Mercurial > repos > galaxyp > fragpipe
annotate workflows/DIA_SpecLib_Quant.workflow @ 7:3f947afe3f71 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
author | galaxyp |
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date | Wed, 01 Oct 2025 22:21:46 +0000 |
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7
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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changeset
|
1 # Workflow: DIA_SpecLib_Quant |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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2 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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3 crystalc.run-crystalc=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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changeset
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4 database.decoy-tag=rev_ |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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5 diann.channel-normalization-strategy=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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6 diann.cmd-opts= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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7 diann.generate-msstats=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff
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8 diann.heavy= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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9 diann.library= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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10 diann.light= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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11 diann.medium= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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12 diann.min-site-prob=0.75 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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13 diann.mod-tag= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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14 diann.q-value=0.01 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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15 diann.quantification-strategy=3 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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16 diann.quantification-strategy-2=2 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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17 diann.run-dia-nn=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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18 diann.run-dia-plex=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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19 diann.run-specific-protein-q-value=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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20 diann.unrelated-runs=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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21 diann.use-predicted-spectra=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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22 diatracer.corr-threshold=0.3 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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changeset
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23 diatracer.delta-apex-im=0.01 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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24 diatracer.delta-apex-rt=3 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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25 diatracer.mass-defect-filter=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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26 diatracer.mass-defect-offset=0.1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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27 diatracer.rf-max=500 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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28 diatracer.run-diatracer=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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29 diatracer.write-intermediate-files=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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30 diaumpire.AdjustFragIntensity=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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31 diaumpire.BoostComplementaryIon=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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32 diaumpire.CorrThreshold=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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33 diaumpire.DeltaApex=0.2 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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34 diaumpire.ExportPrecursorPeak=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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changeset
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35 diaumpire.Q1=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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36 diaumpire.Q2=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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37 diaumpire.Q3=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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changeset
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38 diaumpire.RFmax=500 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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39 diaumpire.RPmax=25 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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40 diaumpire.RTOverlap=0.3 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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41 diaumpire.SE.EstimateBG=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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42 diaumpire.SE.IsoPattern=0.3 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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43 diaumpire.SE.MS1PPM=10 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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44 diaumpire.SE.MS2PPM=20 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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45 diaumpire.SE.MS2SN=1.1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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46 diaumpire.SE.MassDefectFilter=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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47 diaumpire.SE.MassDefectOffset=0.1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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48 diaumpire.SE.NoMissedScan=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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49 diaumpire.SE.SN=1.1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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50 diaumpire.run-diaumpire=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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51 fpop.coadaptr.fpop.fpop_masses= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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52 fpop.coadaptr.fpop.run-fpop-coadaptr=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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53 fpop.fragpipe.fpop.fpop-tmt=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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54 fpop.fragpipe.fpop.label_control= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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55 fpop.fragpipe.fpop.label_fpop= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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56 fpop.fragpipe.fpop.region_size=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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57 fpop.fragpipe.fpop.run-fpop=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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58 fpop.fragpipe.fpop.subtract-control=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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59 freequant.mz-tol=10 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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60 