--- a/picard_SamToFastq.xml	Sun Nov 27 15:11:50 2016 -0500
+++ b/picard_SamToFastq.xml	Tue Dec 06 10:04:41 2016 -0500
@@ -5,16 +5,17 @@
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
-     
+
     echo "BAM" > $report &&    ## This is necessary for output dataset detection (see output tags below)
-    
+
     @java_options@
-    
+    @symlink_element_identifier@
+
     picard
     SamToFastq
-    
-    INPUT="${inputFile}"
-    
+
+    INPUT='$inputFile.element_identifier'
+
     #if str( $output_per_rg ) == "true":
       OUTPUT_PER_RG=true
       OUTPUT_DIR=.
@@ -25,34 +26,34 @@
     #elif str( $output_per_rg ) == "false" and str( $interleave ) == "true":
       FASTQ=INTERLEAVED.fastq
     #end if
-  
+
     RE_REVERSE="${re_reverse}"
     INTERLEAVE="${interleave}"
     INCLUDE_NON_PF_READS="${include_non_pf_reads}"
     CLIPPING_ATTRIBUTE="${clipping_attribute}"
     CLIPPING_ACTION="${clipping_action}"
     READ1_TRIM="${read1_trim}"
-    
+
     #if int($read1_max_bases_to_write) > -1:
       READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}"
     #end if
-    
+
     READ2_TRIM="${read2_trim}"
-    
+
     #if int($read2_max_bases_to_write) > -1:
       READ2_MAX_BASES_TO_WRITE="${read2_max_bases_to_write}"
     #end if
-    
+
     INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"
-    
-    
+
+
     VALIDATION_STRINGENCY="${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"/>
     <param name="output_per_rg" type="boolean" checked="False" label="Do you want to output a fastq file per read group (two fastq files per read group if the group is paired)" help="OUTPUT_PER_RG; default=False"/>
     <param name="re_reverse" type="boolean" checked="True" label="Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq" help="RE_REVERSE; default=True"/>
@@ -65,18 +66,18 @@
     <param name="read2_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 2" help="READ2_TRIM; default=0"/>
     <param name="read2_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 2 after trimming" help="READ2_MAX_BASES_TO_WRITE; If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written; default=null (-1)"/>
     <param name="include_non_primary_alignments" type="boolean" label="If true, include non-primary alignments in the output" help="INCLUDE_NON_PRIMARY_ALIGNMENTS; Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments; default=False"/>
-    
+
     <expand macro="VS" />
-    
-  </inputs> 
-  
+
+  </inputs>
+
   <outputs>
     <!-- here dataset discovery is based on fact that if OUTPUT_PER_RG=true this tool automatically adds .fastq extension to emitted files -->
     <data format="txt" name="report" label="SamToFastq run" hidden="true">
       <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastq" ext="fastqsanger" visible="true"/>
     </data>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
@@ -90,7 +91,7 @@
       <param name="read1_max_bases_to_write" value="-1"/>
       <param name="read2_trim" value="0" />
       <param name="read2_max_bases_to_write" value="-1"/>
-      <param name="include_non_primary_alignments" value="false"/>   
+      <param name="include_non_primary_alignments" value="false"/>
       <output name="report">
         <assert_contents>
           <has_line line="BAM" />
@@ -99,8 +100,8 @@
       </output>
     </test>
   </tests>
-  
-  
+
+
   <help>
 
