--- a/picard_MergeBamAlignment.xml	Sun Nov 27 15:11:50 2016 -0500
+++ b/picard_MergeBamAlignment.xml	Tue Dec 06 10:04:41 2016 -0500
@@ -8,29 +8,29 @@
     @java_options@
     #set $picard_dict = "localref.dict"
     #set $ref_fasta = "localref.fa"     ## This is done because picards "likes" .fa extension
-    
+
     ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
-       
+
     #if str( $reference_source.reference_source_selector ) == "history":
-        
+
       picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
       QUIET=true
       VERBOSITY=ERROR
-      
+
       &&
-      
+
     #else:
-    
+
       #set $ref_fasta = str( $reference_source.ref_file.fields.path )
-    
+
     #end if
-    
+
     picard
     MergeBamAlignment
       UNMAPPED_BAM="${unmapped_bam}"
-      
+
       PAIRED_RUN=true ##This argument is ignored and will be removed. Required. Possible values: {true, false}
-      
+
       #if str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_one_file":
         #for $dataset in $aligned_or_read1_and_read2.aligned_bams:
           ALIGNED_BAM="${dataset.aligned_bam}"
@@ -47,48 +47,48 @@
           READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}"
         #end for
       #end if
-     
+
       OUTPUT="${outFile}"
       REFERENCE_SEQUENCE="${ref_fasta}"
-      
+
       CLIP_ADAPTERS="${clip_adapters}"
       IS_BISULFITE_SEQUENCE="${is_bisulfite_sequence}"
       ALIGNED_READS_ONLY="${aligned_reads_only}"
       MAX_INSERTIONS_OR_DELETIONS="${max_insertions_or_deletions}"
-      
+
       #for $attribute in $attributes_to_retain:
         ATTRIBUTES_TO_RETAIN="${$attribute.attribute}"
       #end for
-      
+
       #for $attribute in $attributes_to_remove:
         ATTRIBUTES_TO_REMOVE="${$attribute.attribute}"
       #end for
-    
+
       READ1_TRIM="${read1_trim}"
       READ2_TRIM="${read2_trim}"
-      
+
       #if str( $orientations ) != "None":
         #for $orientation in str( $orientations ).split(','):   ## See trello card https://trello.com/c/9nW02Zhd
           EXPECTED_ORIENTATIONS="${orientation}"
         #end for
       #end if
-      
-      ALIGNER_PROPER_PAIR_FLAGS="${aligner_proper_pair_flags}"      
+
+      ALIGNER_PROPER_PAIR_FLAGS="${aligner_proper_pair_flags}"
       PRIMARY_ALIGNMENT_STRATEGY="${primary_alignment_strategy}"
       CLIP_OVERLAPPING_READS="${clip_overlapping_reads}"
       INCLUDE_SECONDARY_ALIGNMENTS="${include_secondary_alignments}"
       ADD_MATE_CIGAR="${add_mate_cigar}"
-      
+
       VALIDATION_STRINGENCY="${validation_stringency}"
 
       SORT_ORDER=coordinate
       QUIET=true
       VERBOSITY=ERROR
-      
+
   ]]></command>
-  
+
   <inputs>
-    
+
      <conditional name="reference_source">
       <param name="reference_source_selector" type="select" label="Load reference genome from">
         <option value="cached">Local cache</option>
@@ -103,11 +103,11 @@
           <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
         </param>
       </when>
-      <when value="history"> 
+      <when value="history">
         <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
       </when>
     </conditional>
-    
+
     <param format="sam,bam" name="unmapped_bam" type="data" label="Selected unaligned SAM or BAM with original reads" help="UNMAPPED_BAM; This dataset must be sorted in queryname order (use picard_SortSam to do this)" />
     <conditional name="aligned_or_read1_and_read2">
       <param name="aligned_or_read1_and_read2_selector" type="select" label="What type of aligned data do you have?">
@@ -134,39 +134,39 @@
         </repeat>
       </when>
     </conditional>
-    
+
     <param name="clip_adapters" type="boolean" checked="true" label="Whether to clip adapters where identified" help="CLIP_ADAPTERS; default=True"/>
     <param name="is_bisulfite_sequence" type="boolean" label="Whether the data is from bisulfite sequencing (used when caculating the NM tag)" help="IS_BISULFITE_SEQUENCE; default=False"/>