freequant.rt-tol=0.4 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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61 freequant.run-freequant=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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62 ionquant.excludemods= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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63 ionquant.formula= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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64 ionquant.heavy= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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65 ionquant.imtol=0.05 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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66 ionquant.ionfdr=0.01 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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67 ionquant.light= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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68 ionquant.locprob=0.75 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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69 ionquant.maxlfq=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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70 ionquant.mbr=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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71 ionquant.mbrimtol=0.05 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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72 ionquant.mbrmincorr=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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73 ionquant.mbrrttol=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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74 ionquant.mbrtoprun=10 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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75 ionquant.medium= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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76 ionquant.minfreq=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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77 ionquant.minions=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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78 ionquant.minisotopes=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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79 ionquant.minscans=3 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
80 ionquant.mztol=10 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
81 ionquant.normalization=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
82 ionquant.peptidefdr=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
83 ionquant.proteinfdr=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
84 ionquant.requantify=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
85 ionquant.rttol=0.4 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
86 ionquant.run-ionquant=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
87 ionquant.tp=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
88 ionquant.uniqueness=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
89 ionquant.use-labeling=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
90 ionquant.use-lfq=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
91 ionquant.writeindex=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
92 msbooster.find-best-im-model=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
93 msbooster.find-best-rt-model=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
94 msbooster.find-best-spectra-model=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
95 msbooster.fragmentation-type=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
96 msbooster.im-model=DIA-NN |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
97 msbooster.koina-url= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
98 msbooster.predict-im=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
99 msbooster.predict-rt=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
100 msbooster.predict-spectra=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
101 msbooster.rt-model=DIA-NN |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
102 msbooster.run-msbooster=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
103 msbooster.spectra-model=DIA-NN |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
104 msbooster.spectral-library-path= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
105 msfragger.Y_type_masses= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
106 msfragger.activation_types=all |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
107 msfragger.allowed_missed_cleavage_1=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
108 msfragger.allowed_missed_cleavage_2=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
109 msfragger.analyzer_types=all |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
110 msfragger.calibrate_mass=2 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
111 msfragger.check_spectral_files=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
112 msfragger.clip_nTerm_M=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
113 msfragger.deisotope=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
114 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
115 msfragger.deneutralloss=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
116 msfragger.diagnostic_fragments= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
117 msfragger.diagnostic_intensity_filter=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
118 msfragger.digest_max_length=50 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
119 msfragger.digest_min_length=7 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
120 msfragger.fragment_ion_series=b,y |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
121 msfragger.fragment_mass_tolerance=20 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
122 msfragger.fragment_mass_units=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
123 msfragger.group_variable=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
124 msfragger.intensity_transform=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
125 msfragger.ion_series_definitions= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
126 msfragger.isotope_error=0/1/2 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
127 msfragger.labile_search_mode=off |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
128 msfragger.localize_delta_mass=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
129 msfragger.mass_diff_to_variable_mod=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
130 msfragger.mass_offsets=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
131 msfragger.mass_offsets_detailed= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
132 msfragger.max_fragment_charge=2 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
133 msfragger.max_variable_mods_combinations=5000 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
134 msfragger.max_variable_mods_per_peptide=3 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
135 msfragger.min_fragments_modelling=2 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
136 msfragger.min_matched_fragments=4 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
137 msfragger.min_sequence_matches=2 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
138 msfragger.minimum_peaks=15 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
139 msfragger.minimum_ratio=0.00 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
140 msfragger.misc.fragger.clear-mz-hi=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
141 msfragger.misc.fragger.clear-mz-lo=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
142 msfragger.misc.fragger.digest-mass-hi=5000 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
143 msfragger.misc.fragger.digest-mass-lo=500 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
144 msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
145 msfragger.misc.fragger.enzyme-dropdown-2=null |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
146 msfragger.misc.fragger.precursor-charge-hi=4 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
147 msfragger.misc.fragger.precursor-charge-lo=2 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
148 msfragger.misc.fragger.remove-precursor-range-hi=1.5 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
149 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