 **Purpose**
@@ -120,71 +121,71 @@
 @description@
 
   FASTQ=File
-  F=File                        Output fastq file (single-end fastq or, if paired, first end of the pair fastq).  
+  F=File                        Output fastq file (single-end fastq or, if paired, first end of the pair fastq).
                                 Required.  Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
-  
+
   SECOND_END_FASTQ=File
-  F2=File                       Output fastq file (if paired, second end of the pair fastq).  Default value: null.  
+  F2=File                       Output fastq file (if paired, second end of the pair fastq).  Default value: null.
                                 Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
-  
+
   UNPAIRED_FASTQ=File
-  FU=File                       Output fastq file for unpaired reads; may only be provided in paired-fastq mode  Default 
+  FU=File                       Output fastq file for unpaired reads; may only be provided in paired-fastq mode  Default
                                 value: null.  Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
-  
+
   OUTPUT_PER_RG=Boolean
-  OPRG=Boolean                  Output a fastq file per read group (two fastq files per read group if the group is 
+  OPRG=Boolean                  Output a fastq file per read group (two fastq files per read group if the group is
                                 paired).  Default value: false. Possible values: {true, false}  Cannot be used in
                                 conjuction with option(s) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F)
-  
+
   OUTPUT_DIR=File
-  ODIR=File                     Directory in which to output the fastq file(s).  Used only when OUTPUT_PER_RG is true.  
-                                Default value: null. 
-  
+  ODIR=File                     Directory in which to output the fastq file(s).  Used only when OUTPUT_PER_RG is true.
+                                Default value: null.
+
   RE_REVERSE=Boolean
-  RC=Boolean                    Re-reverse bases and qualities of reads with negative strand flag set before writing them 
-                                to fastq  Default value: true. Possible values: {true, false} 
-  
+  RC=Boolean                    Re-reverse bases and qualities of reads with negative strand flag set before writing them
+                                to fastq  Default value: true. Possible values: {true, false}
+
   INTERLEAVE=Boolean
-  INTER=Boolean                 Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe 
-                                which end it came from  Default value: false. Possible values: {true, false} 
-  
+  INTER=Boolean                 Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe
+                                which end it came from  Default value: false. Possible values: {true, false}
+
   INCLUDE_NON_PF_READS=Boolean
-  NON_PF=Boolean                Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes 
-                                filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads.  
-                                Default value: false. Possible values: {true, false} 
-  
+  NON_PF=Boolean                Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes
+                                filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads.
+                                Default value: false. Possible values: {true, false}
+
   CLIPPING_ATTRIBUTE=String
-  CLIP_ATTR=String              The attribute that stores the position at which the SAM record should be clipped  Default 
-                                value: null. 
-  
+  CLIP_ATTR=String              The attribute that stores the position at which the SAM record should be clipped  Default
+                                value: null.
+
   CLIPPING_ACTION=String
-  CLIP_ACT=String               The action that should be taken with clipped reads: 'X' means the reads and qualities 
-                                should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in 
-                                the clipped region; and any integer means that the base qualities should be set to that 
-                                value in the clipped region.  Default value: null. 
-  
+  CLIP_ACT=String               The action that should be taken with clipped reads: 'X' means the reads and qualities
+                                should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in
+                                the clipped region; and any integer means that the base qualities should be set to that
+                                value in the clipped region.  Default value: null.
+
   READ1_TRIM=Integer
-  R1_TRIM=Integer               The number of bases to trim from the beginning of read 1.  Default value: 0. 
-  
+  R1_TRIM=Integer               The number of bases to trim from the beginning of read 1.  Default value: 0.
+
   READ1_MAX_BASES_TO_WRITE=Integer
-  R1_MAX_BASES=Integer          The maximum number of bases to write from read 1 after trimming. If there are fewer than 
-                                this many bases left after trimming, all will be written.  If this value is null then all 
-                                bases left after trimming will be written.  Default value: null. 
-  
+  R1_MAX_BASES=Integer          The maximum number of bases to write from read 1 after trimming. If there are fewer than
+                                this many bases left after trimming, all will be written.  If this value is null then all
+                                bases left after trimming will be written.  Default value: null.
+
   READ2_TRIM=Integer
-  R2_TRIM=Integer               The number of bases to trim from the beginning of read 2.  Default value: 0. 
-  
+  R2_TRIM=Integer               The number of bases to trim from the beginning of read 2.  Default value: 0.
+
   READ2_MAX_BASES_TO_WRITE=Integer
-  R2_MAX_BASES=Integer          The maximum number of bases to write from read 2 after trimming. If there are fewer than 
-                                this many bases left after trimming, all will be written.  If this value is null then all 
-                                bases left after trimming will be written.  Default value: null. 
-  
+  R2_MAX_BASES=Integer          The maximum number of bases to write from read 2 after trimming. If there are fewer than
+                                this many bases left after trimming, all will be written.  If this value is null then all
+                                bases left after trimming will be written.  Default value: null.
+
   INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean
-                                If true, include non-primary alignments in the output.  Support of non-primary alignments 
-                                in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and 
+                                If true, include non-primary alignments in the output.  Support of non-primary alignments
+                                in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and
                                 there are paired reads with non-primary alignments.  Default value: false.
-                                Possible values: {true, false} 
-  
+                                Possible values: {true, false}
+
 @more_info@
 
   </help>