progressivemauve: progressivemauve.xml annotate

annotate progressivemauve.xml @ 2:bdb752f3c6bb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 7e386c24c2f9f0293abd4877eff708c1fa285751

author	iuc
date	Thu, 07 Feb 2019 05:24:24 -0500
parents	bca52822843e
children	4d869208bd52

rev	line source
0 74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	1 <?xml version="1.0"?>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	2 <tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.0">
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	3 <description>constructs multiple genome alignments</description>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	4 <macros>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	5 <import>macros.xml</import>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	6 </macros>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	7 <expand macro="requirements"/>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	8 <expand macro="stdio"/>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	9 <version_command>progressiveMauve --version</version_command>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	10 <command><![CDATA[
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	11 ## Symlink files in with correct extensions
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	12 #for $file in $sequences:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	13 ln -s $file `basename $file`;
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	14 #end for
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	15
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	16 progressiveMauve
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	17 ## Input Options
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	18
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	19 #if $apply_backbone:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	20 --apply-backbone=$apply_backbone
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	21 #end if
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	22 --island-gap-size=$island_gap_size
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	23 $mums
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	24
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	25 #if $seed_weight:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	26 --seed-weight=$seed_weight
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	27 #end if
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	28
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	29 #if $max_gapped_aligner_length:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	30 --max-gapped-aligner-length=$max_gapped_aligner_length
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	31 #end if
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	32
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	33 #if $match_input:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	34 --match-input=$match_input
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	35 #end if
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	36
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	37 $collinear
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	38 --scoring-scheme=$scoring_scheme
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	39 $no_weight_scaling
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	40
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	41 --max-breakpoint-distance-scale=$max_breakpoint_distance_scale
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	42 --conservation-distance-scale=$conservation_distance_scale
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	43 $skip_refinement
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	44 $skip_gapped_alignment
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	45
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	46 #if $bp_dist_estimate_min_score:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	47 --bp-dist-estimate-min-score=$bp_dist_estimate_min_score
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	48 #end if
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	49
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	50 #if $gap_open:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	51 --gap-open=$gap_open
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	52 #end if
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	53
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	54 #if $gap_extend:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	55 --gap-extend=$gap_extend
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	56 #end if
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	57
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	58 #if $weight:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	59 --weight=$weight
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	60 #end if
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	61
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	62 #if $min_scaled_penalty:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	63 --min-scaled-penalty=$min_scaled_penalty
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	64 #end if
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	65
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	66 --hmm-p-go-homologous=$hmm_p_go_homologous
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	67 --hmm-p-go-unrelated=$hmm_p_go_unrelated
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	68 --hmm-identity=$hmm_identity
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	69
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	70 $seed_family
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	71 $solid_seeds
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	72 $coding_seeds
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	73 $no_recursion
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	74 $disable_backbone
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	75
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	76 ## Outputs
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	77 --output=$output
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	78 #if $output_guide_tree:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	79 --output-guide-tree=$output_guide_tree_file
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	80 #end if
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	81
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	82 #if $output_backbone:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	83 --backbone-output=$output_backbone_file
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	84 #end if
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	85
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	86 ## Sequences
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	87 #for file in $sequences:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	88 `basename "${file}"`
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	89 #end for
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	90
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	91 ]]></command>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	92 <inputs>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	93 <param type="data" format="fasta" name="sequences" multiple="True"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	94 label="Select sequences to align" help="in fasta format" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	95 <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="True"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	96 help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	97
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	98 <param type="integer" label="Island gap size" value="20" name="island_gap_size"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	99 help="Alignment gaps above this size in nucleotides are considered to be islands (--island-gap-size)"/>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	100
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	101 <param type="boolean" truevalue="--disable-backbone" falsevalue="" name="disable_backbone"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	102 label="Disable backbone" help="Disable backbone detection (--disable-backbone)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	103
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	104 <param type="boolean" truevalue="True" falsevalue="" name="output_guide_tree"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	105 label="Output Guide Tree" help="Write out the guide tree used for alignment to a file (--output-guide-tree)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	106
