[0]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	262 #set $pval = $m.groups()[1]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	263 #if $pname not in $config[$category]:
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	264 $config[$category].append($pname)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	265 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	266 #set $config[$pname] = $pval
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	267 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	268 #*
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	269 *#
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	270 #end for
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	271 $fh.close()
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	272 #end for
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	273 #set $wfh = open($merged,'w')
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	274 #if 'TaskType' in $config:
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	275 #silent $wfh.write('%s\n' % $config['TaskType'])
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	276 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	277 #for $category in $config['categories']:
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	278 #silent $wfh.write('\n')
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	279 #silent $wfh.write('%s\n' % $category)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	280 #for $pname in $config[$category]:
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	281 #set $pval = $config[$pname]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	282 #silent $wfh.write('%s = %s\n' % ($pname, $pval))
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	283 #end for
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	284 #end for
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	285 $wfh.close()
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	286 #*
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	287 *#
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	288 #*
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	289 #echo $config
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	290 *#
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	291 #end def
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	292 #if $input_toml
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	293 $merge_tomls([$default_toml,str($input_toml),$user_toml], $task_settings_toml)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	294 #else
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	295 $merge_tomls([$default_toml,$user_toml], $task_settings_toml)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	296 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	297 ln -s '$task_settings_toml' tasksettings.toml &&
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	298
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	299 ]]></token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	300
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	301 <xml name="calibrate_params">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	302 <conditional name="calibration">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	303 <param name="set_calibration" type="select" label="Set Calibration Parameters">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	304 <option value="no">no</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	305 <option value="yes">yes</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	306 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	307 <when value="no"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	308 <when value="yes">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	309 <param argument="MinMS1IsotopicPeaksNeededForConfirmedIdentification" type="integer" value="3" label="MinMS1IsotopicPeaksNeededForConfirmedIdentification"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	310 <param argument="MinMS2IsotopicPeaksNeededForConfirmedIdentification" type="integer" value="2" label="MinMS2IsotopicPeaksNeededForConfirmedIdentification"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	311 <param argument="NumFragmentsNeededForEveryIdentification" type="integer" value="10" label="NumFragmentsNeededForEveryIdentification"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	312 </when>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	313 </conditional>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	314 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	315 <token name="@CALIBRATE_CONFIG@"><![CDATA[
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	316 #if $calibration.set_calibration == 'yes'
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	317 [CalibrationParameters]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	318 WriteIntermediateFiles = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	319 MinMS1IsotopicPeaksNeededForConfirmedIdentification = $calibration.MinMS1IsotopicPeaksNeededForConfirmedIdentification
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	320 MinMS2IsotopicPeaksNeededForConfirmedIdentification = $calibration.MinMS2IsotopicPeaksNeededForConfirmedIdentification
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	321 NumFragmentsNeededForEveryIdentification = $calibration.NumFragmentsNeededForEveryIdentification
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	322 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	323 ]]></token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	324 <xml name="gptmd_params">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	325
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	326 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	327 <token name="@GPTMD_CONFIG@">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	328 TaskType = "Gptmd"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	329
