# HG changeset patch
# User lecorguille
# Date 1490877291 14400
# Node ID b8be2b25957d6ebccd1fa96d280939adbace7233
# Parent  d45e409406edbe837a27ca7f459daf2a384d6f2e
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5583baab62c0f17cabbfe93ba4f2522e8df9b36b

diff -r d45e409406ed -r b8be2b25957d lib.r
--- a/lib.r	Wed Mar 22 16:06:13 2017 -0400
+++ b/lib.r	Thu Mar 30 08:34:51 2017 -0400
@@ -476,9 +476,7 @@
 
 
 # This function get the raw file path from the arguments
-getRawfilePathFromArguments <- function(listArguments) {
-    zipfile = NULL
-    singlefile = NULL
+getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {    
     if (!is.null(listArguments[["zipfile"]]))           zipfile = listArguments[["zipfile"]]
     if (!is.null(listArguments[["zipfilePositive"]]))   zipfile = listArguments[["zipfilePositive"]]
     if (!is.null(listArguments[["zipfileNegative"]]))   zipfile = listArguments[["zipfileNegative"]]
diff -r d45e409406ed -r b8be2b25957d xcms.r
--- a/xcms.r	Wed Mar 22 16:06:13 2017 -0400
+++ b/xcms.r	Thu Mar 30 08:34:51 2017 -0400
@@ -101,7 +101,9 @@
 
 
 if (thefunction %in% c("xcmsSet","retcor","fillPeaks"))  {
-    rawFilePath = getRawfilePathFromArguments(listArguments)
+    if (!exists("singlefile")) singlefile=NULL
+    if (!exists("zipfile")) zipfile=NULL
+    rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
     zipfile = rawFilePath$zipfile
     singlefile = rawFilePath$singlefile
     listArguments = rawFilePath$listArguments