Mercurial > repos > lecorguille > xcms_merge
changeset 9:35b9bb3205d8 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1444e7c7ebd2bb5bdadede71c60a39f560721a98
| author | lecorguille |
|---|---|
| date | Mon, 05 Mar 2018 09:31:22 -0500 |
| parents | 6b5504f877ff |
| children | 47e953d9da82 |
| files | xcms_merge.r |
| diffstat | 1 files changed, 10 insertions(+), 8 deletions(-) [+] |
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--- a/xcms_merge.r Mon Mar 05 04:16:12 2018 -0500 +++ b/xcms_merge.r Mon Mar 05 09:31:22 2018 -0500 @@ -10,19 +10,21 @@ args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects -# Handle infiles -if (!exists("singlefile")) singlefile <- NULL -if (!exists("zipfile")) zipfile <- NULL -rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) -zipfile <- rawFilePath$zipfile -singlefile <- rawFilePath$singlefile -args <- rawFilePath$args -directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) cat("\tXSET MERGING...\n") for(image in args$images) { load(image) + + # Handle infiles + if (!exists("singlefile")) singlefile <- NULL + if (!exists("zipfile")) zipfile <- NULL + rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) + zipfile <- rawFilePath$zipfile + singlefile <- rawFilePath$singlefile + args <- rawFilePath$args + directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) + if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") cat(sampleNamesList$sampleNamesOrigin,"\n") if (!exists("xdata_merged")) {