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	107 <param type="boolean" truevalue="True" falsevalue="" name="output_backbone"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	108 label="Output Backbone" help="Write out the backbone to a file (--backbone-output)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	109
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	110 <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" name="mums"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	111 help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs) (--mums)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	112
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	113 <param type="integer" label="Seed weight" name="seed_weight" value="0" optional="True"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	114 help="Use the specified seed weight for calculating initial anchors (--seed-weight)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	115
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	116 <param type="data" format="tabular" label="Match Input" name="match_input" optional="True"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	117 help="Use specified match file instead of searching for matches (--match-input)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	118
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	119 <!--<param type="file" label="input-id-matrix" help="An identity matrix describing similarity among all pairs of input sequences/alignments (- -input-id-matrix)" />-->
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	120 <param type="integer" label="Max gapped aligner length" value="0" optional="True" name="max_gapped_aligner_length"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	121 help="Maximum number of base pairs to attempt aligning with the gapped aligner (--max-gapped-aligner-length)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	122
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	123 <param type="data" format="nhx" label="input-guide-tree" optional="True" name="input_guide_tree"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	124 help="A phylogenetic guide tree in Newick format that describes the order in which sequences will be aligned (--input-guide-tree)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	125
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	126 <param type="boolean" truevalue="--collinear" falsevalue="" label="Collinear inputs" name="collinear"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	127 help="Assume that input sequences are collinear--they have no rearrangements (--collinear)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	128
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	129 <param type="select" label="Scoring scheme" name="scoring_scheme" help="Selects the anchoring score function. (--scoring-scheme)" >
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	130 <option value="sp" selected="True">Extant sum-of-pairs (sp)</option>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	131 <option value="ancestral_sp">Sum-of-pairs + Ancestral (ancestral_sp)</option>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	132 <option value="ancestral">Ancestral (ancestral)</option>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	133 </param>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	134
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	135 <param type="boolean" truevalue="--no-weight-scaling" falsevalue="" label="No weight scaling" name="no_weight_scaling"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	136 help="Don't scale LCB weights by conservation distance and breakpoint distance (--no-weight-scaling)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	137
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	138 <param type="float" min="0" max="1" label="max-breakpoint-distance-scale" value="0.5" name="max_breakpoint_distance_scale"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	139 help="Set the maximum weight scaling by breakpoint distance. (--max-breakpoint-distance-scale)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	140
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	141 <param type="float" min="0" max="1" label="conservation-distance-scale" value="0.5" name="conservation_distance_scale"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	142 help="Scale conservation distances by this amount. (--conservation-distance-scale)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	143
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	144 <param type="boolean" truevalue="--skip-refinement" falsevalue="" label="Skip refinement" name="skip_refinement"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	145 help="Do not perform iterative refinement (--skip-refinement)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	146 <param type="boolean" truevalue="--skip-gapped-alignment" falsevalue="" label="Skip gapped alignment" name="skip_gapped_alignment"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	147 help="Do not perform gapped alignment (--skip-gapped-alignment)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	148 <param type="integer" label="BP dist estimate min score" name="bp_dist_estimate_min_score" value="0" optional="True"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	149 help="Minimum LCB score for estimating pairwise breakpoint distance (--bp-dist-estimate-min-score)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	150
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	151 <param type="integer" label="Gap open" name="gap_open" value="0" optional="True"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	152 help="Gap open penalty (--gap-open)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	153
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	154 <param type="select" label="Repeat penalty" name="repeat_penalty"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	155 help="Sets whether the repeat scores go negative or go to zero for highly repetitive sequences. (--repeat-penalty)">
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	156 <option value="negative" selected="True">Negative</option>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	157 <option value="zero">Zero</option>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	158 </param>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	159
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	160 <param type="integer" label="Gap extend" name="gap_extend" value="0" optional="True"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	161 help="Gap extend penalty (--gap-extend)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	162
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	163 <!--<param type="data" label="Substitution matrix" -->
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	164 <!--help="Nucleotide substitution matrix in NCBI format (- -substitution-matrix)" />-->
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	165
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	166 <param type="integer" label="Weight" name="weight" value="0" optional="True"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	167 help="Minimum pairwise LCB score (--weight)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	168 <param type="integer" label="Min scaled penalty" name="min_scaled_penalty" value="0" optional="True"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	169 help="Minimum breakpoint penalty after scaling the penalty by expected divergence (--min-scaled-penalty)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	170
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	171 <param type="float" label="HMM p go homologous" name="hmm_p_go_homologous" min="0" max="1" value="0.00001"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	172 help="Probability of transitioning from the unrelated to the homologous state (--hmm-p-go-homologous)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	173 <param type="float" label="HMM p go unrelated" name="hmm_p_go_unrelated" min="0" max="1" value="0.000000001"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	174 help="Probability of transitioning from the homologous to the unrelated state (--hmm-p-go-unrelated)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	175 <param type="float" label="HMM identity" name="hmm_identity" min="0" max="1" value="0.7"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	176 help="Expected level of sequence identity among pairs of sequences(--hmm-identity)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	177