     <param name="aligned_reads_only" type="boolean" label="Whether to output only aligned reads" help="ALIGNED_READS_ONLY; default=False"/>
     <param name="max_insertions_or_deletions" type="integer" value="1" label="The maximum number of insertions or deletions permitted for an alignment to be included" help="MAX_INSERTIONS_OR_DELETIONS; Alignments with more than this many insertions or deletions will be ignored. Set to -1 to allow any number of insertions or deletions. default=1"/>
- 
+
     <repeat name="attributes_to_retain" title="Retain the following alignment attribute" min="0" help="You can provide multiple attributes">
       <param name="attribute" type="text" label="Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over from the alignment data when merging" help="ATTRIBUTES_TO_RETAIN; example: XA"/>
     </repeat>
-    
+
     <repeat name="attributes_to_remove" title="Remove the following alignment attribute" min="0" help="You can provide multiple attributes">
       <param name="attribute" type="text" label="Attributes from the alignment record that should be removed when merging." help="ATTRIBUTES_TO_REMOVE; This overrides ATTRIBUTES_TO_RETAIN if they share common tags"/>
     </repeat>
-    
+
     <param name="read1_trim" type="integer" value="0" label="The number of bases trimmed from the beginning of read 1 prior to alignment" help="READ1_TRIM; default=0"/>
     <param name="read2_trim" type="integer" value="0" label="The number of bases trimmed from the beginning of read 2 prior to alignment" help="READ2_TRIM; default=0"/>
-    
+
     <param name="orientations" type="select" multiple="True" display="checkboxes" label="The expected orientation of proper read pairs" help="EXPECTED_ORIENTATIONS; multiple orinetations can be selected">
       <option value="FR">Forward/Reverse (FR)</option>
       <option value="RF">Reverse/Forward (RF)</option>
       <option value="TANDEM">Tandem</option>
     </param>
- 
-    
+
+
     <param name="aligner_proper_pair_flags" type="boolean" label="Use the aligner's idea of what a proper pair is rather than computing in this program" help="ALIGNER_PROPER_PAIR_FLAGS; default=False"/>
-    
+
     <param name="primary_alignment_strategy" type="select" label="Strategy for selecting primary alignment when the aligner has provided more than one alignment for a pair or fragments" help="PRIMARY_ALIGNMENT_STRATEGY; see help below for more info; default=BestMapq">
       <option value="BestMapq" selected="True">BestMapq</option>
       <option value="EarliestFragment">EarliestFragment</option>
       <option value="BestEndMapq">BestEndMapq</option>
       <option value="MostDistant">MostDistant</option>
     </param>
-    
+
     <param name="clip_overlapping_reads" type="boolean" checked="True" label="For paired reads, soft clip the 3' end of each read if necessary so that it does not extend past the 5' end of its mate" help="CLIP_OVERLAPPING_READS; default=True"/>
     <param name="include_secondary_alignments" type="boolean" checked="True" label="If false, do not write secondary alignments to output" help="INCLUDE_SECONDARY_ALIGNMENTS; default=True"/>
     <param name="add_mate_cigar" type="boolean" checked="True" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
@@ -197,8 +197,8 @@
       <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
-  
-  
+
+
   <help>
 
 .. class:: infomark
@@ -212,96 +212,96 @@
 @description@
 
   UNMAPPED_BAM=File
-  UNMAPPED=File                 Original SAM or BAM file of unmapped reads, which must be in queryname order.  Required. 
-  
+  UNMAPPED=File                 Original SAM or BAM file of unmapped reads, which must be in queryname order.  Required.
+
   ALIGNED_BAM=File
-  ALIGNED=File                  SAM or BAM file(s) with alignment data.  This option may be specified 0 or more times.  
-                                Cannot be used in conjuction with option(s) READ1_ALIGNED_BAM (R1_ALIGNED) 
+  ALIGNED=File                  SAM or BAM file(s) with alignment data.  This option may be specified 0 or more times.
