diff picard_AddCommentsToBam.xml @ 7:08f69add4d06 draft

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

--- a/picard_AddCommentsToBam.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_AddCommentsToBam.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,9 +4,9 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
       AddCommentsToBam
       INPUT="${inputFile}"
       OUTPUT="${outFile}"
@@ -16,8 +16,8 @@
       QUIET=true
       VERBOSITY=ERROR
       VALIDATION_STRINGENCY=${validation_stringency}
-  </command>
-  
+  ]]></command>
+
   <inputs>
     <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
     <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
@@ -31,11 +31,8 @@
   <outputs>
     <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
   </outputs>
-  
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
-  
+
+
   <tests>
   <test>
       <param name="inputFile" value="picard_AddCommentsToBam.bam" />
@@ -57,7 +54,7 @@
 @description@
 
   COMMENT=String
-  C=String          Comments to add to the BAM file  This option may be specified 0 or more times. 
+  C=String          Comments to add to the BAM file  This option may be specified 0 or more times.
 
 @more_info@
   </help>