#if $input_nhx is not None:
            ln -s '$input_nhx' input.nhx &&
        #end if
        ln -s '$input_file' input.$input_file.extension &&
        #set $input_file = 'input.%s' % $input_file.extension
    
        ENV="TOLERATE_NUMERICAL_ERRORS=1;" hyphy busted
            --alignment ./$input_file
            
            #if $input_nhx:
                --tree input.nhx
            #end if
        
            --code $gencodeid
            
        #if $branch_cond.branch_sel == 'specify':
            --branches '$branch_cond.branch_label'
        #else:
            --branches $branch_cond.branch_sel
        #end if
        
            --output '$busted_output'
            --syn-rates $advanced_options.syn_rates
            --rates $advanced_options.rates
            --grid-size $advanced_options.grid_size
            --starting-points $advanced_options.starting_points
            #if $advanced_options.multiple_hits != 'None':
                --multiple-hits $advanced_options.multiple_hits
            #end if
            #if $advanced_options.error_sink:
                --error-sink Yes
            #end if
            #if $advanced_options.save_alternative_model:
                --save-fit alternative_model.nhx
            #end if
            #if $advanced_options.mss.enabled == "true":
                --mss Yes
                --mss-type $advanced_options.mss.mss_type_cond.mss_type
                #if $advanced_options.mss.mss_type_cond.mss_type == "Random":
                    --mss-classes $advanced_options.mss.mss_type_cond.mss_classes
                #elif $advanced_options.mss.mss_type_cond.mss_type == "Empirical":
                    --mss-file $advanced_options.mss.mss_type_cond.mss_file
                #elif $advanced_options.mss.mss_type_cond.mss_type == "File":
                    --mss-file $advanced_options.mss.mss_type_cond.mss_file
                    --mss-neutral $advanced_options.mss.mss_type_cond.mss_neutral
                #elif $advanced_options.mss.mss_type_cond.mss_type == "Codon-file":
                    --mss-file $advanced_options.mss.mss_type_cond.mss_file
                    --mss-neutral $advanced_options.mss.mss_type_cond.mss_neutral
                #end if
            #end if
            --kill-zero-lengths $advanced_options.kill_zero_lengths
            > busted_stdout.md 
        
        ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \$EC