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	330 [GptmdParameters]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	331 ListOfModsGptmd = "Common Biological\tAcetylation on K\t\tCommon Biological\tAcetylation on X\t\tCommon Biological\tADP-ribosylation on S\t\tCommon Biological\tButyrylation on K\t\tCommon Biological\tCarboxylation on D\t\tCommon Biological\tCarboxylation on E\t\tCommon Biological\tCarboxylation on K\t\tCommon Biological\tCitrullination on R\t\tCommon Biological\tCrotonylation on K\t\tCommon Biological\tDimethylation on K\t\tCommon Biological\tDimethylation on R\t\tCommon Biological\tFormylation on K\t\tCommon Biological\tGlu to PyroGlu on Q\t\tCommon Biological\tGlutarylation on K\t\tCommon Biological\tHexNAc on Nxs\t\tCommon Biological\tHexNAc on Nxt\t\tCommon Biological\tHexNAc on S\t\tCommon Biological\tHexNAc on T\t\tCommon Biological\tHydroxybutyrylation on K\t\tCommon Biological\tHydroxylation on K\t\tCommon Biological\tHydroxylation on N\t\tCommon Biological\tHydroxylation on P\t\tCommon Biological\tMalonylation on K\t\tCommon Biological\tMethylation on K\t\tCommon Biological\tMethylation on R\t\tCommon Biological\tNitrosylation on C\t\tCommon Biological\tNitrosylation on Y\t\tCommon Biological\tPhosphorylation on S\t\tCommon Biological\tPhosphorylation on T\t\tCommon Biological\tPhosphorylation on Y\t\tCommon Biological\tPyridoxal phosphate on K\t\tCommon Biological\tSuccinylation on K\t\tCommon Biological\tSulfonation on Y\t\tCommon Biological\tTrimethylation on K\t\tCommon Artifact\tAmmonia loss on C\t\tCommon Artifact\tAmmonia loss on N\t\tCommon Artifact\tCarbamyl on C\t\tCommon Artifact\tCarbamyl on K\t\tCommon Artifact\tCarbamyl on M\t\tCommon Artifact\tCarbamyl on R\t\tCommon Artifact\tCarbamyl on X\t\tCommon Artifact\tDeamidation on N\t\tCommon Artifact\tDeamidation on Q\t\tCommon Artifact\tWater Loss on E\t\tMetal\tCalcium on D\t\tMetal\tCalcium on E\t\tMetal\tCu[I] on D\t\tMetal\tCu[I] on E\t\tMetal\tFe[II] on D\t\tMetal\tFe[II] on E\t\tMetal\tFe[III] on D\t\tMetal\tFe[III] on E\t\tMetal\tMagnesium on D\t\tMetal\tMagnesium on E\t\tMetal\tPotassium on D\t\tMetal\tPotassium on E\t\tMetal\tSodium on D\t\tMetal\tSodium on E\t\tMetal\tZinc on D\t\tMetal\tZinc on E"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	332 </token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	333
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	334 <xml name="search_params">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	335 <conditional name="search_params">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	336 <param name="set_search_params" type="select" label="Set Search Parameters">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	337 <option value="no">no</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	338 <option value="yes">yes</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	339 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	340 <when value="no"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	341 <when value="yes">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	342 <param argument="DoParsimony" type="boolean" truevalue="true" falsevalue="false" checked="true" label="DoParsimony"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	343 <param argument="ModPeptidesAreDifferent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="ModPeptidesAreDifferent"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	344 <param argument="NoOneHitWonders" type="boolean" truevalue="true" falsevalue="false" checked="false" label="NoOneHitWonders"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	345 <param argument="MatchBetweenRuns" type="boolean" truevalue="true" falsevalue="false" checked="false" label="MatchBetweenRuns"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	346 <param argument="Normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Normalize"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	347 <param argument="QuantifyPpmTol" type="float" value="5.0" label="QuantifyPpmTol"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	348 <param argument="DoHistogramAnalysis" type="boolean" truevalue="true" falsevalue="false" checked="false" label="DoHistogramAnalysis"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	349 <param argument="SearchTarget" type="boolean" truevalue="true" falsevalue="false" checked="true" label="SearchTarget"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	350 <param argument="DecoyType" type="select" label="DecoyType">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	351 <option value="Reverse" selected="true">Reverse</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	352 <option value="Slide">Slide</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	353 <option value="None">None</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	354 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	355 <param argument="MassDiffAcceptorType" type="select" label="MassDiffAcceptorType">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	356 <option value="Exact">Exact</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	357 <option value="OneMM" selected="true">OneMM</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	358 <option value="TwoMM">TwoMM</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	359 <option value="ThreeMM">ThreeMM</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	360 <option value="PlusOrMinusThreeMM">PlusOrMinusThreeMM</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	361 <option value="ModOpen">ModOpen</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	362 <option value="Open">Open</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	363 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	364 <param argument="KeepAllUniprotMods" type="boolean" truevalue="true" falsevalue="false" checked="true" label="KeepAllUniprotMods"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	365 <param argument="DoLocalizationAnalysis" type="boolean" truevalue="true" falsevalue="false" checked="true" label="DoLocalizationAnalysis"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	366 <param argument="DoQuantification" type="boolean" truevalue="true" falsevalue="false" checked="true" label="DoQuantification"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	367 <param argument="SearchType" type="select" label="SearchType">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	368 <option value="Classic" selected="true">Classic</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	369 <option value="Modern">Modern</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	370 <option value="NonSpecific">NonSpecific</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	371 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	372 <param argument="LocalFdrCategories" type="select" label="LocalFdrCategories">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	373 <option value="FullySpecific" selected="true">FullySpecific</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	374 <option value="SemiSpecific">SemiSpecific</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	375 <option value="NonSpecific">NonSpecific</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	376 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	377 <param argument="MaxFragmentSize" type="float" value="30000.0" label="MaxFragmentSize"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	378 <param argument="HistogramBinTolInDaltons" type="float" value="0.003" label="HistogramBinTolInDaltons"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	379 <param