## Symlink files in with correct extensions
#for $file in $sequences:
    ln -s $file `basename $file`;
#end for

progressiveMauve
## Input Options

#if $apply_backbone:
    --apply-backbone=$apply_backbone
#end if
--island-gap-size=$island_gap_size
$mums

#if $seed_weight:
    --seed-weight=$seed_weight
#end if

#if $max_gapped_aligner_length:
    --max-gapped-aligner-length=$max_gapped_aligner_length
#end if

#if $match_input:
    --match-input=$match_input
#end if

$collinear
#if $input_guide_tree
    --input-guide-tree='$input_guide_tree'
#end if
--scoring-scheme=$scoring_scheme
$no_weight_scaling

--max-breakpoint-distance-scale=$max_breakpoint_distance_scale
--conservation-distance-scale=$conservation_distance_scale
$skip_refinement
$skip_gapped_alignment

#if $bp_dist_estimate_min_score:
    --bp-dist-estimate-min-score=$bp_dist_estimate_min_score
#end if

#if $gap_open:
    --gap-open=$gap_open
#end if
--repeat-penalty=$repeat_penalty
#if $gap_extend:
    --gap-extend=$gap_extend
#end if

#if $weight:
    --weight=$weight
#end if

#if $min_scaled_penalty:
    --min-scaled-penalty=$min_scaled_penalty
#end if

--hmm-p-go-homologous=$hmm_p_go_homologous
--hmm-p-go-unrelated=$hmm_p_go_unrelated
--hmm-identity=$hmm_identity

$seed_family
$solid_seeds
$coding_seeds
$no_recursion
$disable_backbone

## Outputs
--output=$output
#if $output_guide_tree:
    --output-guide-tree=$output_guide_tree_file
#end if

#if $backbone_output:
    --backbone-output=$output_backbone_file
#end if

## Sequences
#for file in $sequences:
    `basename "${file}"`
#end for