#if $ref.ref_source == 'history':
            #if  $ref.ref_file.is_of_type('fasta'):
                #set $twobit_filename = "out.2bit"
                faToTwoBit '${ref.ref_file}' '$twobit_filename' -stripVersion &&
            #else:
                #set $twobit_filename = $ref.ref_file
            #end if
        #else:
            #set $twobit_filename = $ref.ref_loc.fields.path
        #end if
        find_nested_alt_orfs.py
            --twobit '$twobit_filename'

            --min_length '$min_length'

            --reference '${input.metadata.dbkey}'

            --bed '$input'

            #if $no_canonical_cds:
                --no_canonical_cds '$no_canonical_cds'
            #end if

            --translation_table '$translation_table'

            --bed_out '$bed_out'

            --peptide_fasta_out '$peptide_fasta_out'

            --naltorfs_fasta_out '$naltorfs_fasta_out'

            --cds_fasta_out '$cds_fasta_out'

            $unique_sequences

            #if $write_log:
                --log '$log'
            #end if