diff picard_CollectAlignmentSummaryMetrics.xml @ 7:08f69add4d06 draft

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

--- a/picard_CollectAlignmentSummaryMetrics.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_CollectAlignmentSummaryMetrics.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,22 +4,19 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
 
     #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
 
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     CollectAlignmentSummaryMetrics
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
@@ -40,7 +37,7 @@
     QUIET=true
     VERBOSITY=ERROR
   
-  </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/BAM dataset."/>
     <conditional name="reference_source">