Mercurial > repos > lecorguille > xcms_summary
diff xcms_summary.r @ 42:5d59db39939a draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8"
| author | workflow4metabolomics |
|---|---|
| date | Tue, 12 May 2020 20:38:28 +0000 |
| parents | 1d2cc6c87acf |
| children | 297ee37840ef |
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--- a/xcms_summary.r Wed Feb 12 13:27:00 2020 +0000 +++ b/xcms_summary.r Tue May 12 20:38:28 2020 +0000 @@ -67,18 +67,22 @@ if (!is.null(args$user_email)) user_email = args$user_email; # if the RData come from XCMS 1.x -if (exists("xset")) xobject <- xset -# retrocompatability -if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject))) +if (exists("xset")) { + xobject <- xset + # retrocompatability + if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject))) +} # if the RData come from CAMERA if (exists("xa")) xobject <- xa@xcmsSet # if the RData come from XCMS 3.x -if (exists("xdata")) xobject <- xdata +if (exists("xdata")) { + xobject <- xdata + if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(xdata@phenoData@data$sample_name)) +} if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.") - # ----- MAIN PROCESSING INFO ----- writehtml("<!DOCTYPE html>") writehtml("<HTML lang='en'>")