Mercurial > repos > bzonnedda > exomedepth

changeset 23:a9701c421408 draft default tip

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Uploaded
author bzonnedda
date Fri, 17 Mar 2017 06:38:03 -0400
parents bb063b2b525a
children
files exomedepth.xml
diffstat 1 files changed, 3 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- 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}