diff xcms_merge.r @ 10:47e953d9da82 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309

--- a/xcms_merge.r	Mon Mar 05 09:31:22 2018 -0500
+++ b/xcms_merge.r	Thu Mar 08 05:52:52 2018 -0500
@@ -15,16 +15,15 @@
 
 for(image in args$images) {
     load(image)
-
+    print(args)
     # Handle infiles
     if (!exists("singlefile")) singlefile <- NULL
     if (!exists("zipfile")) zipfile <- NULL
     rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
     zipfile <- rawFilePath$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")) {
@@ -70,18 +69,6 @@
 # Create a sampleMetada file
 sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")
 
-# Get the legacy xcmsSet object
-xset <- getxcmsSetObject(xdata)
-
-cat("\n\n")
-
-
-# -- TIC --
-cat("\t\tGET TIC GRAPH\n")
-#@TODO: one day, use xdata instead of xset to draw the TICs and BPC or a complete other method
-getTICs(xcmsSet=xset, rt="raw", pdfname="TICs.pdf")
-getBPCs(xcmsSet=xset, rt="raw", pdfname="BICs.pdf")
-
 cat("\n\n")
 
 cat("\tXCMSnExp OBJECT INFO\n")