# HG changeset patch
# User lecorguille
# Date 1490878963 14400
# Node ID 97e2c754e81f9efc3ba680641452295a07a7fbe2
# Parent  ddce949e4b35e99010a1265f50ee680ccca94044
planemo upload commit 00bda51a5454373957a0b75024d9fc4282743c4d

diff -r ddce949e4b35 -r 97e2c754e81f CAMERA.r
--- a/CAMERA.r	Tue Mar 28 10:51:55 2017 -0400
+++ b/CAMERA.r	Thu Mar 30 09:02:43 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 ddce949e4b35 -r 97e2c754e81f lib.r
--- a/lib.r	Tue Mar 28 10:51:55 2017 -0400
+++ b/lib.r	Thu Mar 30 09:02:43 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"]]