# HG changeset patch
# User lecorguille
# Date 1490878940 14400
# Node ID 59bdfc86240834fc75409d02597f004bbbfec40e
# Parent  591d26b9027e3525adacbe5a743e469b10ae1481
planemo upload commit 00bda51a5454373957a0b75024d9fc4282743c4d

diff -r 591d26b9027e -r 59bdfc862408 CAMERA.r
--- a/CAMERA.r	Tue Mar 28 10:51:29 2017 -0400
+++ b/CAMERA.r	Thu Mar 30 09:02:20 2017 -0400
@@ -100,7 +100,9 @@
 
 # We unzip automatically the chromatograms from the zip files.
 if (thefunction %in% c("annotatediff"))  {
-    rawFilePath = getRawfilePathFromArguments(listArguments)
+    if (!exists("zipfile")) zipfile=NULL
+    if (!exists("singlefile")) singlefile=NULL
+    rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
     zipfile = rawFilePath$zipfile
     singlefile = rawFilePath$singlefile
     listArguments = rawFilePath$listArguments
diff -r 591d26b9027e -r 59bdfc862408 lib.r
--- a/lib.r	Tue Mar 28 10:51:29 2017 -0400
+++ b/lib.r	Thu Mar 30 09:02:20 2017 -0400
@@ -225,9 +225,7 @@
 }
 
 # 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"]]