diff xcms_retcor.r @ 33:69b5a006fca1 draft

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

--- a/xcms_retcor.r	Tue Mar 06 04:03:16 2018 -0500
+++ b/xcms_retcor.r	Thu Mar 08 05:54:22 2018 -0500
@@ -50,11 +50,6 @@
 args <- rawFilePath$args
 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
 
-# Check some character issues
-md5sumList <- list("origin" = getMd5sum(directory))
-checkXmlStructure(directory)
-checkFilesCompatibilityWithXcms(directory)
-
 
 cat("\n\n")
 
@@ -70,9 +65,6 @@
 print(adjustRtimeParam)
 xdata <- adjustRtime(xdata, param=adjustRtimeParam)
 
-# Get the legacy xcmsSet object
-xset <- getxcmsSetObject(xdata)
-
 cat("\n\n")
 
 
@@ -80,10 +72,6 @@
 cat("\t\tDRAW GRAPHICS\n")
 getPlotAdjustedRtime(xdata)
 
-#@TODO: one day, use xdata instead of xset to draw the TICs and BPC or a complete other method
-getTICs(xcmsSet=xset, rt="corrected", pdfname="TICs.pdf")
-getBPCs(xcmsSet=xset, rt="corrected", pdfname="BICs.pdf")
-
 cat("\n\n")
 
 # ----- EXPORT -----
@@ -93,6 +81,8 @@
 cat("\n\n")
 
 cat("\txcmsSet OBJECT INFO\n")
+# Get the legacy xcmsSet object
+xset <- getxcmsSetObject(xdata)
 print(xset)
 cat("\n\n")