diff picard_AddOrReplaceReadGroups.xml @ 7:08f69add4d06 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92

--- a/picard_AddOrReplaceReadGroups.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_AddOrReplaceReadGroups.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -5,12 +5,12 @@
     <import>read_group_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code">
     @define_read_group_helpers@
     #set $rg_auto_name = $read_group_name_default($inputFile)
     @set_read_group_vars@
     @java_options@
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
       AddOrReplaceReadGroups
       INPUT="${inputFile}"
       $format_read_group("RGLB=", $rg_lb, '"')
@@ -39,9 +39,6 @@
     <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
   </outputs>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <tests>
     <test>