diff picard_DownsampleSam.xml @ 12:05087b27692a draft

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

--- a/picard_DownsampleSam.xml	Wed Nov 11 12:23:17 2015 -0500
+++ b/picard_DownsampleSam.xml	Sun Nov 27 15:11:50 2016 -0500
@@ -4,10 +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
     DownsampleSam
       INPUT="${inputFile}"
       OUTPUT="${outFile}"
@@ -16,7 +15,7 @@
       QUIET=true
       VERBOSITY=ERROR
       VALIDATION_STRINGENCY=${validation_stringency}
-  </command>
+  ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" />
     <param name="probability" type="float" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
@@ -26,9 +25,6 @@
     
   </inputs>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <outputs>
     <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>