argument="MaximumMassThatFragmentIonScoreIsDoubled" type="float" value="0.0" label="MaximumMassThatFragmentIonScoreIsDoubled"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	380 </when>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	381 </conditional>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	382 <param name="search_outputs" type="select" multiple="true" label="Select Optional Search Outputs">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	383 <option value="WriteMzId" selected="true">WriteMzId</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	384 <option value="WritePepXml" selected="false">WritePepXml</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	385 <option value="WritePrunedDatabase" selected="true">WritePrunedDatabase</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	386 <option value="WriteDecoys" selected="false">WriteDecoys</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	387 <option value="WriteContaminants" selected="false">WriteContaminants</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	388 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	389 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	390 <token name="@SEARCH_CONFIG@"><![CDATA[
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	391 [SearchParameters]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	392 #if $search_params.set_search_params == 'yes'
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	393 DisposeOfFileWhenDone = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	394 DoParsimony = $search_params.DoParsimony
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	395 ModPeptidesAreDifferent = $search_params.ModPeptidesAreDifferent
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	396 NoOneHitWonders = $search_params.NoOneHitWonders
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	397 MatchBetweenRuns = $search_params.MatchBetweenRuns
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	398 Normalize = $search_params.Normalize
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	399 QuantifyPpmTol = $search_params.QuantifyPpmTol
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	400 DoHistogramAnalysis = $search_params.DoHistogramAnalysis
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	401 SearchTarget = $search_params.SearchTarget
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	402 DecoyType = "$search_params.DecoyType"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	403 MassDiffAcceptorType = "$search_params.MassDiffAcceptorType"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	404 KeepAllUniprotMods = $search_params.KeepAllUniprotMods
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	405 DoLocalizationAnalysis = $search_params.DoLocalizationAnalysis
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	406 DoQuantification = $search_params.DoQuantification
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	407 SearchType = "$search_params.SearchType"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	408 LocalFdrCategories = ["$search_params.LocalFdrCategories"]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	409 MaxFragmentSize = $search_params.MaxFragmentSize
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	410 HistogramBinTolInDaltons = $search_params.HistogramBinTolInDaltons
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	411 MaximumMassThatFragmentIonScoreIsDoubled = $search_params.MaximumMassThatFragmentIonScoreIsDoubled
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	412 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	413 WritePrunedDatabase = #echo str('WritePrunedDatabase' in $search_outputs).lower()
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	414 WriteMzId = #echo str('WriteMzId' in $search_outputs).lower()
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	415 WritePepXml = #echo str('WritePepXml' in $search_outputs).lower()
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	416 WritePepXml = #echo str('WritePepXml' in $search_outputs).lower()
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	417 WriteDecoys = #echo str('WriteDecoys' in $search_outputs).lower()
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	418 WriteContaminants = #echo str('WriteContaminants' in $search_outputs).lower()
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	419
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	420 [SearchParameters.ModsToWriteSelection]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	421 'N-linked glycosylation' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	422 'O-linked glycosylation' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	423 'Other glycosylation' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	424 'Common Biological' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	425 'Less Common' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	426 Metal = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	427 '2+ nucleotide substitution' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	428 '1 nucleotide substitution' = 3
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	429 UniProt = 2
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	430 ]]></token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	431
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	432 <xml name="dissociation_options">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	433 <option value="Any">Any</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	434 <option value="CID">CID</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	435 <option value="LowCID">LowCID</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	436 <option value="ISCID">ISCID</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	437 <option value="MPD">MPD</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	438 <option value="ECD">ECD</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	439 <option value="PQD">PQD</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	440 <option value="ETD">ETD</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	441 <option value="HCD" selected="true">HCD</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	442 <option value="EThcD">EThcD</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	443 <option value="Custom">Custom</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	444 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	445