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	178 <param type="boolean" truevalue="--seed-family" falsevalue="" label="Seed family" name="seed_family"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	179 help="Use a family of spaced seeds to improve sensitivity (--seed-family)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	180 <param type="boolean" truevalue="--solid-seeds" falsevalue="" label="Solid seeds" name="solid_seeds"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	181 help="Use solid seeds. Do not permit substitutions in anchor matches. (--solid-seeds)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	182 <param type="boolean" truevalue="--coding-seeds" falsevalue="" label="Coding seeds" name="coding_seeds"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	183 help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy. (--coding-seeds)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	184 <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" name="no_recursion"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	185 help="Disable recursive anchor search (--no-recursion)" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	186 </inputs>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	187 <outputs>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	188 <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}">
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	189 <change_format>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	190 <when input="mums" value="--mums" format="tabular" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	191 </change_format>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	192 </data>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	193 <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree">
1 bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7 iuc parents: 0 diff changeset	194 <filter>output_guide_tree</filter>
0 74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	195 </data>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	196 <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone">
2 bdb752f3c6bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 7e386c24c2f9f0293abd4877eff708c1fa285751 iuc parents: 1 diff changeset	197 <filter>output_backbone</filter>
0 74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	198 </data>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	199 </outputs>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	200 <tests>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	201 <test>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	202 <param name="sequences" value="phagey.fa,karma.fa" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	203 <output name="output" file="1.xmfa" lines_diff="20"/>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	204 </test>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	205 <test>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	206 <param name="sequences" value="merged.fa" />
1 bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7 iuc parents: 0 diff changeset	207 <output name="output" file="2.xmfa" lines_diff="20"/>
0 74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	208 </test>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	209 <test>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	210 <param name="sequences" value="merged.fa" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	211 <param name="output_guide_tree" value="True" />
1 bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7 iuc parents: 0 diff changeset	212 <output name="output" file="2.xmfa" lines_diff="20"/>
0 74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	213 <output name="output_guide_tree_file" file="1.nhx" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	214 </test>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	215 <test>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	216 <param name="sequences" value="merged.fa" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	217 <param name="mums" value="True" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	218 <output name="output" file="1.mums" compare="sim_size" delta="1000"/>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	219 </test>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	220 <test>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	221 <param name="sequences" value="merged.fa" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	222 <param name="match_input" value="1.mums" />
1 bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7 iuc parents: 0 diff changeset	223 <output name="output" file="2.xmfa" lines_diff="24"/>
0 74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	224 </test>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	225 </tests>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	226 <help><![CDATA[
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	227 What it does
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	228 ============
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	229
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	230 Mauve is a system for efficiently constructing multiple genome alignments in
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	231 the presence of large-scale evolutionary events such as rearrangement and
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	232 inversion. Multiple genome alignment provides a basis for research into
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	233 comparative genomics and the study of evolutionary dynamics. Aligning whole
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	234 genomes is a fundamentally different problem than aligning short sequences.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	235
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	236 Mauve has been developed with the idea that a multiple genome aligner should
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	237 require only modest computational resources. It employs algorithmic techniques
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	238 that scale well in the amount of sequence being aligned. For example, a pair of
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	239 Y. pestis genomes can be aligned in under a minute, while a group of 9
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	240 divergent Enterobacterial genomes can be aligned in a few hours.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	241
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	242 progressiveMauve XMFA alignment visualized with the Mauve tool:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	243
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	244 .. image:: $PATH_TO_IMAGES/hemolysin.jpg
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	245
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	246 Example Usage
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	247 =============
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	248
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	249 +-----------------------------------+-------------+
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	250 \| Usage \| Notes \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	251 +===================================+=============+
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	252 \| Align genomes \|Simply \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	253 \| \|select as \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	254 \| \|many fasta \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	255 \| \|files with \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	256 \| \|one or more \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	257 \| \|sequences as \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	258 \| \|necessary \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	259 +-----------------------------------+-------------+
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	260 \| Align genomes but also save \|Use the \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	261 \| the guide tree and produce a \|**Output \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	262 \| backbone file \|Guide Tree** \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	263 \| \|and **Output \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	264 \| \|Backbone** \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	265 \| \|options \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	266 +-----------------------------------+-------------+
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	267 \| Align genomes, but do not \|Use the \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	268 \| detect forced alignment of \|**Disable \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	269 \| unrelated sequences \|backbone** \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	270 \| \|option \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	271 +-----------------------------------+-------------+
