# HG changeset patch
# User bzonnedda
# Date 1489747083 14400
# Node ID a9701c42140830c2247e989175266a61d2e4d868
# Parent  bb063b2b525afdd5c34bfd173d21b1cd14e6c103
Uploaded

diff -r bb063b2b525a -r a9701c421408 exomedepth.xml
--- a/exomedepth.xml	Fri Mar 17 06:29:33 2017 -0400
+++ b/exomedepth.xml	Fri Mar 17 06:38:03 2017 -0400
@@ -3,8 +3,8 @@
   <requirements>
 	  <requirement type="package" version="1.1.10">r-exomedepth</requirement>
   </requirements>
-  <command>
-	R CMD BATCH --no-save --no-restore '--args mypars="$args_file"' <!--$__tool_directory__/exomedepth.R-->
+  <command interpreter="Rscript">
+   exomedepth.R $args_file
   </command>
   <inputs>
     <param format="bed" name="targetFile" type="data" label="Target regions (BED)">
@@ -25,8 +25,7 @@
   </inputs>
 
   <configfiles>
-    <configfile name="args_file">
-target=$targetFile
+    <configfile name="args_file">target=$targetFile
 test_vs_ref=$test_vs_ref
 #for $i in $inputs
 bam=${i.input}