--- a/picard_FilterSamReads.xml	Sun Nov 27 15:11:50 2016 -0500
+++ b/picard_FilterSamReads.xml	Tue Dec 06 10:04:41 2016 -0500
@@ -6,35 +6,35 @@
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
-    
+    @symlink_element_identifier@
     ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
-    
+
     picard
     SortSam
-    INPUT="${inputFile}"
+    INPUT='$inputFile.element_identifier'
     OUTPUT=query_sorted_bam.bam
     SORT_ORDER=queryname
     VALIDATION_STRINGENCY=LENIENT
     QUIET=true
     VERBOSITY=ERROR
-    
+
     &&
-    
+
     picard
     FilterSamReads
     INPUT=query_sorted_bam.bam
     FILTER="${filter_type.filter}"
-    
+
     #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ):
       READ_LIST_FILE="${filter_type.read_list_file}"
     #end if
-    
+
     OUTPUT="${outFile}"
     SORT_ORDER=coordinate
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-  
+
   ]]></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"/>
@@ -54,15 +54,15 @@
         <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be EXCLUDED in the output" help="READ_LIST_FILE"/>
       </when>
     </conditional>
-    
+
     <expand macro="VS" />
-    
-  </inputs> 
-  
+
+  </inputs>
+
   <outputs>
     <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
@@ -79,8 +79,8 @@
       <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
-  
-  
+
+
   <help>
 
 **Purpose**
@@ -93,32 +93,32 @@
 
 **Warning on using this tool on BWA-MEM output**
 
-This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts. 
+This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts.
 
 @dataset_collections@
 
 @description@
 
   FILTER=Filter                 Filter.  Required. Possible values:
-                                includeAligned [OUTPUT SAM/BAM will contain aligned 
-                                reads only. (Note that *both* first and 
+                                includeAligned [OUTPUT SAM/BAM will contain aligned
+                                reads only. (Note that *both* first and
                                 second of paired reads must be aligned to be included
-                                in the OUTPUT SAM or BAM)], 
-                                
+                                in the OUTPUT SAM or BAM)],
+
                                 excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only.
-                                (Note that *both* first and second of pair must be aligned to be 
+                                (Note that *both* first and second of pair must be aligned to be
                                 excluded from the OUTPUT SAM or BAM)]
-                                
-                                includeReadList [OUTPUT SAM/BAM will contain reads 
+
+                                includeReadList [OUTPUT SAM/BAM will contain reads
                                 that are supplied in the READ_LIST_FILE file]
-                                
-                                excludeReadList [OUTPUT bam will contain 
-                                reads that are *not* supplied in the READ_LIST_FILE file]} 
+
+                                excludeReadList [OUTPUT bam will contain
+                                reads that are *not* supplied in the READ_LIST_FILE file]}
 
   READ_LIST_FILE=File
-  RLF=File                      Read List File containing reads that will be included or excluded from the OUTPUT SAM or 
-                                BAM file.  Default value: null. 
-  
+  RLF=File                      Read List File containing reads that will be included or excluded from the OUTPUT SAM or
+                                BAM file.  Default value: null.
+
 @more_info@
 
   </help>