Mercurial > repos > yguitton > metams_rungc
comparison metaMS_runGC.r @ 8:d1ce2634135f draft
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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| 7:89af36e05548 | 8:d1ce2634135f |
|---|---|
| 112 rtrange=NULL | 112 rtrange=NULL |
| 113 cat("rtrange= ",rtrange) | 113 cat("rtrange= ",rtrange) |
| 114 } | 114 } |
| 115 | 115 |
| 116 nSlaves=args$nSlaves | 116 nSlaves=args$nSlaves |
| 117 | 117 # peakpicking parameters are not needed anymore xcms does it before runGC but keep it for protocolName and chrom type (2020-06-18 Yann Guitton) |
| 118 GALAXY.GC <- | 118 GALAXY.GC <- |
| 119 metaMSsettings("protocolName" = "GALAXY.GC", | 119 metaMSsettings("protocolName" = "GALAXY.GC", |
| 120 "chrom" = "GC", | 120 "chrom" = "GC", |
| 121 PeakPicking = list( | 121 PeakPicking = list( |
| 122 method = "matchedFilter", | 122 method = "matchedFilter", |
| 123 step = 0.5, | 123 step = 0.5, |
| 124 steps = 2, | 124 steps = 2, |
| 125 mzdiff = .5, | 125 mzdiff = .5, |
| 126 fwhm = fwhmparam, | 126 fwhm = 5, |
| 127 snthresh = 2, | 127 snthresh = 2, |
| 128 max = 500), | 128 max = 500), |
| 129 CAMERA = list(perfwhm = 1)) | 129 CAMERA = list(perfwhm = 1)) |
| 130 | 130 |
| 131 metaSetting(GALAXY.GC, "DBconstruction") <- list( | 131 metaSetting(GALAXY.GC, "DBconstruction") <- list( |