_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 up input files

    #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
    

    picard CollectAlignmentSummaryMetrics
    --INPUT '$escaped_element_identifier'
    --OUTPUT '${outFile}'
    --MAX_INSERT_SIZE ${maxinsert}
    #for $sequence in $adapters:
        --ADAPTER_SEQUENCE '${sequence.adapter}'
    #end for
    #for $level in str($metric_accumulation_level).split(','):
        --METRIC_ACCUMULATION_LEVEL '${level}'
    #end for
    --IS_BISULFITE_SEQUENCED '${bisulphite}'

    --REFERENCE_SEQUENCE '${reference_fasta_filename}'

    --ASSUME_SORTED '${assume_sorted}'

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