# HG changeset patch
# User lecorguille
# Date 1488460957 18000
# Node ID 38fa090ae98ff8c01deed854145e312fc49e9046
# Parent  411d2b9ea412502b70481a67421a5b77ad96b6e1
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312

diff -r 411d2b9ea412 -r 38fa090ae98f xcms.r
--- a/xcms.r	Wed Mar 01 16:57:27 2017 -0500
+++ b/xcms.r	Thu Mar 02 08:22:37 2017 -0500
@@ -161,6 +161,11 @@
 cat("\t\tCOMPUTE\n")
 xset = do.call(thefunction, listArguments)
 
+# check if there are no peaks
+if (nrow(peaks(xset)) == 0) {
+    stop("No peaks were detected. You should review your settings")
+}
+
 
 cat("\n\n")
 
@@ -170,7 +175,6 @@
 
     #transform the files absolute pathways into relative pathways
     xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
-    print(zipfile)
     if(exists("zipfile") && !is.null(zipfile) && (zipfile!="")) {
 
         #Modify the samples names (erase the path)