Mercurial > repos > yguitton > metams_rungc

diff metaMS_runGC.r @ 8:d1ce2634135f draft

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planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 88163f9ba0e3e95f00e18247c67b95cf7791fa98-dirty
author workflow4metabolomics
date Mon, 06 Jul 2020 03:04:16 -0400
parents 89af36e05548
children
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--- a/metaMS_runGC.r	Thu May 07 06:24:39 2020 -0400
+++ b/metaMS_runGC.r	Mon Jul 06 03:04:16 2020 -0400
@@ -114,16 +114,16 @@
     }
 
     nSlaves=args$nSlaves
-
+# peakpicking parameters are not needed anymore xcms does it before runGC but keep it for protocolName and chrom type (2020-06-18 Yann Guitton)
     GALAXY.GC <- 
-        metaMSsettings("protocolName" = "GALAXY.GC",
+       metaMSsettings("protocolName" = "GALAXY.GC",
                        "chrom" = "GC",
                        PeakPicking = list(
                         method = "matchedFilter",
                         step = 0.5,
                         steps = 2,
                         mzdiff = .5,
-                        fwhm = fwhmparam,
+                        fwhm = 5,
                         snthresh = 2,
                         max = 500),
                        CAMERA = list(perfwhm = 1))