--- a/picard_CollectBaseDistributionByCycle.xml	Sun Nov 27 15:11:50 2016 -0500
+++ b/picard_CollectBaseDistributionByCycle.xml	Tue Dec 06 10:04:41 2016 -0500
@@ -8,30 +8,31 @@
   </expand>
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
+    @symlink_element_identifier@
     ##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}" &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
-    
+
     picard
     CollectBaseDistributionByCycle
-    INPUT="${inputFile}"
+    INPUT='$inputFile.element_identifier'
     OUTPUT="${outFile}"
     CHART_OUTPUT="${pdfFile}"
     ALIGNED_READS_ONLY="${aligned_reads_only}"
     PF_READS_ONLY="${pf_reads_only}"
     REFERENCE_SEQUENCE="${reference_fasta_filename}"
     ASSUME_SORTED="${assume_sorted}"
-    
+
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-  
+
   ]]></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."/>
@@ -51,19 +52,19 @@
         <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
       </when>
     </conditional>
-    <param name="aligned_reads_only" type="boolean" label="Calculate the base distribution over aligned reads only" checked="true" truevalue="true" falsevalue="false" help="ALIGNED_READS_ONLY"/> 
-    <param name="pf_reads_only" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/> 
-    <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> 
-    
+    <param name="aligned_reads_only" type="boolean" label="Calculate the base distribution over aligned reads only" checked="true" truevalue="true" falsevalue="false" help="ALIGNED_READS_ONLY"/>
+    <param name="pf_reads_only" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/>
+    <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
+
     <expand macro="VS" />
-    
+
   </inputs>
-  
+
   <outputs>
     <data format="tabular" name="outFile"/>
     <data format="pdf" name="pdfFile"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="aligned_reads_only" value="true" />
@@ -75,8 +76,8 @@
       <output name="outFile" file="picard_CollectBaseDistributionByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
     </test>
   </tests>
-  
-  
+
+
   <help>
 
 .. class:: infomark
@@ -89,19 +90,19 @@
 
 @description@
 
-  ALIGNED_READS_ONLY=Boolean    If set to true, calculate the base distribution over aligned reads only.  Default value: 
-                                false. This option can be set to 'null' to clear the default value. Possible values: 
-                                {true, false} 
+  ALIGNED_READS_ONLY=Boolean    If set to true, calculate the base distribution over aligned reads only.  Default value:
+                                false. This option can be set to 'null' to clear the default value. Possible values:
+                                {true, false}
 
-  PF_READS_ONLY=Boolean         If set to true calculate the base distribution over PF reads only.  Default value: false. 
-                                This option can be set to 'null' to clear the default value. Possible values: {true, 
-                                false} 
+  PF_READS_ONLY=Boolean         If set to true calculate the base distribution over PF reads only.  Default value: false.
+                                This option can be set to 'null' to clear the default value. Possible values: {true,
+                                false}
 
   REFERENCE_SEQUENCE=File
-  R=File                        Reference sequence fasta  Default value: null. 
+  R=File                        Reference sequence fasta  Default value: null.
 
   ASSUME_SORTED=Boolean
-  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default 
+  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default
 
 @more_info@