_JAVA_OPTIONS=\${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=\${TMPDIR:-\${_GALAXY_JOB_TMPDIR}}"} &&
    export _JAVA_OPTIONS &&
    
    
    #import re
    #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
    ln -sf '$inputFile' '$escaped_element_identifier' &&
    
    #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
    ReorderSam
      --INPUT '$escaped_element_identifier'
      --OUTPUT '${outFile}'
      --SEQUENCE_DICTIONARY '${ref_fasta}'
      --ALLOW_INCOMPLETE_DICT_CONCORDANCE '${allow_incomplete_dict_concordance}'
      --ALLOW_CONTIG_LENGTH_DISCORDANCE '${allow_contig_length_discordance}'

      --VALIDATION_STRINGENCY '${validation_stringency}'
      --QUIET true
      --VERBOSITY ERROR