#import re
        #set $filenames = list()
        ## Roary resolves symbolic links and breaks if there is whitespace in the path.
        ## Copying and renaming the files resolves that issue.
        #for $gff in $gff_input.gffs
            #set $filename = '%s.gff' % re.sub('[^\w_-]', '_', str($gff.element_identifier))
            cp '$gff' $filename &&
            $filenames.append(str($filename))
        #end for

        roary
            -f out
            -p \${GALAXY_SLOTS:-1}
            -e
            -z
            -n
            -i '$percent_ident'
            -cd '$core_diff'
            -g '$advanced.maxclust'
            $advanced.split_para
            -t '$advanced.trans_tab'
            -iv '$advanced.mcl'

            #for $f in $filenames
                '$f'
            #end for