annotate progressivemauve.xml @ 3:97a43bcbf44d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fc61c9d4850614a6580d25f92e3032dc8edbc10d"
author iuc
date Fri, 26 Jun 2020 05:35:25 -0400
parents bdb752f3c6bb
children 4d869208bd52
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74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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1 <?xml version="1.0"?>
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2 <tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.0">
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3 <description>constructs multiple genome alignments</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <version_command>progressiveMauve --version</version_command>
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10 <command><![CDATA[
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11 ## Symlink files in with correct extensions
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12 #for $file in $sequences:
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13 ln -s $file `basename $file`;
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14 #end for
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16 progressiveMauve
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17 ## Input Options
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19 #if $apply_backbone:
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20 --apply-backbone=$apply_backbone
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21 #end if
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22 --island-gap-size=$island_gap_size
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23 $mums
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25 #if $seed_weight:
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26 --seed-weight=$seed_weight
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27 #end if
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29 #if $max_gapped_aligner_length:
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30 --max-gapped-aligner-length=$max_gapped_aligner_length
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31 #end if
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33 #if $match_input:
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34 --match-input=$match_input
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35 #end if
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37 $collinear
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38 --scoring-scheme=$scoring_scheme
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39 $no_weight_scaling
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41 --max-breakpoint-distance-scale=$max_breakpoint_distance_scale
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42 --conservation-distance-scale=$conservation_distance_scale
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43 $skip_refinement
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44 $skip_gapped_alignment
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46 #if $bp_dist_estimate_min_score:
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47 --bp-dist-estimate-min-score=$bp_dist_estimate_min_score
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48 #end if
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50 #if $gap_open:
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51 --gap-open=$gap_open
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52 #end if
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54 #if $gap_extend:
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55 --gap-extend=$gap_extend
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56 #end if
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57
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58 #if $weight:
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59 --weight=$weight
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60 #end if
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61
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62 #if $min_scaled_penalty:
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63 --min-scaled-penalty=$min_scaled_penalty
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64 #end if
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65
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66 --hmm-p-go-homologous=$hmm_p_go_homologous
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67 --hmm-p-go-unrelated=$hmm_p_go_unrelated
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68 --hmm-identity=$hmm_identity
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69
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70 $seed_family
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71 $solid_seeds
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72 $coding_seeds
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73 $no_recursion
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74 $disable_backbone
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75
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76 ## Outputs
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77 --output=$output
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78 #if $output_guide_tree:
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79 --output-guide-tree=$output_guide_tree_file
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80 #end if
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81
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82 #if $output_backbone:
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83 --backbone-output=$output_backbone_file
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84 #end if
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85
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86 ## Sequences
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87 #for file in $sequences:
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88 `basename "${file}"`
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89 #end for
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90
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91 ]]></command>
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92 <inputs>
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93 <param type="data" format="fasta" name="sequences" multiple="True"
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94 label="Select sequences to align" help="in fasta format" />
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95 <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="True"
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96 help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" />
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97
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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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
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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
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100
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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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
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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
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diff changeset
109
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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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
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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
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diff changeset
112
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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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
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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
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diff changeset
115
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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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
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diff changeset
118
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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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
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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:
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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
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125
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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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:
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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
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diff changeset
128
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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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
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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
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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
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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
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diff changeset
133 </param>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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134
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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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
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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
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diff changeset
137
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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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:
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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
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diff changeset
140
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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parents:
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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
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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:
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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
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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
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diff changeset
150
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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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
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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:
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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
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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
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157 <option value="zero">Zero</option>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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diff changeset
158 </param>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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parents:
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159
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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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
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162
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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parents:
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163 <!--<param type="data" label="Substitution matrix" -->
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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parents:
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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
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165
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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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:
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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:
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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:
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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
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parents:
diff changeset
170
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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parents:
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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:
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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:
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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:
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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:
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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
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parents:
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177
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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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
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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:
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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:
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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:
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183 help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy. (--coding-seeds)" />
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184 <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" name="no_recursion"
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185 help="Disable recursive anchor search (--no-recursion)" />
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186 </inputs>
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187 <outputs>
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188 <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}">
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189 <change_format>
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190 <when input="mums" value="--mums" format="tabular" />
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191 </change_format>
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192 </data>
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193 <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree">
1
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194 <filter>output_guide_tree</filter>
0
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195 </data>
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196 <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone">
2
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197 <filter>output_backbone</filter>
0
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198 </data>
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199 </outputs>
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200 <tests>
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201 <test>
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202 <param name="sequences" value="phagey.fa,karma.fa" />
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203 <output name="output" file="1.xmfa" lines_diff="20"/>
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204 </test>
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205 <test>
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206 <param name="sequences" value="merged.fa" />
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207 <output name="output" file="2.xmfa" lines_diff="20"/>
0
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208 </test>
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209 <test>
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210 <param name="sequences" value="merged.fa" />
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211 <param name="output_guide_tree" value="True" />
1
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212 <output name="output" file="2.xmfa" lines_diff="20"/>
0
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213 <output name="output_guide_tree_file" file="1.nhx" />
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214 </test>
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215 <test>
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216 <param name="sequences" value="merged.fa" />
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217 <param name="mums" value="True" />
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218 <output name="output" file="1.mums" compare="sim_size" delta="1000"/>
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219 </test>
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220 <test>
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221 <param name="sequences" value="merged.fa" />
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222 <param name="match_input" value="1.mums" />
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223 <output name="output" file="2.xmfa" lines_diff="24"/>
0
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224 </test>
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225 </tests>
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226 <help><![CDATA[
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227 What it does
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228 ============
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229
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230 Mauve is a system for efficiently constructing multiple genome alignments in
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231 the presence of large-scale evolutionary events such as rearrangement and
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232 inversion. Multiple genome alignment provides a basis for research into
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233 comparative genomics and the study of evolutionary dynamics. Aligning whole
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234 genomes is a fundamentally different problem than aligning short sequences.
