Mercurial > repos > galaxyp > dia_umpire
annotate test-data/se_params @ 0:e8f7be6a6e59 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
author | galaxyp |
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date | Tue, 23 Jan 2018 14:45:50 -0500 |
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e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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1 #DIA-Umpire (version 1.4) |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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2 #Data Independent Acquisition data processing and analysis package (Signal extraction module) |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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3 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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4 # 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 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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5 # 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 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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6 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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7 #No of threads |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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8 Thread = 6 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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9 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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10 #Report peak |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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11 ExportPrecursorPeak = false |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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12 ExportFragmentPeak = false |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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13 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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14 #Signal extraction parameters |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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15 SE.MS1PPM = 30.0 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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16 SE.MS2PPM = 40 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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17 SE.Resolution = 17000 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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18 SE.StartCharge = 2 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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19 SE.EndCharge = 4 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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20 SE.MS2StartCharge = 2 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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21 SE.MS2EndCharge = 4 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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22 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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23 #Fragment grouping parameters |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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24 RPmax = 25 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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25 RFmax = 300 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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26 CorrThreshold = 0.2 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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27 DeltaApex = 0.6 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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28 AdjustFragIntensity = true |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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29 BoostComplementaryIon = true |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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30 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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31 #Signal extraction parameters |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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32 SE.SN = 2 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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33 SE.MS2SN = 2 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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34 SE.MinMSIntensity = 5 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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35 SE.MinMSMSIntensity = 1 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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36 SE.MaxCurveRTRange = 1 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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37 SE.NoMissedScan = 1 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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38 SE.MinFrag=10 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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39 SE.EstimateBG = true |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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40 SE.MinNoPeakCluster = 2 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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41 SE.MaxNoPeakCluster = 3 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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42 WindowType = SWATH |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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43 WindowSize = 25 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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44 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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45 Thread = 8 |