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	272 \| Detect forced alignment of \|Use the \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	273 \| unrelated sequence in the \|**Apply \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	274 \| alignment produced \|Backbone** \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	275 \| in previous example, use \|option and \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	276 \| custom Homology HMM transition \|specify the \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	277 \| parameters. \|XMFA file \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	278 \| \|produced \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	279 \| \|in the \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	280 \| \|previous \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	281 \| \|example \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	282 +-----------------------------------+-------------+
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	283 \| Compute ungapped \|Use the \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	284 \| local-multiple alignments among \|MUMs \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	285 \| the input sequences \|option \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	286 +-----------------------------------+-------------+
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	287 \| Compute an alignment of the \|Set the \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	288 \| same genomes, using previously \|**Match \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	289 \| computed local-multiple \|Input** to \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	290 \| alignments \|the tabular \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	291 \| \|MUMs file \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	292 \| \|produced in \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	293 \| \|the previous \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	294 \| \|example \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	295 +-----------------------------------+-------------+
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	296 \| Set a minimum scaled \|Use the \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	297 \| breakpoint penalty to cope with \|**Min Scaled \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	298 \| the case where most genomes \|Penalty** and\|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	299 \| are aligned correctly, but manual \|set to a \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	300 \| inspection reveals that \|value like \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	301 \| a divergent genome has too \|5000 \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	302 \| many predicted rearrangements. \| \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	303 +-----------------------------------+-------------+
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	304 \| Globally align a set of \|Use the \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	305 \| collinear virus \|Colinear,\|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	306 \| genomes, using seed families \|**Seed \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	307 \| to improve anchoring sensitivity \|Family** \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	308 \| in regions below 70% sequence \|options \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	309 \| identity. \| \|
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	310 +-----------------------------------+-------------+
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	311
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	312
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	313 The progressiveMauve algorithm: addressing limitations of the original algorithm
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	314 ================================================================================
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	315
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	316 Comparative genomics has revealed that closely-related bacteria often have
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	317 highly divergent gene content. While the original Mauve algorithm could align
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	318 regions conserved among all organisms, the portion of the genome conserved
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	319 among all taxa (the core genome) shrinks as more taxa are added to the
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	320 analysis. As such, the original Mauve algorithm did not scale well to large
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	321 numbers of taxa because it could not align regions conserved among subsets of
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	322 the genomes under study. progressiveMauve employs a different algorithmic
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	323 approach to scoring alignments that allows alignment of segments conserved
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	324 among subsets of taxa. The progressiveMauve algorithm has been described in
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	325 Aaron Darling's Ph.D. Thesis, and is also the subject of a manuscript published
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	326 in PLoS ONE. A brief overview is given here.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	327
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	328 Finding initial local multiple alignments
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	329 -----------------------------------------
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	330
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	331 progressiveMauve elaborates on the original algorithm for finding local
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	332 multiple alignments. Instead of using a single seed pattern for match
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	333 filtration, progressiveMauve uses a combination of three seed patterns for
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	334 improved sensitivity. The palindromic seed patterns have been described in
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	335 Darling et al. 2006 "Procrastination leads to efficient filtration for local
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	336 multiple alignment"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	337
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	338 Seed matches which represent a unique subsequence shared by two or more input
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	339 genomes are subjected to ungapped extension until the seed pattern no longer
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	340 matches. The result is an ungapped local multiple alignment with at most one
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	341 component from each of the input genome sequences.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	342
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	343 Computing a pairwise genome content distance matrix and guide tree
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	344 ------------------------------------------------------------------
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	345
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	346 progressiveMauve builds up genome alignments progressively according to a guide
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	347 tree. The guide tree is computed based on an estimate of the shared gene
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	348 content among each pair of input genomes. For a pair of input genomes, g.x and
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	349 g.y, shared gene content is estimated by counting the number of nucleotides in
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	350 gx and gy aligned to each other in the initial set of local multiple
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	351 alignments. The count is normalized to a similarity value between 0 and 1 by
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	352 dividing by the average size of gx and gy. The similarity value is subtracted
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	353 from 1 to arrive at a distance estimate. Neighbor joining is then applied to
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	354 the matrix of distance estimates to yield a guide tree topology. Note that the
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	355 guide tree is not intended to be a phylogeny indicative of the genealogy of
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	356 input genomes. It is merely a computational crutch for progressive genome