150 msfragger.misc.slice-db=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
151 msfragger.num_enzyme_termini=2 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
152 msfragger.output_format=pepXML_pin |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
153 msfragger.output_max_expect=50 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
154 msfragger.output_report_topN=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
155 msfragger.output_report_topN_dda_plus=5 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
156 msfragger.output_report_topN_dia1=5 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
157 msfragger.override_charge=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
158 msfragger.precursor_mass_lower=-20 |
3f947afe3f71
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159 msfragger.precursor_mass_mode=selected |
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160 msfragger.precursor_mass_units=1 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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161 msfragger.precursor_mass_upper=20 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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162 msfragger.precursor_true_tolerance=20 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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163 msfragger.precursor_true_units=1 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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164 msfragger.remainder_fragment_masses= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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165 msfragger.remove_precursor_peak=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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166 msfragger.report_alternative_proteins=true |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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167 msfragger.require_precursor=true |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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168 msfragger.restrict_deltamass_to=all |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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169 msfragger.reuse_dia_fragment_peaks=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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170 msfragger.run-msfragger=true |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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171 msfragger.search_enzyme_cut_1=KR |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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172 msfragger.search_enzyme_cut_2= |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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173 msfragger.search_enzyme_name_1=stricttrypsin |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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174 msfragger.search_enzyme_name_2=null |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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175 msfragger.search_enzyme_nocut_1= |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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176 msfragger.search_enzyme_nocut_2= |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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177 msfragger.search_enzyme_sense_1=C |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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178 msfragger.search_enzyme_sense_2=C |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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179 msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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180 msfragger.table.var-mods=15.9949,M,true,1; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 0.0,site_06,false,1; 0.0,site_07,false,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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181 msfragger.track_zero_topN=0 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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182 msfragger.use_all_mods_in_first_search=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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183 msfragger.use_detailed_offsets=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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184 msfragger.use_topN_peaks=1000 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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185 msfragger.write_calibrated_mzml=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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186 msfragger.zero_bin_accept_expect=0 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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187 msfragger.zero_bin_mult_expect=1 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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188 opair.activation1=HCD |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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189 opair.activation2=ETD |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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190 opair.allowed_sites= |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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191 opair.filterOxonium=true |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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192 opair.glyco_db= |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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193 opair.max_glycans=4 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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194 opair.max_isotope_error=2 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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195 opair.min_isotope_error=0 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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196 opair.ms1_tol=20 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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197 opair.ms2_tol=20 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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198 opair.oxonium_filtering_file= |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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199 opair.oxonium_minimum_intensity=0.05 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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200 opair.reverse_scan_order=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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201 opair.run-opair=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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202 opair.single_scan_type=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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203 peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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204 peptide-prophet.combine-pepxml=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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205 peptide-prophet.run-peptide-prophet=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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206 percolator.cmd-opts=--no-terminate --post-processing-tdc --subset-max-train 500000 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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207 percolator.keep-tsv-files=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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208 percolator.min-prob=0.7 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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209 percolator.run-percolator=true |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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210 phi-report.dont-use-prot-proph-file=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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211 phi-report.filter=--picked --prot 0.01 --minPepLen 8 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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212 phi-report.pep-level-summary=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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213 phi-report.print-decoys=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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214 