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	446 <xml name="common_params">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	447 <conditional name="common">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	448 <param name="set_common" type="select" label="Set Common Parameters">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	449 <option value="no">no</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	450 <option value="yes">yes</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	451 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	452 <when value="no"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	453 <when value="yes">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	454 <param argument="UseProvidedPrecursorInfo" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Provided Precursor"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	455 <param argument="DoPrecursorDeconvolution" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Deconvolute Precursor"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	456 <param argument="DeconvolutionMaxAssumedChargeState" type="integer" value="12" label="Deconvolution Max Assumed Charge State"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	457 <param argument="DeconvolutionIntensityRatio" type="float" value="3.0" label="DeconvolutionIntensityRatio"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	458 <param argument="DeconvolutionMassTolerance" type="float" value="4.0000" label="DeconvolutionMassTolerance in PPM"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	459 <param argument="TotalPartitions" type="integer" value="1" label="TotalPartitions"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	460 <param argument="PrecursorMassTolerance" type="float" value="15.0000" label="PrecursorMassTolerance in PPM"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	461 <param argument="ProductMassTolerance" type="float" value="25.0000" label="ProductMassTolerance in PPM"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	462 <param argument="AddCompIons" type="boolean" truevalue="true" falsevalue="false" checked="false" label="AddCompIons"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	463 <param argument="ScoreCutoff" type="float" value="5.0" label="ScoreCutoff"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	464 <param argument="ReportAllAmbiguity" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ReportAllAmbiguity"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	465 <param argument="NumberOfPeaksToKeepPerWindow" type="integer" value="200" label="NumberOfPeaksToKeepPerWindow"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	466 <param argument="MinimumAllowedIntensityRatioToBasePeak" type="float" value="0.01" label="MinimumAllowedIntensityRatioToBasePeak"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	467 <param argument="NormalizePeaksAccrossAllWindows" type="boolean" truevalue="true" falsevalue="false" checked="false" label="NormalizePeaksAccrossAllWindows"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	468 <param argument="TrimMs1Peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="TrimMs1Peaks"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	469 <param argument="TrimMsMsPeaks" type="boolean" truevalue="true" falsevalue="false" checked="true" label="TrimMsMsPeaks"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	470 <param argument="UseDeltaScore" type="boolean" truevalue="true" falsevalue="false" checked="false" label="UseDeltaScore"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	471 <param argument="QValueOutputFilter" type="float" value="1.0" label="QValueOutputFilter"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	472 <param argument="MaxHeterozygousVariants" type="integer" value="4" label="MaxHeterozygousVariants"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	473 <param argument="MinVariantDepth" type="integer" value="1" label="MinVariantDepth"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	474 <param argument="SeparationType" type="select" label="SeparationType">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	475 <option value="HPLC" selected="true">HPLC</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	476 <option value="CZE">CZE</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	477 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	478 <param argument="DissociationType" type="select" label="DissociationType">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	479 <expand macro="dissociation_options"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	480 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	481 <param argument="MS2ChildScanDissociationType" type="select" label="MS2ChildScanDissociationType">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	482 <expand macro="dissociation_options"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	483 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	484 <param argument="MS3ChildScanDissociationType" type="select" label="MS2ChildScanDissociationType">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	485 <expand macro="dissociation_options"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	486 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	487 </when>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	488 </conditional>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	489 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	490 <token name="@COMMON_CONFIG@">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	491 [CommonParameters]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	492 TaskDescriptor = "CalibrateTask"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	493 MaxThreadsToUsePerFile = 11
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	494 #if $common.set_common == 'yes'
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	495 DoPrecursorDeconvolution = $common.DoPrecursorDeconvolution
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	496 UseProvidedPrecursorInfo = $common.UseProvidedPrecursorInfo
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	497 DeconvolutionIntensityRatio = $common.DeconvolutionIntensityRatio
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	498 DeconvolutionMaxAssumedChargeState = $common.DeconvolutionMaxAssumedChargeState
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	499 DeconvolutionMassTolerance = "±${common.DeconvolutionMassTolerance} PPM"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	500 TotalPartitions = $common.TotalPartitions
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	501 ProductMassTolerance = "±${common.ProductMassTolerance} PPM"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	502 PrecursorMassTolerance = "±${common.PrecursorMassTolerance} PPM"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	503 AddCompIons = $common.AddCompIons
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	504 ScoreCutoff = $common.ScoreCutoff
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	505 ReportAllAmbiguity = $common.ReportAllAmbiguity
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	506 NumberOfPeaksToKeepPerWindow = $common.NumberOfPeaksToKeepPerWindow
