#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
    
        hyphy fade
            --alignment $input_file
            
            #if $input_nhx:
                --tree input.nhx
            #end if
        
            
        #if $branch_cond.branch_sel == 'specify':
            --branches '$branch_cond.branch_label'
        #else:
            --branches $branch_cond.branch_sel
        #end if
        
            --model '$model'
            --method '$advanced_options.posteriorEstimationMethod.method'
            
            #if $posteriorEstimationMethod.method != "Variational-Bayes"
                --chains '$posteriorEstimationMethod.chains'
                --chain-length '$posteriorEstimationMethod.chain_length'
                --burn-in '$posteriorEstimationMethod.samples'
                --samples '$posteriorEstimationMethod.samples_per_chain'
            #end if
    
            --grid '$advanced_options.grid_points'
            --concentration_parameter '$advanced_options.concentration'
            --output '$fade_output'
            > fade_stdout.md 
        
        ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \$EC