diff xcms_fillpeaks.r @ 44:1b5fb5a27f5e draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"

--- a/xcms_fillpeaks.r	Mon Apr 29 06:14:27 2019 -0400
+++ b/xcms_fillpeaks.r	Wed Feb 12 13:25:04 2020 +0000
@@ -53,15 +53,9 @@
 # Handle infiles
 if (!exists("singlefile")) singlefile <- NULL
 if (!exists("zipfile")) zipfile <- NULL
-rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
+rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
 zipfile <- rawFilePath$zipfile
 singlefile <- rawFilePath$singlefile
-directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
-
-# Check some character issues
-md5sumList <- list("origin" = getMd5sum(directory))
-checkXmlStructure(directory)
-checkFilesCompatibilityWithXcms(directory)
 
 
 cat("\n\n")
@@ -81,7 +75,7 @@
 
 # back compatibility between xcms-3.0.0 and xcms-3.5.2
 xdata <- updateObject(xdata)
-
+register(SerialParam())
 xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam)
 
 if (exists("intval")) {