_JAVA_OPTIONS=\${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=\${TMPDIR:-\${_GALAXY_JOB_TMPDIR}}"} &&
    export _JAVA_OPTIONS &&
    
    #set $picard_dict = "localref.dict"
    #set $ref_fasta = "localref.fa"     ## This is done because picards "likes" .fa extension

    ln -sf '${reference_source.ref_file}' '${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}'
        #end for
      #elif str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_two_files":
        #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams:
            --READ1_ALIGNED_BAM '${dataset.read1_aligned_bam}'
        #end for
        #for $dataset in $aligned_or_read1_and_read2.read2_aligned_bams:
            --READ2_ALIGNED_BAM '${dataset.read2_aligned_bam}'
        #end for
      #else
        #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams:
            --READ1_ALIGNED_BAM '${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 '${aligner_proper_pair_flags}'
      --PRIMARY_ALIGNMENT_STRATEGY '${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