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	507 MinimumAllowedIntensityRatioToBasePeak = $common.MinimumAllowedIntensityRatioToBasePeak
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	508 NormalizePeaksAccrossAllWindows = $common.NormalizePeaksAccrossAllWindows
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	509 TrimMs1Peaks = $common.TrimMs1Peaks
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	510 TrimMsMsPeaks = $common.TrimMsMsPeaks
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	511 UseDeltaScore = $common.UseDeltaScore
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	512 QValueOutputFilter = $common.QValueOutputFilter
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	513 ## CustomIons = $common.CustomIons
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	514 AssumeOrphanPeaksAreZ1Fragments = $common.AssumeOrphanPeaksAreZ1Fragments
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	515 MaxHeterozygousVariants = $common.MaxHeterozygousVariants
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	516 MinVariantDepth = $common.MinVariantDepth
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	517 DissociationType = $common.DissociationType
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	518 SeparationType = $common.SeparationType
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	519 MS2ChildScanDissociationType = $common.MS2ChildScanDissociationType
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	520 MS3ChildScanDissociationType = $common.MS3ChildScanDissociationType
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	521 #else
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	522 DoPrecursorDeconvolution = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	523 UseProvidedPrecursorInfo = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	524 DeconvolutionIntensityRatio = 3.0
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	525 DeconvolutionMaxAssumedChargeState = 12
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	526 DeconvolutionMassTolerance = "±4.0000 PPM"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	527 TotalPartitions = 1
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	528 ProductMassTolerance = "±25.0000 PPM"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	529 PrecursorMassTolerance = "±15.0000 PPM"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	530 AddCompIons = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	531 ScoreCutoff = 5.0
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	532 ReportAllAmbiguity = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	533 NumberOfPeaksToKeepPerWindow = 200
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	534 MinimumAllowedIntensityRatioToBasePeak = 0.01
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	535 NormalizePeaksAccrossAllWindows = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	536 TrimMs1Peaks = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	537 TrimMsMsPeaks = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	538 UseDeltaScore = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	539 QValueOutputFilter = 1.0
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	540 CustomIons = []
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	541 AssumeOrphanPeaksAreZ1Fragments = true
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	542 MaxHeterozygousVariants = 4
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	543 MinVariantDepth = 1
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	544 DissociationType = "HCD"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	545 SeparationType = "HPLC"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	546 MS2ChildScanDissociationType = "Unknown"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	547 MS3ChildScanDissociationType = "Unknown"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	548 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	549 </token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	550 <xml name="mods_params">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	551 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	552 <token name="@MODS_CONFIG@">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	553 ListOfModsFixed = "Common Fixed\tCarbamidomethyl on C\t\tCommon Fixed\tCarbamidomethyl on U"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	554 ListOfModsVariable = "Common Variable\tOxidation on M"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	555 </token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	556 <xml name="digest_params">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	557 <conditional name="digest">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	558 <param name="set_digest" type="select" label="Set Digest Parameters">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	559 <option value="no">no</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	560 <option value="yes">yes</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	561 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	562 <when value="no"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	563 <when value="yes">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	564 <param name="Protease" type="select" label="Protease">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	565 <option value="Any">Any</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	566 <option value="Arg-C">Arg-C</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	567 <option value="Asp-N">Asp-N</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	568 <option value="chymotrypsin (don't cleave before proline)">chymotrypsin (don't cleave before proline)</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	569 <option value="chymotrypsin (cleave before proline)">chymotrypsin (cleave before proline)</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	570 <option value="CNBr">CNBr</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	571 <option value="Glu-C">Glu-C</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	572 <option value="Glu-C (with asp)">Glu-C (with asp)</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	573 <option value="Lys-C (don't cleave before proline)">Lys-C (don't cleave before proline)</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	574 <option value="Lys-C (cleave before proline)">Lys-C (cleave before proline)</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	575 <option value="Lys-N">Lys-N</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	576 <option value="semi-trypsin">semi-trypsin</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	577 <option value="trypsin" selected="true">trypsin</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	578 <option value="tryptophan