##set the maximum number of open file to hard maximum or 4096 if on a mac (mac gives 'unlimited' as output of `ulimit -Hn` command

    [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn`

    &&

    ##set up input files
    
    #import re
    #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
    ln -sf '$inputFile' '$escaped_element_identifier' &&
    
    #set $reference_fasta_filename = "localref.fa"

    #if str( $reference_source.reference_source_selector ) == "history":
        ln -sf '${reference_source.ref_file}' '${reference_fasta_filename}' &&
    #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if

    
    _JAVA_OPTIONS=\${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=\${TMPDIR:-\${_GALAXY_JOB_TMPDIR}}"} &&
    export _JAVA_OPTIONS &&
    

    picard ValidateSamFile

    --INPUT '$escaped_element_identifier'
    --OUTPUT '${outFile}'
    --MODE '${mode}'

    #if str( $ignore ) != "None":
      #for $element in str( $ignore ).split(','):   ## See trello card https://trello.com/c/9nW02Zhd
        --IGNORE '${element}'
      #end for
    #end if

    --MAX_OUTPUT '${max_output}'
    --REFERENCE_SEQUENCE '${reference_fasta_filename}'
    --IGNORE_WARNINGS '${ignore_warnings}'
    --IS_BISULFITE_SEQUENCED '${is_bisulfite_sequenced}'
    --MAX_OPEN_TEMP_FILES `ulimit -Sn`

    --VERBOSITY ERROR
    --QUIET true