_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 $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 CollectSequencingArtifactMetrics 
    --I '$escaped_element_identifier'
    --O 'OutPut'
    --R '${reference_fasta_filename}'
    --AS ${assume_sorted}
    --CONTEXT_SIZE ${context_size}
    --INCLUDE_DUPLICATES '${duplicates}'
    #if $contexts_to_print 
        #for $context in str($contexts_to_print).split(','):
          --CONTEXTS_TO_PRINT '${context}'
        #end for;
    #end if;
    --MINIMUM_QUALITY_SCORE '${min_quality_score}'
    --INCLUDE_UNPAIRED '${unpaired}'
    --MAXIMUM_INSERT_SIZE '${max_size}'
    --MINIMUM_INSERT_SIZE '${min_size}'
    --MINIMUM_MAPPING_QUALITY '${minim_map_quality}'
    --VALIDATION_STRINGENCY '${validation_stringency}';