Mercurial > repos > galaxyp > fragpipe

annotate workflows/TMT10.workflow @ 3:da9ebef968bd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit b1b03bb7cd31c1ec806b286d6c9444428b358e15
author galaxyp
date Thu, 12 Sep 2024 08:06:44 +0000
parents 14785481da2b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1 # Workflow: TMT10
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:
diff 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
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:
diff changeset
7 diann.library=
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
8 diann.light=
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
9 diann.medium=
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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
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
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:
diff changeset
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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=0
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
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
53 ionquant.medium=
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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
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
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
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
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
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
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
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
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
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
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 changeset
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
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
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
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 changeset
69 ionquant.writeindex=0
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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
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 changeset
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
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 changeset
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
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
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 changeset
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 changeset
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
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
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 changeset
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=-1/0/1/2/3
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=131.5
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=125.5
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=200
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=-18.01056 79.96633
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; 229.16293,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; 229.16293,n^,true,1; 229.16293,S,true,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
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
parents:
diff changeset
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 changeset
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 changeset
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 changeset
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 changeset
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:
diff changeset
178 phi-report.filter=--sequential --picked --prot 0.01
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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
parents:
diff changeset
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 changeset
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 changeset
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 changeset
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 changeset
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 changeset
185 protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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:
diff changeset
187 ptmprophet.cmdline=
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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=true
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=false
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
galaxyp
parents:
diff changeset
236 ptmshepherd.precursor_tol=0.01
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
237 ptmshepherd.print_decoys=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
245 ptmshepherd.remainder_masses=
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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
parents:
diff changeset
247 ptmshepherd.run-shepherd=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
248 ptmshepherd.spectra_maxfragcharge=2
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
249 ptmshepherd.spectra_ppmtol=20
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
250 ptmshepherd.varmod_masses=
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
251 quantitation.run-label-free-quant=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
252 run-psm-validation=true
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
253 run-validation-tab=true
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
254 saintexpress.fragpipe.cmd-opts=
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
255 saintexpress.max-replicates=3
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
256 saintexpress.run-saint-express=true
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
257 saintexpress.virtual-controls=100
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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
galaxyp
parents:
diff changeset
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
galaxyp
parents:
diff changeset
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
galaxyp
parents:
diff changeset
261 speclibgen.easypqp.fragment.a=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
262 speclibgen.easypqp.fragment.b=true
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
263 speclibgen.easypqp.fragment.c=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
264 speclibgen.easypqp.fragment.x=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
265 speclibgen.easypqp.fragment.y=true
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
266 speclibgen.easypqp.fragment.z=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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
galaxyp
parents:
diff changeset
268 speclibgen.easypqp.neutral_loss=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
269 speclibgen.easypqp.rt-cal=noiRT
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
270 speclibgen.easypqp.select-file.text=
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
271 speclibgen.easypqp.select-im-file.text=
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
272 speclibgen.keep-intermediate-files=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
273 speclibgen.run-speclibgen=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
274 tab-run.delete_calibrated_mzml=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
275 tab-run.delete_temp_files=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
278 tmtintegrator.add_Ref=1
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
279 tmtintegrator.aggregation_method=0
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
280 tmtintegrator.allow_overlabel=true
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
281 tmtintegrator.allow_unlabeled=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
282 tmtintegrator.best_psm=true
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
283 tmtintegrator.channel_num=TMT-10
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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
parents:
diff changeset
285 tmtintegrator.glyco_qval=-1
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
286 tmtintegrator.groupby=0
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
287 tmtintegrator.log2transformed=true
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
288 tmtintegrator.max_pep_prob_thres=0.9
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
289 tmtintegrator.min_ntt=0
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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
parents:
diff changeset
291 tmtintegrator.min_percent=0.05
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
292 tmtintegrator.min_purity=0.5
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
293 tmtintegrator.min_site_prob=-1
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
294 tmtintegrator.mod_tag=none
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
295 tmtintegrator.ms1_int=true
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
296 tmtintegrator.outlier_removal=true
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
297 tmtintegrator.print_RefInt=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
298 tmtintegrator.prot_exclude=none
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
299 tmtintegrator.prot_norm=1
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
300 tmtintegrator.psm_norm=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
301 tmtintegrator.quant_level=2
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
302 tmtintegrator.ref_tag=Bridge
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
303 tmtintegrator.run-tmtintegrator=true
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
304 tmtintegrator.tolerance=20
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
305 tmtintegrator.top3_pep=true
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
306 tmtintegrator.unique_gene=0
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
307 tmtintegrator.unique_pep=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
308 tmtintegrator.use_glycan_composition=false
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
309 workflow.description=<p style\="margin-top\: 0">Basic TMT 10-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.</p>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
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:
diff changeset
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
parents:
diff changeset
312 workflow.saved-with-ver=20.0-build5