diff xcms_retcor.r @ 34:9714270678a7 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a

--- a/xcms_retcor.r	Thu Mar 08 05:54:22 2018 -0500
+++ b/xcms_retcor.r	Tue Apr 03 11:39:48 2018 -0400
@@ -29,7 +29,7 @@
 cat("\tARGUMENTS PROCESSING INFO\n")
 
 #saving the specific parameters
-method <- args$method; args$method <- NULL
+method <- args$method
 
 cat("\n\n")
 
@@ -47,7 +47,6 @@
 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
 zipfile <- rawFilePath$zipfile
 singlefile <- rawFilePath$singlefile
-args <- rawFilePath$args
 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
 
 
@@ -61,6 +60,9 @@
 cat("\t\tCOMPUTE\n")
 
 cat("\t\t\tAlignment/Retention Time correction\n")
+# clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
+args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))]
+
 adjustRtimeParam <- do.call(paste0(method,"Param"), args)
 print(adjustRtimeParam)
 xdata <- adjustRtime(xdata, param=adjustRtimeParam)