--- a/picard_MergeBamAlignment.xml	Wed Nov 11 12:23:17 2015 -0500
+++ b/picard_MergeBamAlignment.xml	Sun Nov 27 15:11:50 2016 -0500
@@ -4,20 +4,20 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     #set $picard_dict = "localref.dict"
     #set $ref_fasta = "localref.fa"     ## This is done because picards "likes" .fa extension
     
-    ln -s "${reference_source.ref_file}" "${ref_fasta}" &amp;&amp;
+    ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
        
     #if str( $reference_source.reference_source_selector ) == "history":
         
-      java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
+      picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
       QUIET=true
       VERBOSITY=ERROR
       
-      &amp;&amp;
+      &&
       
     #else:
     
@@ -25,7 +25,7 @@
     
     #end if
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     MergeBamAlignment
       UNMAPPED_BAM="${unmapped_bam}"
       
@@ -85,7 +85,7 @@
       QUIET=true
       VERBOSITY=ERROR
       
-  </command>
+  ]]></command>
   
   <inputs>
     
@@ -194,13 +194,10 @@
       <param name="clip_overlapping_reads" value="True"/>
       <param name="include_secondary_alignments" value="True"/>
       <param name="add_mate_cigar" value="True"/>
-      <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="2"/>
+      <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>