+                                Cannot be used in conjuction with option(s) READ1_ALIGNED_BAM (R1_ALIGNED)
                                 READ2_ALIGNED_BAM (R2_ALIGNED)
-  
+
   READ1_ALIGNED_BAM=File
-  R1_ALIGNED=File               SAM or BAM file(s) with alignment data from the first read of a pair.  This option may be 
-                                specified 0 or more times.  Cannot be used in conjuction with option(s) ALIGNED_BAM 
+  R1_ALIGNED=File               SAM or BAM file(s) with alignment data from the first read of a pair.  This option may be
+                                specified 0 or more times.  Cannot be used in conjuction with option(s) ALIGNED_BAM
                                 (ALIGNED)
-  
+
   READ2_ALIGNED_BAM=File
-  R2_ALIGNED=File               SAM or BAM file(s) with alignment data from the second read of a pair.  This option may 
-                                be specified 0 or more times.  Cannot be used in conjuction with option(s) ALIGNED_BAM 
+  R2_ALIGNED=File               SAM or BAM file(s) with alignment data from the second read of a pair.  This option may
+                                be specified 0 or more times.  Cannot be used in conjuction with option(s) ALIGNED_BAM
                                 (ALIGNED)
-  
+
   PAIRED_RUN=Boolean
-  PE=Boolean                    This argument is ignored and will be removed.  Required. Possible values: {true, false} 
-  
+  PE=Boolean                    This argument is ignored and will be removed.  Required. Possible values: {true, false}
+
   JUMP_SIZE=Integer
-  JUMP=Integer                  The expected jump size (required if this is a jumping library). Deprecated. Use 
-                                EXPECTED_ORIENTATIONS instead  Default value: null.  Cannot be used in conjuction with 
+  JUMP=Integer                  The expected jump size (required if this is a jumping library). Deprecated. Use
+                                EXPECTED_ORIENTATIONS instead  Default value: null.  Cannot be used in conjuction with
                                 option(s) EXPECTED_ORIENTATIONS (ORIENTATIONS)
-  
-  CLIP_ADAPTERS=Boolean         Whether to clip adapters where identified.  Default value: true. Possible values: {true, false} 
-  
-  IS_BISULFITE_SEQUENCE=Boolean Whether the lane is bisulfite sequence (used when caculating the NM tag).  Default value: 
-                                false. Possible values: {true, false} 
-  
-  ALIGNED_READS_ONLY=Boolean    Whether to output only aligned reads. Default value: false. Possible values: {true, false} 
-  
+
+  CLIP_ADAPTERS=Boolean         Whether to clip adapters where identified.  Default value: true. Possible values: {true, false}
+
+  IS_BISULFITE_SEQUENCE=Boolean Whether the lane is bisulfite sequence (used when caculating the NM tag).  Default value:
+                                false. Possible values: {true, false}
+
+  ALIGNED_READS_ONLY=Boolean    Whether to output only aligned reads. Default value: false. Possible values: {true, false}
+
   MAX_INSERTIONS_OR_DELETIONS=Integer
-  MAX_GAPS=Integer              The maximum number of insertions or deletions permitted for an alignment to be included. 
-                                Alignments with more than this many insertions or deletions will be ignored. Set to -1 to 
+  MAX_GAPS=Integer              The maximum number of insertions or deletions permitted for an alignment to be included.
+                                Alignments with more than this many insertions or deletions will be ignored. Set to -1 to
                                 allow any number of insertions or deletions.  Default value: 1.
-  
-  ATTRIBUTES_TO_RETAIN=String   Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over 
-                                from the alignment data when merging.  This option may be specified 0 or more times. 
-  
-  ATTRIBUTES_TO_REMOVE=String   Attributes from the alignment record that should be removed when merging.  This overrides 
-                                ATTRIBUTES_TO_RETAIN if they share common tags.  This option may be specified 0 or more 
-                                times. 
-  
+
+  ATTRIBUTES_TO_RETAIN=String   Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over
+                                from the alignment data when merging.  This option may be specified 0 or more times.
+
+  ATTRIBUTES_TO_REMOVE=String   Attributes from the alignment record that should be removed when merging.  This overrides
+                                ATTRIBUTES_TO_RETAIN if they share common tags.  This option may be specified 0 or more
+                                times.
+
   READ1_TRIM=Integer
-  R1_TRIM=Integer               The number of bases trimmed from the beginning of read 1 prior to alignment  Default 
-                                value: 0. 
-  
+  R1_TRIM=Integer               The number of bases trimmed from the beginning of read 1 prior to alignment  Default
+                                value: 0.
+
   READ2_TRIM=Integer
-  R2_TRIM=Integer               The number of bases trimmed from the beginning of read 2 prior to alignment  Default 
-                                value: 0. 
-  
+  R2_TRIM=Integer               The number of bases trimmed from the beginning of read 2 prior to alignment  Default
+                                value: 0.
