diff test-data/se_params @ 0:e8f7be6a6e59 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/se_params	Tue Jan 23 14:45:50 2018 -0500
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+#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