cmalign
            ## Infernal Options
            --cpu "\${GALAXY_SLOTS:-2}"
            -o '$outfile'

            $alignment_algorithm_cont.alignment_algorithm.alignment_algorithm_selector
            #if $alignment_algorithm_cont.alignment_algorithm.alignment_algorithm_selector=="--sample"
                --seed $alignment_algorithm_cont.alignment_algorithm.seed
            #end if
            $alignment_algorithm_cont.notrunc_opt.notrunc
            #if $alignment_algorithm_cont.notrunc_opt.notrunc=="--notrunc"
                $alignment_algorithm_cont.notrunc_opt.sub
            #end if
            $speed_memory_cont.hmm_banding.banding_selector
            #if $speed_memory_cont.hmm_banding.banding_selector=="--hbanded"
                --tau $speed_memory_cont.hmm_banding.tau
                --mxsize $speed_memory_cont.hmm_banding.mxsize
                $speed_memory_cont.hmm_banding.fixedtau
                --maxtau $speed_memory_cont.hmm_banding.maxtau
            #end if
            #if $speed_memory_cont.hmm_banding.banding_selector=="--nonbanded"
                --mxsize $speed_memory_cont.hmm_banding.mxsize
            #end if

            #if $other_opts.mapali_opt.mapali_cond=="true"
                --mapali '$other_opts.mapali_opt.mapali'
                $other_opts.mapali_opt.mapstr
            #end if

            --informat $seqdb.ext
            --outformat $other_opts.outformat_selector
            $other_opts.dnaout
            $other_opts.noprob
            $other_opts.matchonly
            $other_opts.ileaved

            ##--small requirements according to cmalign.c

            #if $alignment_algorithm_cont.alignment_algorithm.alignment_algorithm_selector=="--cyk" \
                and $other_opts.noprob \
                and $speed_memory_cont.hmm_banding.banding_selector=="--nonbanded" \
                and $alignment_algorithm_cont.notrunc_opt.notrunc=="--notrunc"
                    $speed_memory_cont.small
            #end if

            ## CM file from the history or stored as database on disc
            #if $cm_opts.cm_opts_selector == "db":
                $cm_opts.database.fields.path
            #else:
                '$cm_opts.cmfile'
            #end if
            ## sequence file
            '$seqdb'