oxidation">tryptophan oxidation</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	579 <option value="non-specific">non-specific</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	580 <option value="top-down">top-down</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	581 <option value="singleN">singleN</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	582 <option value="singleC">singleC</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	583 <option value="collagenase">collagenase</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	584 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	585 <param name="SpecificProtease" type="select" label="SpecificProtease">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	586 <option value="Any">Any</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	587 <option value="Arg-C">Arg-C</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	588 <option value="Asp-N">Asp-N</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	589 <option value="chymotrypsin (don't cleave before proline)">chymotrypsin (don't cleave before proline)</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	590 <option value="chymotrypsin (cleave before proline)">chymotrypsin (cleave before proline)</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	591 <option value="CNBr">CNBr</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	592 <option value="Glu-C">Glu-C</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	593 <option value="Glu-C (with asp)">Glu-C (with asp)</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	594 <option value="Lys-C (don't cleave before proline)">Lys-C (don't cleave before proline)</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	595 <option value="Lys-C (cleave before proline)">Lys-C (cleave before proline)</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	596 <option value="Lys-N">Lys-N</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	597 <option value="semi-trypsin">semi-trypsin</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	598 <option value="trypsin" selected="true">trypsin</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	599 <option value="tryptophan oxidation">tryptophan oxidation</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	600 <option value="non-specific">non-specific</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	601 <option value="top-down">top-down</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	602 <option value="singleN">singleN</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	603 <option value="singleC">singleC</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	604 <option value="collagenase">collagenase</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	605 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	606 <param name="InitiatorMethionineBehavior" type="select" label="InitiatorMethionineBehavior">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	607 <option value="Variable" selected="true">Variable</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	608 <option value="Undefined">Undefined</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	609 <option value="Retain">Retain</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	610 <option value="Cleave">Cleave</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	611 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	612 <param name="SearchModeType" type="select" label="SearchModeType">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	613 <option value="Full" selected="true">Full</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	614 <option value="None">None</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	615 <option value="Semi">Semi</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	616 <option value="SingleN">SingleN</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	617 <option value="SingleC">SingleC</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	618 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	619 <param name="FragmentationTerminus" type="select" label="FragmentationTerminus">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	620 <option value="Both" selected="true">Both</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	621 <option value="None">None</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	622 <option value="N">N</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	623 <option value="C">C</option>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	624 </param>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	625 <param name="MaxMissedCleavages" type="integer" value="2" min="0" max="5" label="MaxMissedCleavages"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	626 <param name="MinPeptideLength" type="integer" value="7" min="4" label="MinPeptideLength"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	627 <param name="MaxPeptideLength" type="integer" value="2147483647" max="2147483647" label="MaxPeptideLength"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	628 <param name="MaxModificationIsoforms" type="integer" value="1024" min="0" max="5000" label="MaxModificationIsoforms"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	629 <param name="MaxModsForPeptide" type="integer" value="2" min="0" max="10" label="MaxModsForPeptide"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	630 <param name="GeneratehUnlabeledProteinsForSilac" type="boolean" truevalue="true" falsevalue="false" checked="false" label="GeneratehUnlabeledProteinsForSilac"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	631 </when>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	632 </conditional>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	633 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	634 <token name="@DIGEST_CONFIG@">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	635 [CommonParameters.DigestionParams]
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	636 #if $digest.set_digest == 'yes'
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	637 MaxMissedCleavages = $digest.MaxMissedCleavages
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	638 InitiatorMethionineBehavior = "$digest.InitiatorMethionineBehavior"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	639 MinPeptideLength = $digest.MinPeptideLength
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	640 MaxPeptideLength = $digest.MaxPeptideLength
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	641 MaxModificationIsoforms = $digest.MaxModificationIsoforms
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	642 MaxModsForPeptide = $digest.MaxModsForPeptide
