Mercurial > repos > galaxyp > maxquant

diff test-data/08/config.yml @ 12:0839f84def5e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
author galaxyp
date Sun, 20 Jun 2021 16:37:41 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/08/config.yml	Sun Jun 20 16:37:41 2021 +0000
@@ -0,0 +1,58 @@
+
+            fastaFiles: [/tmp/tmpd7w978vs/files/0/f/c/dataset_0fc77a17-694f-4046-a911-98d071f76050.dat]
+            parseRules:
+              identifierParseRule: '>([^\s]*)'
+              descriptionParseRule: '>(.*)'
+            minUniquePeptides: 0
+            minPepLen: 7
+            maxPeptideMass: 4600
+            calcPeakProperties: False
+            writeMzTab: False
+            separateLfq: False
+            lfqStabilizeLargeRatios: True
+            lfqRequireMsms: True
+            advancedSiteIntensities: True
+            matchBetweenRuns: False
+            includeContaminants: True
+            minPeptideLengthForUnspecificSearch: 8
+            maxPeptideLengthForUnspecificSearch: 25
+            decoyMode: revert
+            peptideFdr: 0.01
+            proteinFdr: 0.01
+            quantMode: 1
+            restrictProteinQuantification: True
+            restrictMods: [Oxidation (M),Acetyl (Protein N-term)]
+            useCounterparts: True
+            paramGroups:
+              - files: ['tmt_data.mzXML']
+                maxMissedCleavages: 2
+                fixedModifications: []
+                variableModifications: [Oxidation (M)]
+                enzymes: [Trypsin/P]
+                enzymeMode: 0
+                lcmsRunType: 'Reporter ion MS2'
+                reporterMassTolerance: 0.003
+                reporterPif: 0
+                reporterFraction: 0
+                reporterBasePeakRatio: 0
+                filterPif: False
+                isobaricLabels:
+                    
+                    - [TMTpro16plex-Lys127N,TMTpro16plex-Nter127N,0,0,0,0,True]
+                    - [TMTpro16plex-Lys127C,TMTpro16plex-Nter127C,0,0,0,0,True]
+                    - [TMTpro16plex-Lys128N,TMTpro16plex-Nter128N,0,0,0,0,True]
+                    - [TMTpro16plex-Lys128C,TMTpro16plex-Nter128C,0,0,0,0,True]
+                    - [TMTpro16plex-Lys129N,TMTpro16plex-Nter129N,0,0,0,0,True]
+                    - [TMTpro16plex-Lys129C,TMTpro16plex-Nter129C,0,0,0,0,True]
+                    - [TMTpro16plex-Lys130N,TMTpro16plex-Nter130N,0,0,0,0,True]
+                    - [TMTpro16plex-Lys130C,TMTpro16plex-Nter130C,0,0,0,0,True]
+                    - [TMTpro16plex-Lys131N,TMTpro16plex-Nter131N,0,0,0,0,True]
+                    - [TMTpro16plex-Lys131C,TMTpro16plex-Nter131C,0,0,0,0,True]
+                    - [TMTpro16plex-Lys132N,TMTpro16plex-Nter132N,0,0,0,0,True]
+                    - [TMTpro16plex-Lys132C,TMTpro16plex-Nter132C,0,0,0,0,True]
+                    - [TMTpro16plex-Lys133N,TMTpro16plex-Nter133N,0,0,0,0,True]
+                    - [TMTpro16plex-Lys133C,TMTpro16plex-Nter133C,0,0,0,0,True]
+                    - [TMTpro16plex-Lys134N,TMTpro16plex-Nter134N,0,0,0,0,True]
+                    - [TMTpro16plex-Lys126C,TMTpro16plex-Nter126C,0,0,0,0,True]
+    
+        
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