Mercurial > repos > lecorguille > xcms_fillpeaks

changeset 24:7a01dfc8be41 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312
author lecorguille
date Thu, 02 Mar 2017 08:23:17 -0500
parents 7e289788d37d
children 9ca8133a2b9f
files xcms.r
diffstat 1 files changed, 5 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/xcms.r	Wed Mar 01 16:58:07 2017 -0500
+++ b/xcms.r	Thu Mar 02 08:23:17 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)