+
   EXPECTED_ORIENTATIONS=PairOrientation
-  ORIENTATIONS=PairOrientation  The expected orientation of proper read pairs. Replaces JUMP_SIZE  Possible values: {FR, 
-                                RF, TANDEM} This option may be specified 0 or more times.  Cannot be used in conjuction 
+  ORIENTATIONS=PairOrientation  The expected orientation of proper read pairs. Replaces JUMP_SIZE  Possible values: {FR,
+                                RF, TANDEM} This option may be specified 0 or more times.  Cannot be used in conjuction
                                 with option(s) JUMP_SIZE (JUMP)
-  
+
   ALIGNER_PROPER_PAIR_FLAGS=Boolean
-                                Use the aligner's idea of what a proper pair is rather than computing in this program.  
-                                Default value: false. Possible values: {true, false} 
-  
+                                Use the aligner's idea of what a proper pair is rather than computing in this program.
+                                Default value: false. Possible values: {true, false}
+
   SORT_ORDER=SortOrder
   SO=SortOrder                  The order in which the merged reads should be output.  Default value: coordinate.
-                                Possible values: {unsorted, queryname, coordinate} 
-  
+                                Possible values: {unsorted, queryname, coordinate}
+
   PRIMARY_ALIGNMENT_STRATEGY=PrimaryAlignmentStrategy
-                                Strategy for selecting primary alignment when the aligner has provided more than one 
-                                alignment for a pair or fragment, and none are marked as primary, more than one is marked 
-                                as primary, or the primary alignment is filtered out for some reason. BestMapq expects 
-                                that multiple alignments will be correlated with HI tag, and prefers the pair of 
-                                alignments with the largest MAPQ, in the absence of a primary selected by the aligner. 
-                                EarliestFragment prefers the alignment which maps the earliest base in the read. Note 
-                                that EarliestFragment may not be used for paired reads. BestEndMapq is appropriate for 
-                                cases in which the aligner is not pair-aware, and does not output the HI tag. It simply 
-                                picks the alignment for each end with the highest MAPQ, and makes those alignments 
-                                primary, regardless of whether the two alignments make sense together.MostDistant is also 
-                                for a non-pair-aware aligner, and picks the alignment pair with the largest insert size. 
-                                If all alignments would be chimeric, it picks the alignments for each end with the best 
+                                Strategy for selecting primary alignment when the aligner has provided more than one
+                                alignment for a pair or fragment, and none are marked as primary, more than one is marked
+                                as primary, or the primary alignment is filtered out for some reason. BestMapq expects
+                                that multiple alignments will be correlated with HI tag, and prefers the pair of
+                                alignments with the largest MAPQ, in the absence of a primary selected by the aligner.
+                                EarliestFragment prefers the alignment which maps the earliest base in the read. Note
+                                that EarliestFragment may not be used for paired reads. BestEndMapq is appropriate for
+                                cases in which the aligner is not pair-aware, and does not output the HI tag. It simply
+                                picks the alignment for each end with the highest MAPQ, and makes those alignments
+                                primary, regardless of whether the two alignments make sense together.MostDistant is also
+                                for a non-pair-aware aligner, and picks the alignment pair with the largest insert size.
+                                If all alignments would be chimeric, it picks the alignments for each end with the best
                                 MAPQ.  For all algorithms, ties are resolved arbitrarily.  Default value: BestMapq.
-                                Possible values: {BestMapq, EarliestFragment, BestEndMapq, MostDistant} 
-  
-  CLIP_OVERLAPPING_READS=BooleanFor paired reads, soft clip the 3' end of each read if necessary so that it does not 
-                                extend past the 5' end of its mate.  Default value: true. Possible values: {true, false} 
-  
+                                Possible values: {BestMapq, EarliestFragment, BestEndMapq, MostDistant}
+
+  CLIP_OVERLAPPING_READS=BooleanFor paired reads, soft clip the 3' end of each read if necessary so that it does not
+                                extend past the 5' end of its mate.  Default value: true. Possible values: {true, false}
+
   INCLUDE_SECONDARY_ALIGNMENTS=Boolean
                                 If false, do not write secondary alignments to output.  Default value: true.
-                                Possible values: {true, false} 
-  
+                                Possible values: {true, false}
+
   ADD_MATE_CIGAR=Boolean
-  MC=Boolean                    Adds the mate CIGAR tag (MC) if true, does not if false. Possible values: {true, false} 
+  MC=Boolean                    Adds the mate CIGAR tag (MC) if true, does not if false. Possible values: {true, false}