Mercurial > repos > galaxyp > maxquant

diff test-data/10/config.yml @ 15:97a7f34fcb6a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
author galaxyp
date Wed, 11 Aug 2021 09:24:23 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/10/config.yml	Wed Aug 11 09:24:23 2021 +0000
@@ -0,0 +1,38 @@
+
+            fastaFiles: [/tmp/tmps9fy8_y6/files/0/d/3/dataset_0d32c02a-47ca-47c8-83b6-1e955f377a96.dat]
+            parseRules:
+              identifierParseRule: '^>.*\|(.*)\|.*$'
+              descriptionParseRule: '^>.*\|.*\|[^ ]+ (.*) OS.*$'
+            minUniquePeptides: 1
+            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: ['thermo.raw.thermo.raw']
+                maxMissedCleavages: 1
+                fixedModifications: [Carbamidomethyl (C)]
+                variableModifications: [Oxidation (M)]
+                enzymes: [Trypsin/P]
+                enzymeMode: 0
+                lfqMode: 1
+                lfqNormType: 1
+                lfqMinEdgesPerNode: 3
+                lfqAvEdgesPerNode: 6
+                lfqMinRatioCount: 2
+        
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