phi-report.prot-level-summary=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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215 phi-report.remove-contaminants=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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216 phi-report.run-report=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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217 protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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218 protein-prophet.run-protein-prophet=true |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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219 ptmprophet.cmdline= |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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220 ptmprophet.override-defaults=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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221 ptmprophet.run-ptmprophet=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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222 ptmshepherd.adv_params=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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223 ptmshepherd.annotation-common=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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224 ptmshepherd.annotation-custom=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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225 ptmshepherd.annotation-glyco=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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226 ptmshepherd.annotation-unimod=true |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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227 ptmshepherd.annotation_file= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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228 ptmshepherd.annotation_tol=0.01 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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229 ptmshepherd.cap_y_ions= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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230 ptmshepherd.decoy_type=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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231 ptmshepherd.diag_ions= |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
232 ptmshepherd.diagmine_diagMinFoldChange=3.0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
233 ptmshepherd.diagmine_diagMinSpecDiff=25 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
234 ptmshepherd.diagmine_fragMinFoldChange=3.0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
235 ptmshepherd.diagmine_fragMinPropensity=12.5 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
236 ptmshepherd.diagmine_fragMinSpecDiff=25 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
237 ptmshepherd.diagmine_minIonsPerSpec=2 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
238 ptmshepherd.diagmine_minPeps=25 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
239 ptmshepherd.diagmine_pepMinFoldChange=3.0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
240 ptmshepherd.diagmine_pepMinSpecDiff=25 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
241 ptmshepherd.glyco_fdr=1.00 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
242 ptmshepherd.glyco_isotope_max=3 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff
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|
243 ptmshepherd.glyco_isotope_min=-1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
244 ptmshepherd.glyco_ppm_tol=50 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
245 ptmshepherd.glycodatabase= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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|
246 ptmshepherd.histo_smoothbins=2 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
247 ptmshepherd.iontype_a=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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|
248 ptmshepherd.iontype_b=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff
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|
249 ptmshepherd.iontype_c=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
250 ptmshepherd.iontype_x=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
251 ptmshepherd.iontype_y=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
252 ptmshepherd.iontype_z=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
253 ptmshepherd.iterloc_maxEpoch=100 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
254 ptmshepherd.iterloc_mode=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
255 ptmshepherd.localization_allowed_res= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
256 ptmshepherd.n_glyco=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
257 ptmshepherd.normalization-psms=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
258 ptmshepherd.normalization-scans=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
259 ptmshepherd.output_extended=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
260 ptmshepherd.peakpicking_mass_units=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
261 ptmshepherd.peakpicking_minPsm=10 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
262 ptmshepherd.peakpicking_promRatio=0.3 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
263 ptmshepherd.peakpicking_width=0.002 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
264 ptmshepherd.precursor_mass_units=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
265 ptmshepherd.precursor_tol=0.01 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
266 ptmshepherd.print_decoys=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
267 ptmshepherd.print_full_glyco_params=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
268 ptmshepherd.prob_mass=0.5 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
269 ptmshepherd.remainder_masses= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
270 ptmshepherd.remove_glycan_delta_mass=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
271 ptmshepherd.run-shepherd=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
272 ptmshepherd.run_diagextract_mode=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
273 ptmshepherd.run_diagmine_mode=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
274 ptmshepherd.run_glyco_mode=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
275 ptmshepherd.spectra_condPeaks=150 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
276 ptmshepherd.spectra_condRatio=0.0001 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
277 ptmshepherd.spectra_maxPrecursorCharge=4 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
278 ptmshepherd.spectra_maxfragcharge=2 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
279 ptmshepherd.spectra_ppmtol=20 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
280 ptmshepherd.varmod_masses= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
281 quantitation.run-label-free-quant=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
282 run-psm-validation=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
283 run-validation-tab=true |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
284 saintexpress.cmd-opts= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
285 saintexpress.max-replicates=10 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
286 saintexpress.run-saint-express=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
287 saintexpress.virtual-controls=100 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
288 skyline.run-skyline=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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289 skyline.skyline=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
290 skyline.skyline-custom=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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291 skyline.skyline-custom-path= |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
292 skyline.skyline-daily=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
293 skyline.skyline-fragment-tolerance=10 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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294 skyline.skyline-mods-mode=Default |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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295 skyline.skyline-precursor-tolerance=10 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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296 skyline.use-ssl=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