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	357 alignment. Also note that alignments are later refined independently of a
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	358 single guide tree toplogy to avoid biasing later phylogenetic inference.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	359
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	360 Computing a pairwise breakpoint distance matrix
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	361 -----------------------------------------------
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	362
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	363 Prior to alignment, progressiveMauve attempts to compute a conservative
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	364 estimate of the number of rearrangement breakpoints among any pair of genomes.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	365 For each pair of genomes, pairwise alignments are created from the
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	366 local-multiple alignments and the pairwise alignments are subjected to greedy
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	367 breakpoint elimination. The breakpoint penalty used for greedy breakpoint
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	368 elimination is set high for closely related genomes and scaled downward
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	369 according to the estimate of genomic content distance. Because the breakpoint
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	370 penalty is high, the resulting set of locally collinear blocks represent
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	371 robustly supported segmental homology, and a conservative estimate of the
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	372 breakpoint distance can be made on this basis. The conservative estimate of
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	373 breakpoint distance is used later during progressive alignment to scale
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	374 breakpoint penalties.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	375
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	376 Progressive genome alignment
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	377 ----------------------------
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	378
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	379 A genome alignment is progressively built up according to the guide tree. At
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	380 each step of the progressive genome alignment, alignment anchors are selected
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	381 from the initial set of local multiple alignments. Anchors are selected so that
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	382 they maximize a Sum-of-pairs scoring scheme which applies a penalty for
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	383 predicting breakpoints among any pair of genomes. Because rates of genomic
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	384 rearrangement are highly variable, especially in some bacterial pathogens, some
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	385 genomes may be expected to exhibit greater rearrangement than others. As such,
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	386 a single choice of scoring penalty is unlikely to yield accurate alignments for
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	387 all genomes. To cope with this phenomenon, progressiveMauve scales the
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	388 breakpoint penalty according to the expected level of sequence divergence and
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	389 the number of well-supported genomic rearrangements among the pair of input
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	390 genomes. These scaling values are taken from the distance matrices computed
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	391 earlier in the algorithm.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	392
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	393 Anchored alignment
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	394 ------------------
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	395
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	396 Once anchors have been computed at a node in the guide tree, a global alignment
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	397 is computed on the basis of the anchors. Given a set of anchors among two
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	398 genomes, a genome and an alignment, or a pair of alignments, a modified MUSCLE
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	399 global alignment algorithm is applied to compute an anchored profile-profile
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	400 alignment. MUSCLE is then used to perform tree-independent iterative refinement
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	401 on the global genome alignment.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	402
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	403 Rejecting alignment of unrelated sequence
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	404 -----------------------------------------
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	405
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	406 Although we compute a global alignment among sequences, genomes often contain
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	407 lineage-specific sequence and are thus not globally related. The global
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	408 alignment will often contain forced alignment of unrelated sequence. A simple
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	409 hidden Markov model structure is used to detect forced alignment of unrelated
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	410 sequence, which are then removed from the alignment.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	411
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	412 Strengths of the progressiveMauve algorithm
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	413 -------------------------------------------
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	414
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	415 - It can be applied to a much larger number of genomes than the original Mauve
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	416 algorithm
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	417 - It can align more divergent genomes than the original algorithm. Genomes
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	418 with as little as 50% nucleotide identity can be alignable
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	419 - Manual adjustment of the alignment scoring parameters is usually not
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	420 necessary
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	421 - It aligns the pan-genome, e.g. regions conserved among subsets of the input
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	422 genomes
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	423 - It is more accurate than the previous Mauve algorithm
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	424
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	425 Notes on Reproducibility
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	426 ------------------------
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	427
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	428 The command line programme progressiveMauve seems to behave differently when::
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	429
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	430 --max-breakpoint-distance-scale=0.5 --conservation-distance-scale=0.5
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	431
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	432 are passed to the tool, compared to when those options are not passed. This
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	433 means that if you wish to precisely replicate the results you see in Galaxy at
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	434 the command line, you'll need to pass these flags with their "default" values.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	435
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	436 @ATTRIBUTION@
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	437 ]]></help>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	438 <expand macro="citation" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8 iuc parents: diff changeset	439 </tool>

Mercurial > repos > iuc > progressivemauve

annotate progressivemauve.xml @ 2:bdb752f3c6bb draft