# HG changeset patch
# User tomnl
# Date 1525339292 14400
# Node ID 1965e2b5a3d085d74549f451f9b861522a7eb9b0
# Parent  df281fb2c27988f73fddfbe3f10fe5756f192b22
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit d4159f1962ef3fe37dd4f3047e4050afe013c15a-dirty

diff -r df281fb2c279 -r 1965e2b5a3d0 cameradims.R
--- a/cameradims.R	Mon Apr 23 05:45:23 2018 -0400
+++ b/cameradims.R	Thu May 03 05:21:32 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,
diff -r df281fb2c279 -r 1965e2b5a3d0 cameradims.xml
--- a/cameradims.xml	Mon Apr 23 05:45:23 2018 -0400
+++ b/cameradims.xml	Thu May 03 05:21:32 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="cameradims" name="CAMERA_DIMS" version="0.1.13">
+<tool id="cameradims" name="CAMERA_DIMS" version="0.1.14">
     <description>Modification of the R package CAMERA to work on DIMS data</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
@@ -59,6 +59,7 @@
             <param name="ruleset" type="select" label="Rules for adducts" >
                 <option value="primary adducts" >Primary adducts ([M+Na]+, [M+K]+ and [M+NH4]+")</option>
                 <option value="extended" selected="true" >Extended adducts</option>
+                <option value="extended_large" selected="true" >Extended adducts (large)</option>
                 <option value="user" >Provide a csv file of the rules to use</option>
             </param>
             <when value="user">