cmbuild
        -F
        #if $is_summery_output:
            -o '$summary_outfile'
        #end if
        ## to many outputs, is that one really needed?
        ##-O $annotated_source_alignment_outfile
        $model_construction_opts.model_construction_opts_selector
        #if $model_construction_opts.model_construction_opts_selector == '--fast':
            --symfrac $model_construction_opts.symfrac
        #end if
        $noss
        $relative_weights_opts.relative_weights_opts_selector
        #if $relative_weights_opts.relative_weights_opts_selector == '--wblosum':
            --wid $relative_weights_opts.wid
        #end if
        --p7ere $controlling_filter_p7_hmm.p7ere
        $controlling_filter_p7_hmm.p7ml
        --EmN $controlling_filter_p7_hmm.EmN
        --EvN $controlling_filter_p7_hmm.EvN
        --ElfN $controlling_filter_p7_hmm.ElfN
        --EgfN $controlling_filter_p7_hmm.EgfN
        $effective_opts.effective_opts_selector
        #if str($effective_opts.effective_opts_selector) == '--eent':
            #if $effective_opts.ere
                --ere $effective_opts.ere
            #end if
            #if $effective_opts.eminseq
                --eminseq $effective_opts.eminseq
            #end if
            #if $effective_opts.emaxseq
                --emaxseq $effective_opts.emaxseq
            #end if
            #if $effective_opts.ehmmre
                --ehmmre $effective_opts.ehmmre
            #end if
            #if $effective_opts.eset
                --eset $effective_opts.eset
            #end if
        #end if
        #if str($refining_opts.refining_opts_selector) == '--refine':
            #if $refining_opts.refine_output:
                --refine '$refined_multiple_alignment_output'
            #else:
                --refine /dev/null
            #end if
            $refining_opts.l
            $refining_opts.gibbs_opts.gibbs_opts_selector
            #if str($refining_opts.gibbs_opts.gibbs_opts_selector) == '--gibbs':
                --seed $refining_opts.gibbs_opts.random_seed
            #end if
            $refining_opts.notrunc
            $refining_opts.cyk
        #end if
        '$cmfile_outfile'
        '$alignment_infile'


    #if $Calibrate.selector=="true"
        && cmcalibrate
            -L $Calibrate.L
            #if $Calibrate.output_options_cond.selector == "extra"
                #if str($Calibrate.output_options_cond.output_options) != 'None'
                    #for j in $Calibrate.output_options_cond.output_options.value:
                        --$j $getVar($j)
                    #end for
                #end if
            #end if
            #if $Calibrate.cont_exp_tails_fits.selector == "top_n"
                --gtailn $Calibrate.cont_exp_tails_fits.gtailn
                --ltailn $Calibrate.cont_exp_tails_fits.ltailn
            #elif $Calibrate.cont_exp_tails_fits.selector == "frac"
                --tailp $Calibrate.cont_exp_tails_fits.tailp
            #end if
            --seed $Calibrate.add_opts.seed
            --beta $Calibrate.add_opts.beta
            $Calibrate.add_opts.nonbanded
            $Calibrate.add_opts.nonull3
            $Calibrate.add_opts.random
            #if str($Calibrate.add_opts.gc) != 'None'
                --gc '$Calibrate.add_opts.gc'
            #end if
            --cpu "\${GALAXY_SLOTS:-2}"
            '$cmfile_outfile'
    #end if