--- a/picard_CleanSam.xml	Sun Nov 27 15:11:50 2016 -0500
+++ b/picard_CleanSam.xml	Tue Dec 06 10:04:41 2016 -0500
@@ -6,35 +6,36 @@
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
+    @symlink_element_identifier@
     picard
     CleanSam
-    INPUT="${inputFile}"
+    INPUT='$inputFile.element_identifier'
     OUTPUT="${outFile}"
     QUIET=true
     VERBOSITY=ERROR
     VALIDATION_STRINGENCY=${validation_stringency}
   ]]></command>
-  
+
   <inputs>
     <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
-    
+
     <expand macro="VS" />
-    
+
   </inputs>
-  
+
   <outputs>
     <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
     </data>
   </outputs>
-  
-  
+
+
   <tests>
     <test>
       <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
-      <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" />
+      <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
-  
+
   <help>
 
 .. class:: infomark
@@ -45,9 +46,9 @@
 
  1. to soft-clip an alignment that hangs off the end of its reference sequence.
  2. to set MAPQ to 0 if a read is unmapped.
- 
+
 @dataset_collections@
- 
+
 @more_info@
 
   </help>