if [[ -n "\$GALAXY_MEMORY_MB" ]]; then
    MEMORY="-m \$((GALAXY_MEMORY_MB * 1024))";
fi;

megahit
    --num-cpu-threads \${GALAXY_SLOTS:-4}
    #if $input_option.choice == 'paired'
        -1 '${input_option.fastq_input1}'
        -2 '${input_option.fastq_input2}'
    #else if $input_option.choice == 'paired_collection'

        #if $input_option.batchmode.processmode == 'merge':
            -1 ${ ','.join(['"%s"' % x.forward for x in $input_option.batchmode.pair_input_list]) }
            -2 ${ ','.join(['"%s"' % x.reverse for x in $input_option.batchmode.pair_input_list]) }
        #else:
            -1 '${input_option.batchmode.pair_input.forward}'
            -2 '${input_option.batchmode.pair_input.reverse}'
        #end if
    #else if $input_option.choice == 'interleaved'
        --12 '${input_option.interleaved_file}'
    #else
        -r '${input_option.single_files}'
    #end if
    ##basic assembly
    --min-count '${basic_section.min_count}'
    #if $basic_section.k_mer.k_mer_method == "klist_method":
        --k-list '${basic_section.k_mer.k_list}'
    #else:
        --k-step '${basic_section.k_mer.k_step}'
        --k-min '${basic_section.k_mer.k_min}'
        --k-max '${basic_section.k_mer.k_max}'
    #end if
    ##advanced assembly
    ${advanced_section.nomercy}
    --bubble-level '${advanced_section.bubble_level}'
    --merge-level '${advanced_section.merge_level}'
    --prune-level '${advanced_section.prune_level}'
    --prune-depth '${advanced_section.prune_depth}'
	--disconnect-ratio '${advanced_section.disconnect_ratio}'
    --low-local-ratio '${advanced_section.low_local_ratio}'
	--cleaning-rounds '${advanced_section.cleaning_rounds}'					  
    ${advanced_section.nolocal}
    ${advanced_section.kmin1pass}
    --min-contig-len '${output_section.min_contig_len}'
    \$MEMORY