#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
    
        export TERM="vt100"; 
        \${GALAXY_MPIRUN:-mpirun --allow-run-as-root --oversubscribe -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI  fel
            --alignment ./$input_file
            
            #if $input_nhx:
                --tree input.nhx
            #end if
        
            --code '$gencodeid'
            --multiple-hits $multiple_hits_conditional.multiple_hits
            
        #if $branch_cond.branch_sel == 'specify':
            --branches '$branch_cond.branch_label'
        #else:
            --branches $branch_cond.branch_sel
        #end if
        
            --srv '$include_srv'
            --pvalue '$p_value'
            
            #if $resample:
                --resample $resample
            #end if
        
            #if $restrict_sites_conditional.restrict_sites_flag == "true":
            --limit-to-sites '$restrict_sites_conditional.limit_to_sites'
            --save-lf-for-sites '$restrict_sites_conditional.save_lf_for_sites'
            #end if
            --precision $precision
            $ci
            --output '$fel_output'
            #if $multiple_hits_conditional.multiple_hits != "None":
            --site-multihit $multiple_hits_conditional.site_multihit
            #end if

            --kill-zero-lengths $kill_zero_lengths
            #if $full_model:
            --full-model $full_model
            #end if
            > fel_stdout.md 
        
        ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \$EC