--- a/picard_CollectRnaSeqMetrics.xml	Sun Nov 27 15:11:50 2016 -0500
+++ b/picard_CollectRnaSeqMetrics.xml	Tue Dec 06 10:04:41 2016 -0500
@@ -9,33 +9,33 @@
     <command detect_errors="exit_code"><![CDATA[
 
       ## Set up input files
-      
+      @symlink_element_identifier@
       ## Reference sequences
 
       #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
-      
+
       ## refFlat data
       ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format
-      
+
       grep -v '^#' ${refFlat} | awk '{print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab &&
-      
+
       ## Start picard command
-      
+
       @java_options@
       picard
       CollectRnaSeqMetrics
       REF_FLAT=refFlat.tab
-      
+
       #if str( $ribosomal_intervals ) != "None":
 	 RIBOSOMAL_INTERVALS="${ribosomal_intervals}"
       #end if
-      
+
       STRAND_SPECIFICITY="${strand_specificity}"
       MINIMUM_LENGTH="${minimum_length}"
       CHART_OUTPUT="${pdfFile}"
@@ -43,20 +43,20 @@
       #for $sequence_to_ignore in $ignore_list:
 	 IGNORE_SEQUENCE="${sequence_to_ignore.sequence}"
       #end for
-      
+
       RRNA_FRAGMENT_PERCENTAGE="${rrna_fragment_percentage}"
       METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
-      INPUT="${inputFile}"
+      INPUT='$inputFile.element_identifier'
       OUTPUT="${outFile}"
       REFERENCE_SEQUENCE="${reference_fasta_filename}"
       ASSUME_SORTED="${assume_sorted}"
-     
+
       QUIET=true
       VERBOSITY=ERROR
       VALIDATION_STRINGENCY=${validation_stringency}
-    
+
    ]]></command>
-   
+
    <inputs>
       <param format="sam,bam" type="data" name="inputFile" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
       <conditional name="reference_source">
@@ -73,7 +73,7 @@
 	 <when value="history">
 	    <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>        
+      </conditional>
       <param format="tabular" name="refFlat" type="data" label="Gene annotations in refFlat form" help="See &quot;Obtaining gene annotations in refFlat format&quot; below for help" />
       <param name="ribosomal_intervals" format="picard_interval_list" type="data" optional="True" label="Location of rRNA sequences in genome, in interval_list format" help="RIBOSOMAL_INTERVALS; If not specified no bases will be identified as being ribosomal. The list of intervals can be geberated from BED or Interval datasets using Galaxy BedToIntervalList tool"/>
       <param name="strand_specificity" type="select" label="What is the RNA-seq library strand specificity" help="STRAND_SPECIFICITY; For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand.">
@@ -93,7 +93,7 @@
 	 <option value="READ_GROUP">Read group</option>
       </param>
       <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>
@@ -101,7 +101,7 @@
       <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
       <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="reference_source_selector" value="history"/>
@@ -156,41 +156,41 @@
    8. Click **Send query to Galaxy**
    9. A new dataset will appear in the current Galaxy history
    10. Use this dataset as the input for **Gene annotations in refFlat form** dropdown of this tool
-   
+
 .. _refFlat: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat
 
 @description@
 
-   REF_FLAT=File                 Gene annotations in refFlat form.  Format described here: 
-                                 http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat  Required. 
+   REF_FLAT=File                 Gene annotations in refFlat form.  Format described here:
+                                 http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat  Required.
 
-   RIBOSOMAL_INTERVALS=File      Location of rRNA sequences in genome, in interval_list format.  If not specified no bases 
-                                 will be identified as being ribosomal. Format described here: 
+   RIBOSOMAL_INTERVALS=File      Location of rRNA sequences in genome, in interval_list format.  If not specified no bases
+                                 will be identified as being ribosomal. Format described here:
                                  http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html  and can be
 				 generated from BED datasetes using Galaxy's wrapper for picard_BedToIntervalList tool
 
    STRAND_SPECIFICITY=StrandSpecificity
-   STRAND=StrandSpecificity      For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND 
-                                 if the reads are expected to be on the transcription strand.  Required. Possible values: 
-                                 {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND} 
+   STRAND=StrandSpecificity      For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND
+                                 if the reads are expected to be on the transcription strand.  Required. Possible values:
+                                 {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND}
 
-   MINIMUM_LENGTH=Integer        When calculating coverage based values (e.g. CV of coverage) only use transcripts of this 
+   MINIMUM_LENGTH=Integer        When calculating coverage based values (e.g. CV of coverage) only use transcripts of this
                                  length or greater.  Default value: 500.
 
-   IGNORE_SEQUENCE=String        If a read maps to a sequence specified with this option, all the bases in the read are 
-                                 counted as ignored bases.  
+   IGNORE_SEQUENCE=String        If a read maps to a sequence specified with this option, all the bases in the read are
+                                 counted as ignored bases.
 
    RRNA_FRAGMENT_PERCENTAGE=Double
-                                 This percentage of the length of a fragment must overlap one of the ribosomal intervals 
-                                 for a read or read pair by this must in order to be considered rRNA.  Default value: 0.8. 
+                                 This percentage of the length of a fragment must overlap one of the ribosomal intervals
+                                 for a read or read pair by this must in order to be considered rRNA.  Default value: 0.8.
 
    METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
-   LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics.    Possible values: {ALL_READS, SAMPLE, 
+   LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics.    Possible values: {ALL_READS, SAMPLE,
                                  LIBRARY, READ_GROUP} This option may be specified 0 or more times.
-				 
+
    ASSUME_SORTED=Boolean
-   AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default 
-                                 value: true. Possible values: {true, false} 
+   AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default
+                                 value: true. Possible values: {true, false}
 
 @more_info@