#import re

        ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
        ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
        #set $named_input_files = ''
        #for $input_file in $input_files
            ## Add single quotes around each input file identifier
            #set $_input_file = "'{}'".format($input_file.element_identifier)
            ln -s '${input_file}' ${_input_file} &&
            #set $named_input_files = $named_input_files + ' ' + $_input_file
        #end for

        mlst --nopath
        --threads "\${GALAXY_SLOTS:-1}"
        #if str($settings.advanced) == "advanced"
            #if str($settings.minid)
                --minid=$settings.minid
            #end if
            #if str($settings.mincov)
                --mincov=$settings.mincov
            #end if
            #if $settings.novel
                --novel '${novel_alleles}'
            #end if
            #if str($settings.scheme_condition.set_scheme) == "auto"
                #if str($settings.scheme_condition.minscore)
                    --minscore=$settings.scheme_condition.minscore
                #end if
                #if str($settings.scheme_condition.exclude)
                    --exclude '${settings.scheme_condition.exclude}'
                #end if
            #elif str($settings.scheme_condition.set_scheme) == "list" or str($settings.scheme_condition.set_scheme) == "manual"
                #if str($settings.scheme_condition.scheme)
                    --scheme='${settings.scheme_condition.scheme}'
                #end if
                $settings.scheme_condition.legacy
            #end if
        #end if
        ${named_input_files}
        > "$report"