view test-data/se_params @ 0:e8f7be6a6e59 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8

#DIA-Umpire (version 1.4)
#Data Independent Acquisition data processing and analysis package (Signal extraction module)

# LongSwath_UPS1_1ug_rep2.mzXML LongSwath_UPS1_1ug_rep2.mzXML /panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/189/dataset_189909.dat
# LongSwath_UPS1_1ug_rep1.mzXML LongSwath_UPS1_1ug_rep1.mzXML /panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/189/dataset_189910.dat

#No of threads
Thread = 6

#Report peak
ExportPrecursorPeak = false
ExportFragmentPeak = false

#Signal extraction parameters
SE.MS1PPM = 30.0
SE.MS2PPM = 40
SE.Resolution = 17000
SE.StartCharge = 2
SE.EndCharge = 4
SE.MS2StartCharge = 2
SE.MS2EndCharge = 4

#Fragment grouping parameters
RPmax = 25
RFmax = 300
CorrThreshold = 0.2
DeltaApex = 0.6
AdjustFragIntensity = true
BoostComplementaryIon = true

#Signal extraction parameters
SE.SN = 2
SE.MS2SN = 2
SE.MinMSIntensity = 5
SE.MinMSMSIntensity = 1
SE.MaxCurveRTRange = 1
SE.NoMissedScan = 1
SE.MinFrag=10
SE.EstimateBG = true
SE.MinNoPeakCluster = 2
SE.MaxNoPeakCluster = 3
WindowType = SWATH
WindowSize = 25
     
Thread = 8