# HG changeset patch
# User tomnl
# Date 1525345084 14400
# Node ID 9c3d764b2e5b1b638f206a280ff89f3acdf4f124
# Parent  e91c400c6ca60ffd710b340d10e92193bf5a6058
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 578fd07833b93847193666c11744ba0bca1aaf57-dirty

diff -r e91c400c6ca6 -r 9c3d764b2e5b cameradims.R
--- a/cameradims.R	Thu May 03 06:42:15 2018 -0400
+++ b/cameradims.R	Thu May 03 06:58:04 2018 -0400
@@ -81,12 +81,16 @@
 
 
 if (opt$rule_type=='extended_large'){
+
+   rule_sep=','
    opt$rule_type <- 'user'
    if(opt$polarity=='pos'){
-	opt$rule_path <-  read.csv(system.file("rules", "CAMERA_rules_PosFinal_PlusLi.csv", package = "cameraDIMS"),  header=TRUE)
+	opt$rule_path <-  system.file("rules", "CAMERA_rules_PosFinal_PlusLi.csv", package = "cameraDIMS")
    }else{
-	opt$rule_path <-  read.csv(system.file("rules", "CAMERA_rules_NegFinal_PlusLi.csv", package = "cameraDIMS"),  header=TRUE)
+	opt$rule_path <-  system.file("rules", "CAMERA_rules_NegFinal_PlusLi.csv", package = "cameraDIMS")
    }   
+}else{
+   rule_sep='\t'
 }
 
 cameraOut <- cameraDIMS(data=df,
@@ -94,7 +98,7 @@
                         params_adduct=paramadduct,
                         rule_type=opt$rule_type,
                         rule_pth=opt$rule_path,
-                        rule_sep='\t',
+                        rule_sep=rule_sep,
                         rule_export=rule_export)