Mercurial > repos > yguitton > metams_rungc
changeset 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 | 93508ea69eb5 |
| files | lib_metams.r macros.xml metaMS_runGC.r |
| diffstat | 3 files changed, 15 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/lib_metams.r Thu May 07 06:24:39 2020 -0400 +++ b/lib_metams.r Mon Jul 06 03:04:16 2020 -0400 @@ -433,7 +433,8 @@ par (mar=c(5, 4, 4, 2) + 0.1) #For each unknown for (l in 1:length(unkn)){ - #recordPlot + print("la") + #recordPlot perpage=3 #if change change layout also! dev.new(width=21/2.54, height=29.7/2.54, file=paste("Unknown_",unkn[l],".pdf", sep="")) #A4 pdf # par(mfrow=c(perpage,2)) @@ -446,7 +447,7 @@ on.exit(par(o.par)) #For each sample for (c in 1:length(resGC$xset)) { - #get sample name + #get sample name sampname<-basename(resGC$xset[[c]]@xcmsSet@filepaths) #remove .cdf, .mzXML filepattern filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", @@ -472,13 +473,18 @@ pcgrp <- helpannotation[[a]][r,"pspvector"] par (mar=c(0, 0, 0, 0) + 0.1) #Write title + print("on plot le new") plot.new() box() text(0.5, 0.5, title1, cex=2) par (mar=c(3, 2.5, 3, 1.5) + 0.1) #Window for EIC + print("plot eic") + print(an) + print(pcgrp) plotEICs(an, pspec=pcgrp, maxlabel=2) #Window for pseudospectra + print("plotPsSpectrum") plotPsSpectrum(an, pspec=pcgrp, maxlabel=2) } } @@ -502,5 +508,7 @@ } } graphics.off() + print("graph off") }#end for unkn[l] + print("fin unkn") }#end function
--- a/macros.xml Thu May 07 06:24:39 2020 -0400 +++ b/macros.xml Mon Jul 06 03:04:16 2020 -0400 @@ -2,7 +2,7 @@ <macros> - <token name="@TOOL_VERSION@">1.22.0</token> + <token name="@TOOL_VERSION@">1.22.1</token> <xml name="stdio"> <stdio> @@ -104,4 +104,4 @@ </citations> </xml> -</macros> \ No newline at end of file +</macros>
--- 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))