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	643 Protease = "$digest.Protease"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	644 SearchModeType = "$digest.SearchModeType"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	645 FragmentationTerminus = "$digest.FragmentationTerminus"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	646 SpecificProtease = "$digest.SpecificProtease"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	647 GeneratehUnlabeledProteinsForSilac = $digest.GeneratehUnlabeledProteinsForSilac
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	648 #else
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	649 MaxMissedCleavages = 2
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	650 InitiatorMethionineBehavior = "Variable"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	651 MinPeptideLength = 7
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	652 MaxPeptideLength = 2147483647
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	653 MaxModificationIsoforms = 1024
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	654 MaxModsForPeptide = 2
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	655 Protease = "trypsin"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	656 SearchModeType = "Full"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	657 FragmentationTerminus = "Both"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	658 SpecificProtease = "trypsin"
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	659 GeneratehUnlabeledProteinsForSilac = false
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	660 #end if
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	661 </token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	662
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	663
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	664 <xml name="output_settings_toml">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	665 <data name="settings_toml" format="toml" label="${tool.name} on ${on_string} tasksettings.toml" from_work_dir="tasksettings.toml" />
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	666 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	667 <xml name="calibrated_outputs">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	668 <collection name="calibrated_scans" type="list" label="${tool.name} on ${on_string} Calibrated Spectrums">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	669 <discover_datasets pattern="^(?P<name>.+\.mzML)$" ext="mzml" directory="output/Task1CalibrationTask" />
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	670 </collection>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	671 <collection name="calibratation_toml" type="list" label="${tool.name} on ${on_string} Calibration TOMLs">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	672 <discover_datasets pattern="^(?P<name>.+\.toml)$" ext="toml" directory="output/Task1CalibrationTask" />
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	673 </collection>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	674 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	675 <xml name="search_collection_outputs">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	676 <collection name="mzids" type="list" label="${tool.name} on ${on_string} Spectrum Search mzIdent">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	677 <filter>search_outputs and 'WriteMzId' in search_outputs</filter>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	678 <discover_datasets pattern="^(?P<name>.+\.mzID)$" ext="mzid" directory="output/Task1SearchTask/Individual File Results" />
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	679 </collection>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	680 <collection name="pepxmls" type="list" label="${tool.name} on ${on_string} Spectrum Search pep.xml">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	681 <filter>search_outputs and 'WritePepXml' in search_outputs</filter>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	682 <discover_datasets pattern="^(?P<name>.+\.pep\.XML)$" ext="pepxml" directory="output/Task1SearchTask/Individual File Results" />
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	683 </collection>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	684 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	685
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	686 <token name="@METAMORPHEUS_HELP@"><![CDATA[
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	687 MetaMorpheus
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	688
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	689 MetaMorpheus_ is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability.
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	690 See the wiki page for details: https://github.com/smith-chem-wisc/MetaMorpheus/wiki
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	691
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	692 Typical MetaMorpheus Workflow:
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	693
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	694 1. MetaMorpheus Calibration - of MassSpec Spectrum files using a reference protein database (preferably in Uniprot XML format)
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	695 2. MetaMorpheus G-PTM-D - Post-translational modification (PTM) discovery from the Calibrated Spectrum files
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	696 3. MetaMorpheus Database Search - Proetomics Search using the Calibrated Spectrum files and the GPTMD protein database
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	697
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	698 .. image:: MetaMorpheusWorkflow.png
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	699 :width: 823
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	700 :height: 759
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	701
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	702 .. _MetaMorpheus: https://github.com/smith-chem-wisc/MetaMorpheus
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	703
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	704 ]]></token>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	705
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	706 <xml name="citations">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	707 <citations>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	708 <citation type="doi">10.1021/acs.jproteome.7b00873</citation>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	709 <yield />
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	710 </citations>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	711 </xml>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	712
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty" galaxyp parents: diff changeset	713 </macros>

Mercurial > repos > galaxyp > metamorpheus

annotate macros.xml @ 0:e8d7b7dc55fc draft