# HG changeset patch
# User tomnl
# Date 1525339337 14400
# Node ID 21d2cd76bb1b0f4fd379e447b1e16d7a7f6cddb8
# Parent  1c7c55ac84f82c8c400291f55da2b98368221661
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit d4159f1962ef3fe37dd4f3047e4050afe013c15a-dirty

diff -r 1c7c55ac84f8 -r 21d2cd76bb1b cameradims.R
--- a/cameradims.R	Mon Apr 23 05:46:16 2018 -0400
+++ b/cameradims.R	Thu May 03 05:22:17 2018 -0400
@@ -79,6 +79,15 @@
 
 df <- df[df$i>opt$intensity_filter,]
 
+
+if (opt$rule_type=='extended_large'){
+   if(opt$polarity=='pos'){
+	opt$rule_path <-  read.csv(system.file("rules", "CAMERA_rules_PosFinal_PlusLi.csv", package = "cameraDIMS"),  header=TRUE)
+   }else{
+	opt$rule_path <-  read.csv(system.file("rules", "CAMERA_rules_NegFinal_PlusLi.csv", package = "cameraDIMS"),  header=TRUE)
+   }   
+}
+
 cameraOut <- cameraDIMS(data=df,
                         params_iso=paramiso,
                         params_adduct=paramadduct,