Mercurial > repos > lecorguille > xcms_xcmsset

changeset 27:8e46e9bd7c50 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5583baab62c0f17cabbfe93ba4f2522e8df9b36b
author lecorguille
date Thu, 30 Mar 2017 08:33:25 -0400
parents 626d3db664ef
children b90e4f92e8b5
files lib.r xcms.r
diffstat 2 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/lib.r	Wed Mar 22 16:04:45 2017 -0400
+++ b/lib.r	Thu Mar 30 08:33:25 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"]]
--- a/xcms.r	Wed Mar 22 16:04:45 2017 -0400
+++ b/xcms.r	Thu Mar 30 08:33:25 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