297 speclibgen.convert-pepxml=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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298 speclibgen.convert-psm=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
299 speclibgen.easypqp.extras.max_delta_ppm=15 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
300 speclibgen.easypqp.extras.max_delta_unimod=0.02 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
301 speclibgen.easypqp.extras.max_glycan_qval=1 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
302 speclibgen.easypqp.extras.rt_lowess_fraction=0 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
303 speclibgen.easypqp.fragment.a=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
304 speclibgen.easypqp.fragment.b=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
changeset
|
305 speclibgen.easypqp.fragment.c=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
diff
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|
306 speclibgen.easypqp.fragment.x=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
307 speclibgen.easypqp.fragment.y=true |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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|
308 speclibgen.easypqp.fragment.z=false |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents:
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309 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM |
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310 speclibgen.easypqp.labile_mode=Regular (not glyco) |
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311 speclibgen.easypqp.neutral_loss=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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312 speclibgen.easypqp.rt-cal=noiRT |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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313 speclibgen.easypqp.select-file.text= |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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314 speclibgen.easypqp.select-im-file.text= |
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315 speclibgen.keep-intermediate-files=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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316 speclibgen.run-speclibgen=true |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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317 tab-run.delete_calibrated_mzml=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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318 tab-run.delete_temp_files=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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319 tab-run.export_matched_fragments=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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320 tab-run.sub_mzml_prob_threshold=0.5 |
3f947afe3f71
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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321 tab-run.write_sub_mzml=false |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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322 tmtintegrator.add_Ref=-1 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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323 tmtintegrator.aggregation_method=0 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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324 tmtintegrator.allow_overlabel=true |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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325 tmtintegrator.allow_unlabeled=true |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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326 tmtintegrator.best_psm=true |
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327 tmtintegrator.channel_num=TMT-6 |
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328 tmtintegrator.extraction_tool=IonQuant |
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329 tmtintegrator.glyco_qval=-1 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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330 tmtintegrator.groupby=-1 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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331 tmtintegrator.log2transformed=true |
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332 tmtintegrator.max_pep_prob_thres=0 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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333 tmtintegrator.min_ntt=0 |
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334 tmtintegrator.min_pep_prob=0.9 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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335 tmtintegrator.min_percent=0.05 |
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336 tmtintegrator.min_purity=0.5 |
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337 tmtintegrator.min_resolution=0 |
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338 tmtintegrator.min_site_prob=-1 |
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339 tmtintegrator.min_snr=0 |
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340 tmtintegrator.mod_tag=none |
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341 tmtintegrator.ms1_int=true |
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342 tmtintegrator.outlier_removal=true |
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343 tmtintegrator.philosopher-msstats=false |
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344 tmtintegrator.print_RefInt=false |
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345 tmtintegrator.prot_exclude=none |
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346 tmtintegrator.prot_norm=0 |
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347 tmtintegrator.psm_norm=false |
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348 tmtintegrator.quant_level=2 |
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349 tmtintegrator.ref_d_tag=Pool |
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350 tmtintegrator.ref_tag=Bridge |
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351 tmtintegrator.run-tmtintegrator=false |
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352 tmtintegrator.tolerance=20 |
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353 tmtintegrator.top3_pep=true |
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354 tmtintegrator.unique_gene=0 |
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355 tmtintegrator.unique_pep=false |
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356 tmtintegrator.use_glycan_composition=false |
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357 workflow.description=<p style\="margin-top\: 0">Complete workflow for DIA analysis using spectral library building and quantification using DIA-NN.</p>\n<p style\="margin-top\: 0"></p>\n<p style\="margin-top\: 0">Spectral library can be built from DDA data and/or DIA data, with direct identification from DIA data using MSFragger-DIA. All data are processed together using MSFragger (in DDA or DIA mode, respectively) - MSBooster - Percolator - ProteinProphet (Philosopher) - EasyPQP. The library is filtered to 1% FDR at the protein and peptide levels. DIA files annotated as 'DIA-Quant' are used for quantification only (i.e. not used for spectral library building). If building the library from fractionated DDA data only, in EasyPQP tab change RT Calibration option to "ciRT", or "iRT" if using organisms other than yeast or human (requires iRT peptides).</p>\n<p style\="margin-top\: 0"></p>\n<p style\="margin-top\: 0">Supports DDA RAW/.d files, mzML, and MGF files. DIA files with staggered windows should be mzML files demultiplexed using Proteowizard. For quantification using DIA-NN, Thermo/Sciex DIA files should be in mzML format, and .d for Bruker's timsTOF. diaPASEF DIA data will only be used for quantification (i.e. automatically considered as 'DIA-Quant' data type).</p> |
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358 workflow.input.data-type.im-ms=false |
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359 workflow.input.data-type.regular-ms=true |
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360 workflow.misc.save-sdrf=true |
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361 workflow.misc.sdrf-type=Default |
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362 workflow.saved-with-ver=23.0-build14 |