diff xcms_merge.r @ 8:6b5504f877ff draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f

--- a/xcms_merge.r	Thu Mar 01 04:15:19 2018 -0500
+++ b/xcms_merge.r	Mon Mar 05 04:16:12 2018 -0500
@@ -23,6 +23,7 @@
 
 for(image in args$images) {
     load(image)
+    if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
     cat(sampleNamesList$sampleNamesOrigin,"\n")
     if (!exists("xdata_merged")) {
         xdata_merged <- xdata
@@ -63,7 +64,23 @@
         stop(error_message)
     }
 }
-save.image()
+
+# 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")
 print(pData(xdata))