Mercurial > repos > galaxyp > fragpipe
annotate workflows/LFQ-MBR.workflow @ 2:ef46866326ef draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit e75f095a55caa325cd97127114c9703e4557ad50
author | galaxyp |
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date | Tue, 16 Jul 2024 06:55:53 +0000 |
parents | 14785481da2b |
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rev | line source |
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14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
1 # Workflow: LFQ-MBR |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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changeset
|
3 crystalc.run-crystalc=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
4 database.decoy-tag=rev_ |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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5 diann.fragpipe.cmd-opts= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
6 diann.heavy= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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changeset
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7 diann.library= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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8 diann.light= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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9 diann.medium= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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10 diann.q-value=0.01 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
11 diann.quantification-strategy=3 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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12 diann.run-dia-nn=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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13 diann.run-dia-plex=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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changeset
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14 diann.run-specific-protein-q-value=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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15 diann.unrelated-runs=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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16 diann.use-predicted-spectra=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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17 diaumpire.AdjustFragIntensity=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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18 diaumpire.BoostComplementaryIon=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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19 diaumpire.CorrThreshold=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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20 diaumpire.DeltaApex=0.2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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21 diaumpire.ExportPrecursorPeak=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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22 diaumpire.Q1=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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23 diaumpire.Q2=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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24 diaumpire.Q3=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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25 diaumpire.RFmax=500 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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26 diaumpire.RPmax=25 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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27 diaumpire.RTOverlap=0.3 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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28 diaumpire.SE.EstimateBG=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
29 diaumpire.SE.IsoPattern=0.3 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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30 diaumpire.SE.MS1PPM=10 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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31 diaumpire.SE.MS2PPM=20 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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32 diaumpire.SE.MS2SN=1.1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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33 diaumpire.SE.MassDefectFilter=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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34 diaumpire.SE.MassDefectOffset=0.1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
35 diaumpire.SE.NoMissedScan=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
36 diaumpire.SE.SN=1.1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
37 diaumpire.run-diaumpire=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
38 freequant.mz-tol=10 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
39 freequant.rt-tol=0.4 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
40 freequant.run-freequant=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
41 ionquant.excludemods= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
42 ionquant.heavy= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
43 ionquant.imtol=0.05 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
44 ionquant.ionfdr=0.01 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
45 ionquant.light= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
46 ionquant.locprob=0.75 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
47 ionquant.maxlfq=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
48 ionquant.mbr=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
49 ionquant.mbrimtol=0.05 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
50 ionquant.mbrmincorr=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
51 ionquant.mbrrttol=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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52 ionquant.mbrtoprun=10 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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53 ionquant.medium= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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54 ionquant.minfreq=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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55 ionquant.minions=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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56 ionquant.minisotopes=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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57 ionquant.minscans=3 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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58 ionquant.mztol=10 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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59 ionquant.normalization=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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60 ionquant.peptidefdr=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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61 ionquant.proteinfdr=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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62 ionquant.requantify=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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63 ionquant.rttol=0.4 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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64 ionquant.run-ionquant=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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65 ionquant.tp=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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66 ionquant.uniqueness=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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67 ionquant.use-labeling=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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68 ionquant.use-lfq=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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69 ionquant.writeindex=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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70 msbooster.predict-rt=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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71 msbooster.predict-spectra=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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72 msbooster.run-msbooster=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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73 msbooster.use-correlated-features=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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74 msfragger.Y_type_masses= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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75 msfragger.activation_types=all |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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76 msfragger.add_topN_complementary=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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77 msfragger.allowed_missed_cleavage_1=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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78 msfragger.allowed_missed_cleavage_2=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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79 msfragger.calibrate_mass=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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80 msfragger.check_spectral_files=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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81 msfragger.clip_nTerm_M=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
