diff msnbase_readmsdata.r @ 13:226fb89cacc4 draft

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

--- a/msnbase_readmsdata.r	Tue Jan 07 04:30:02 2020 -0500
+++ b/msnbase_readmsdata.r	Wed Feb 12 08:27:38 2020 -0500
@@ -38,16 +38,12 @@
 # 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)
+files <- rawFilePath$files
 
-# Check some character issues
-md5sumList <- list("origin" = getMd5sum(directory))
-checkXmlStructure(directory)
-checkFilesCompatibilityWithXcms(directory)
-
+md5sumList <- list("origin" = getMd5sum(files))
 
 cat("\n\n")
 
@@ -58,9 +54,6 @@
 
 cat("\t\tCOMPUTE\n")
 
-## Get the full path to the files
-files <- getMSFiles(directory)
-
 cat("\t\t\tCreate a phenodata data.frame\n")
 s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x),"/")), n=1))
 s_name <- tools::file_path_sans_ext(basename(files))