_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' &&
    

    picard SamToFastq

    --INPUT '$escaped_element_identifier'

    #if str($single_or_paired) == "pe_interleaved":
      --FASTQ '${interleaved_fastq}'
      --INTERLEAVE TRUE
    #else if str($single_or_paired) == "pe_sep":
      --F '${fq1}'
      --F2 '${fq2}'
      --FU '${fq_u}'
    #else
      --F '${fq_single}'
    #end if

    --RE_REVERSE '${re_reverse}'

    -INCLUDE_NON_PF_READS '${include_non_pf_reads}'
    #if len(str($clipping_attribute)) > 0:
       --CLIPPING_ATTRIBUTE '${clipping_attribute}'
    #end if
    #if len(str($clipping_action)) > 0:
       --CLIPPING_ACTION '${clipping_action}'
    #end if
    --READ1_TRIM '${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