82 msfragger.deisotope=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
83 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
84 msfragger.deneutralloss=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
85 msfragger.diagnostic_fragments= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
86 msfragger.diagnostic_intensity_filter=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
87 msfragger.digest_max_length=50 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
88 msfragger.digest_min_length=7 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
89 msfragger.fragment_ion_series=b,y |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
90 msfragger.fragment_mass_tolerance=20 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
91 msfragger.fragment_mass_units=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
92 msfragger.group_variable=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
93 msfragger.intensity_transform=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
94 msfragger.ion_series_definitions= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
95 msfragger.isotope_error=0/1/2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
96 msfragger.labile_search_mode=off |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
97 msfragger.localize_delta_mass=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
98 msfragger.mass_diff_to_variable_mod=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
99 msfragger.mass_offsets=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
100 msfragger.max_fragment_charge=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
101 msfragger.max_variable_mods_combinations=5000 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
102 msfragger.max_variable_mods_per_peptide=3 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
103 msfragger.min_fragments_modelling=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
104 msfragger.min_matched_fragments=4 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
105 msfragger.min_sequence_matches=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
106 msfragger.minimum_peaks=15 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
107 msfragger.minimum_ratio=0.01 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
108 msfragger.misc.fragger.clear-mz-hi=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
109 msfragger.misc.fragger.clear-mz-lo=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
110 msfragger.misc.fragger.digest-mass-hi=5000 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
111 msfragger.misc.fragger.digest-mass-lo=500 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
112 msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
113 msfragger.misc.fragger.enzyme-dropdown-2=null |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
114 msfragger.misc.fragger.precursor-charge-hi=4 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
115 msfragger.misc.fragger.precursor-charge-lo=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
116 msfragger.misc.fragger.remove-precursor-range-hi=1.5 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
117 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
118 msfragger.misc.slice-db=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
119 msfragger.num_enzyme_termini=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
120 msfragger.output_format=pepXML_pin |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
121 msfragger.output_max_expect=50 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
122 msfragger.output_report_topN=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
123 msfragger.output_report_topN_dia1=5 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
124 msfragger.output_report_topN_dia2=3 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
125 msfragger.override_charge=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
126 msfragger.precursor_mass_lower=-20 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
127 msfragger.precursor_mass_mode=selected |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
128 msfragger.precursor_mass_units=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
129 msfragger.precursor_mass_upper=20 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
130 msfragger.precursor_true_tolerance=20 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
131 msfragger.precursor_true_units=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
132 msfragger.remainder_fragment_masses= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
133 msfragger.remove_precursor_peak=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
134 msfragger.report_alternative_proteins=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
135 msfragger.require_precursor=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
136 msfragger.restrict_deltamass_to=all |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
137 msfragger.reuse_dia_fragment_peaks=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
138 msfragger.run-msfragger=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
139 msfragger.search_enzyme_cut_1=KR |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
140 msfragger.search_enzyme_cut_2= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
141 msfragger.search_enzyme_name_1=stricttrypsin |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
142 msfragger.search_enzyme_name_2=null |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
143 msfragger.search_enzyme_nocut_1= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
144 msfragger.search_enzyme_nocut_2= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
145 msfragger.search_enzyme_sense_1=C |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
146 msfragger.search_enzyme_sense_2=C |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
147 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 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
148 msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 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 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
149 msfragger.track_zero_topN=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
150 msfragger.use_all_mods_in_first_search=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
151 msfragger.use_topN_peaks=150 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
152 msfragger.write_calibrated_mzml=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
153 msfragger.write_uncalibrated_mgf=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
154 msfragger.zero_bin_accept_expect=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
155 msfragger.zero_bin_mult_expect=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
156 opair.activation1=HCD |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
157 opair.activation2=ETD |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
158 opair.filterOxonium=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
159 opair.glyco_db= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
160 opair.max_glycans=4 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
161 opair.max_isotope_error=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
162 opair.min_isotope_error=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
163 opair.ms1_tol=20 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
164 opair.ms2_tol=20 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
