mlocarna
    '$input_data'
    #if 'stockholm' in str($outputs).split(","):
    --stockholm
    #end if

    --tgtdir mlocarna_results
    ## maybe reenable later? see  https://github.com/s-will/LocARNA/issues/77
    ## --width 60
    
    ## -------------------- alignment mode and specific option--------- #
    #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
        $alignment_mode.free_endgaps
    #elif str($alignment_mode.alignment_mode_selector) == "local_locarna"
        --sequ-local on
    #elif str($alignment_mode.alignment_mode_selector) == "probabilistic"
        --probabilistic
        $alignment_mode.consistency_transformation
        
        #if str($alignment_mode.iterate) == "true"
            --iterate
            --iterations $alignment_mode.iterations
        #end if
    #elif str($alignment_mode.alignment_mode_selector) == "sparse"
        --sparse
    #end if
    
    
        ## -------------------- scoring parameters
        --indel $Scoring.indel
        --indel-opening $Scoring.indel_opening
        --struct-weight $Scoring.struct_weight
        --tau $Scoring.tau
        
        #if str($Scoring.sequence_score.sequence_score_selector) == "match"
            --match $Scoring.sequence_score.match
            --mismatch $Scoring.sequence_score.mismatch
        #elif str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
            --use-ribosum true
        #elif str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
            --ribofit true
        #end if
    

    
        ## -------------------- folding parameters
        #if float($Folding.rnafold_temperature) != 37.0
            --rnafold-temperature $Folding.rnafold_temperature
        #end if
    
    #if $Folding.plfold_span>=0
        --plfold-span $Folding.plfold_span
        --plfold-winsize $Folding.plfold_winsize
    #end if
    $Folding.alifold_consensus_dp

    
        ## -------------------- heuristic parameters
        -p $Heuristics.min_prob

        #if str($Heuristics.max_diff_mode.max_diff_mode_selector) == "off"
            --max-diff -1
        #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff"
            --max-diff $Heuristics.max_diff_mode.max_diff
        #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-at-am"
            --max-diff -1
            --max-diff-at-am $Heuristics.max_diff_mode.max_diff_at_am
        #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-aln"
            --max-diff $Heuristics.max_diff_mode.max_diff
            --max-diff-aln '$Heuristics.max_diff_mode.max_diff_aln'
            $Heuristics.max_diff_mode.max_diff_relax
        #end if
        
        --max-diff-am $Heuristics.max_diff_am
    
        #if float($Heuristics.max_bps_length_ratio) > 0.0
            --max-bps-length-ratio $Heuristics.max_bps_length_ratio
        #end if
    

    #if str($alignment_mode.alignment_mode_selector) == "sparse"
        --pw-aligner-options " 
           --prob-unpaired-in-loop $alignment_mode.HeuristicsSparse.prob_unpaired_in_loop_threshold
           --prob-basepair-in-loop $alignment_mode.HeuristicsSparse.prob_basepair_in_loop_threshold

     "
    #end if

    
    
        ## -------------------- constraint parameters
        $Constraints.lonely_pairs
        
        #if $Constraints.maxBPspan != -1
            --maxBPspan $Constraints.maxBPspan
        #end if

        $Constraints.ignore_constraints
    
    
    #if str($Constraints.bed_anchors.bed_anchors_selector) == "yes"
        --anchor-constraints $Constraints.bed_anchors.bed_anchors_file
    #end if

    
        $stdout_verbosity
        
        #if str($stdout_verbosity) != "--quiet":
            > '$stdout'
        #end if
    

    #if 'strict' in str($outputs).split(",")
        && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln
    #end if