exonerate

        --query '$query'

        #if str( $ref_seq.ref_seq_selector ) == "personal"
            --target '${ref_seq.input_fasta}'
        #else
            --target '${ref_seq.input_fasta.fields.path}'
        #end if

        --score $score
        --percent $percent
        --bestn $bestn
        --verbose 0

        #if str($model) != "ungapped"
            --model '${model}'
        #end if

        #if str($model) == "est2genome"
            --querytype dna --targettype dna
        #elif str($model) == "protein2genome"
            --querytype protein --targettype dna
        #elif str($model) == "coding2coding"
            --querytype dna --targettype dna
        #end if

        #if $minintron
            --minintron ${minintron}
        #end if

        #if $maxintron
            --maxintron ${maxintron}
        #end if

        --cores \${GALAXY_SLOTS:-1}

        #if str($outformat) == "alignment"
            --showalignment yes --showvulgar no > '${output_ali}'
        #elif str($outformat) == "targetgff"
            --showalignment no --showvulgar no --showtargetgff yes --showquerygff no > '${output_gff}'
        #elif str($outformat) == "querygff"
            --showalignment no --showvulgar no --showtargetgff no --showquerygff yes > '${output_gff}'
        #end if

        ## Produce a more standard GFF3
        #if str($outformat) in ["targetgff", "querygff"]
            && python '$__tool_directory__/exonerategff_to_gff3.py' '${output_gff}' > '${output_gff3}'
        #end if