Mercurial > repos > galaxyp > maxquant

comparison test-data/05/config.yml @ 9:fe479bf15bd3 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
author galaxyp
date Fri, 12 Mar 2021 08:39:34 +0000
parents
children 057bf124c80e
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8:55f8e3f91e0b 9:fe479bf15bd3
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2 fastaFiles: [/tmp/tmp0wswhy4o/files/4/7/7/dataset_4770959a-66d4-405f-a5b5-48d25389063a.dat]
3 parseRules:
4 identifierParseRule: '^>.*\|(.*)\|.*$'
5 descriptionParseRule: '^>.*\|.*\|[^ ]+ (.*) OS.*$'
6 minUniquePeptides: 1
7 minPepLen: 7
8 maxPeptideMass: 4600
9 calcPeakProperties: False
10 writeMzTab: False
11 ibaq: True
12 ibaqLogFit: False
13 separateLfq: False
14 lfqStabilizeLargeRatios: True
15 lfqRequireMsms: True
16 advancedSiteIntensities: True
17 matchBetweenRuns: True
18 matchingTimeWindow: 0.7
19 matchingIonMobilityWindow: 0.05
20 alignmentTimeWindow: 20
21 alignmentIonMobilityWindow: 1
22 matchUnidentifiedFeatures: False
23 includeContaminants: True
24 minPeptideLengthForUnspecificSearch: 8
25 maxPeptideLengthForUnspecificSearch: 25
26 decoyMode: revert
27 peptideFdr: 0.01
28 proteinFdr: 0.01
29 quantMode: 1
30 restrictProteinQuantification: True
31 restrictMods: [Oxidation (M),Acetyl (Protein N-term)]
32 useCounterparts: True
33 paramGroups:
34 - files: ['BSA_min_22.mzxml']
35 maxMissedCleavages: 1
36 fixedModifications: [Carbamidomethyl (C)]
37 variableModifications: [Oxidation (M)]
38 enzymes: [Trypsin/P]
39 enzymeMode: 0
40 lfqMode: 1
41 lfqSkipNorm: True
42 lfqMinEdgesPerNode: 3
43 lfqAvEdgesPerNode: 6
44 lfqMinRatioCount: 2
45