165 opair.oxonium_filtering_file= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
166 opair.oxonium_minimum_intensity=0.05 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
167 opair.reverse_scan_order=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
168 opair.run-opair=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
169 opair.single_scan_type=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
170 peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
171 peptide-prophet.combine-pepxml=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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172 peptide-prophet.run-peptide-prophet=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
173 percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
174 percolator.keep-tsv-files=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
175 percolator.min-prob=0.5 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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176 percolator.run-percolator=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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177 phi-report.dont-use-prot-proph-file=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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178 phi-report.filter=--sequential --prot 0.01 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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|
179 phi-report.pep-level-summary=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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180 phi-report.philosoher-msstats=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
181 phi-report.print-decoys=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
182 phi-report.prot-level-summary=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
183 phi-report.remove-contaminants=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
184 phi-report.run-report=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
185 protein-prophet.cmd-opts=--maxppmdiff 2000000 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
186 protein-prophet.run-protein-prophet=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
187 ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
188 ptmprophet.run-ptmprophet=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
189 ptmshepherd.adv_params=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
190 ptmshepherd.annotation-common=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
191 ptmshepherd.annotation-custom=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
192 ptmshepherd.annotation-glyco=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
193 ptmshepherd.annotation-unimod=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
194 ptmshepherd.annotation_file= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
195 ptmshepherd.annotation_tol=0.01 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
196 ptmshepherd.cap_y_ions= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
197 ptmshepherd.decoy_type=1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
198 ptmshepherd.diag_ions= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
199 ptmshepherd.diagextract_mode=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
200 ptmshepherd.diagmine_diagMinFoldChange=3.0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
201 ptmshepherd.diagmine_diagMinSpecDiff=00.2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
202 ptmshepherd.diagmine_fragMinFoldChange=3.0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
203 ptmshepherd.diagmine_fragMinPropensity=00.1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
204 ptmshepherd.diagmine_fragMinSpecDiff=00.1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
205 ptmshepherd.diagmine_minIonsPerSpec=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
206 ptmshepherd.diagmine_minPeps=25 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
207 ptmshepherd.diagmine_mode=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
208 ptmshepherd.diagmine_pepMinFoldChange=3.0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
209 ptmshepherd.diagmine_pepMinSpecDiff=00.2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
210 ptmshepherd.glyco_adducts= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
211 ptmshepherd.glyco_fdr=1.00 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
212 ptmshepherd.glyco_isotope_max=3 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
213 ptmshepherd.glyco_isotope_min=-1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
214 ptmshepherd.glyco_mode=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
215 ptmshepherd.glyco_ppm_tol=50 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
216 ptmshepherd.glycodatabase= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
217 ptmshepherd.histo_smoothbins=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
218 ptmshepherd.iontype_a=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
219 ptmshepherd.iontype_b=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
220 ptmshepherd.iontype_c=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
221 ptmshepherd.iontype_x=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
222 ptmshepherd.iontype_y=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
223 ptmshepherd.iontype_z=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
224 ptmshepherd.localization_allowed_res= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
225 ptmshepherd.localization_background=4 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
226 ptmshepherd.max_adducts=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
227 ptmshepherd.n_glyco=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
228 ptmshepherd.normalization-psms=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
229 ptmshepherd.normalization-scans=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
230 ptmshepherd.output_extended=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
231 ptmshepherd.peakpicking_mass_units=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
232 ptmshepherd.peakpicking_minPsm=10 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
233 ptmshepherd.peakpicking_promRatio=0.3 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
234 ptmshepherd.peakpicking_width=0.002 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
235 ptmshepherd.precursor_mass_units=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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236 ptmshepherd.precursor_tol=0.01 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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237 ptmshepherd.print_decoys=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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238 ptmshepherd.prob_dhexOx=2,0.5,0.1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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239 ptmshepherd.prob_dhexY=2,0.5 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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240 ptmshepherd.prob_neuacOx=2,0.05,0.2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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241 ptmshepherd.prob_neugcOx=2,0.05,0.2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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242 ptmshepherd.prob_phosphoOx=2,0.05,0.2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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243 ptmshepherd.prob_regY=5,0.5 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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244 ptmshepherd.prob_sulfoOx=2,0.05,0.2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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245 ptmshepherd.remainder_masses= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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246 ptmshepherd.remove_glycan_delta_mass=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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247 ptmshepherd.run-shepherd=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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248 ptmshepherd.spectra_maxfragcharge=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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249 ptmshepherd.spectra_ppmtol=20 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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250 ptmshepherd.varmod_masses= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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251 quantitation.run-label-free-quant=true |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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252 run-psm-validation=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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253 run-validation-tab=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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254 saintexpress.fragpipe.cmd-opts= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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255 saintexpress.max-replicates=10 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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256 saintexpress.run-saint-express=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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257 saintexpress.virtual-controls=100 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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258 speclibgen.easypqp.extras.max_delta_ppm=15 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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259 speclibgen.easypqp.extras.max_delta_unimod=0.02 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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260 speclibgen.easypqp.extras.rt_lowess_fraction=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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261 speclibgen.easypqp.fragment.a=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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262 speclibgen.easypqp.fragment.b=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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263 speclibgen.easypqp.fragment.c=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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264 speclibgen.easypqp.fragment.x=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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265 speclibgen.easypqp.fragment.y=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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266 speclibgen.easypqp.fragment.z=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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267 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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268 speclibgen.easypqp.neutral_loss=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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269 speclibgen.easypqp.rt-cal=noiRT |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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270 speclibgen.easypqp.select-file.text= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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271 speclibgen.easypqp.select-im-file.text= |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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272 speclibgen.keep-intermediate-files=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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273 speclibgen.run-speclibgen=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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274 tab-run.delete_calibrated_mzml=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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275 tab-run.delete_temp_files=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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276 tab-run.sub_mzml_prob_threshold=0.5 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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277 tab-run.write_sub_mzml=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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278 tmtintegrator.add_Ref=-1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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279 tmtintegrator.aggregation_method=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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280 tmtintegrator.allow_overlabel=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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281 tmtintegrator.allow_unlabeled=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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282 tmtintegrator.best_psm=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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283 tmtintegrator.channel_num=TMT-6 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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284 tmtintegrator.dont-run-fq-lq=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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285 tmtintegrator.glyco_qval=-1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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286 tmtintegrator.groupby=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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287 tmtintegrator.log2transformed=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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288 tmtintegrator.max_pep_prob_thres=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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289 tmtintegrator.min_ntt=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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290 tmtintegrator.min_pep_prob=0.9 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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291 tmtintegrator.min_percent=0.05 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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292 tmtintegrator.min_purity=0.5 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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293 tmtintegrator.min_site_prob=-1 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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294 tmtintegrator.mod_tag=none |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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295 tmtintegrator.ms1_int=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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296 tmtintegrator.outlier_removal=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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297 tmtintegrator.print_RefInt=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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298 tmtintegrator.prot_exclude=none |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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299 tmtintegrator.prot_norm=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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300 tmtintegrator.psm_norm=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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301 tmtintegrator.quant_level=2 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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302 tmtintegrator.ref_tag=Bridge |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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303 tmtintegrator.run-tmtintegrator=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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304 tmtintegrator.tolerance=20 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
305 tmtintegrator.top3_pep=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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306 tmtintegrator.unique_gene=0 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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307 tmtintegrator.unique_pep=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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308 tmtintegrator.use_glycan_composition=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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|
309 workflow.description=Perform closed search, followed by label free quantification with match-between-runs using IonQuant. If using mzML files, need to choose the right MS data type (Regular MS vs IM-MS). Need to assign runs to experiments. |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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310 workflow.input.data-type.im-ms=false |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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311 workflow.input.data-type.regular-ms=true |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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312 workflow.saved-with-ver=20.0-build5 |