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235
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236 Mauve has been developed with the idea that a multiple genome aligner should
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237 require only modest computational resources. It employs algorithmic techniques
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238 that scale well in the amount of sequence being aligned. For example, a pair of
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239 Y. pestis genomes can be aligned in under a minute, while a group of 9
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240 divergent Enterobacterial genomes can be aligned in a few hours.
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241
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242 progressiveMauve XMFA alignment visualized with the Mauve tool:
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243
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244 .. image:: $PATH_TO_IMAGES/hemolysin.jpg
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245
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246 Example Usage
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247 =============
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248
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249 +-----------------------------------+-------------+
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250 | Usage | Notes |
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251 +===================================+=============+
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252 | Align genomes |Simply |
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253 | |select as |
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254 | |many fasta |
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255 | |files with |
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256 | |one or more |
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257 | |sequences as |
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258 | |necessary |
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259 +-----------------------------------+-------------+
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260 | Align genomes but also save |Use the |
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261 | the guide tree and produce a |**Output |
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262 | backbone file |Guide Tree** |
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263 | |and **Output |
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264 | |Backbone** |
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265 | |options |
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266 +-----------------------------------+-------------+
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267 | Align genomes, but do not |Use the |
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268 | detect forced alignment of |**Disable |
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269 | unrelated sequences |backbone** |
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270 | |option |
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271 +-----------------------------------+-------------+
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272 | Detect forced alignment of |Use the |
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273 | unrelated sequence in the |**Apply |
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274 | alignment produced |Backbone** |
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275 | in previous example, use |option and |
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276 | custom Homology HMM transition |specify the |
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277 | parameters. |XMFA file |
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278 | |produced |
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279 | |in the |
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280 | |previous |
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281 | |example |
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282 +-----------------------------------+-------------+
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283 | Compute ungapped |Use the |
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284 | local-multiple alignments among |**MUMs** |
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285 | the input sequences |option |
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286 +-----------------------------------+-------------+
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287 | Compute an alignment of the |Set the |
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288 | same genomes, using previously |**Match |
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289 | computed local-multiple |Input** to |
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290 | alignments |the tabular |
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291 | |MUMs file |
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292 | |produced in |
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293 | |the previous |
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294 | |example |
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295 +-----------------------------------+-------------+
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296 | Set a minimum scaled |Use the |
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297 | breakpoint penalty to cope with |**Min Scaled |
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298 | the case where most genomes |Penalty** and|
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299 | are aligned correctly, but manual |set to a |
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300 | inspection reveals that |value like |
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301 | a divergent genome has too |5000 |
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302 | many predicted rearrangements. | |
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303 +-----------------------------------+-------------+
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304 | Globally align a set of |Use the |
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305 | collinear virus |**Colinear**,|
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306 | genomes, using seed families |**Seed |
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307 | to improve anchoring sensitivity |Family** |
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308 | in regions below 70% sequence |options |
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309 | identity. | |
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310 +-----------------------------------+-------------+
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311
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312
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313 The progressiveMauve algorithm: addressing limitations of the original algorithm
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314 ================================================================================
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315
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316 Comparative genomics has revealed that closely-related bacteria often have
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317 highly divergent gene content. While the original Mauve algorithm could align
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318 regions conserved among all organisms, the portion of the genome conserved
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319 among all taxa (the core genome) shrinks as more taxa are added to the
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320 analysis. As such, the original Mauve algorithm did not scale well to large
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321 numbers of taxa because it could not align regions conserved among subsets of
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322 the genomes under study. progressiveMauve employs a different algorithmic
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323 approach to scoring alignments that allows alignment of segments conserved
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324 among subsets of taxa. The progressiveMauve algorithm has been described in
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325 Aaron Darling's Ph.D. Thesis, and is also the subject of a manuscript published
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326 in PLoS ONE. A brief overview is given here.
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327
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328 Finding initial local multiple alignments
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329 -----------------------------------------
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330
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331 progressiveMauve elaborates on the original algorithm for finding local
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332 multiple alignments. Instead of using a single seed pattern for match
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333 filtration, progressiveMauve uses a combination of three seed patterns for
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334 improved sensitivity. The palindromic seed patterns have been described in
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335 Darling et al. 2006 "Procrastination leads to efficient filtration for local
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336 multiple alignment"
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337
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338 Seed matches which represent a unique subsequence shared by two or more input
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339 genomes are subjected to ungapped extension until the seed pattern no longer
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340 matches. The result is an ungapped local multiple alignment with at most one
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341 component from each of the input genome sequences.
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342
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343 Computing a pairwise genome content distance matrix and guide tree
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344 ------------------------------------------------------------------
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345
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346 progressiveMauve builds up genome alignments progressively according to a guide
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347 tree. The guide tree is computed based on an estimate of the shared gene
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348 content among each pair of input genomes. For a pair of input genomes, g.x and
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349 g.y, shared gene content is estimated by counting the number of nucleotides in
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350 gx and gy aligned to each other in the initial set of local multiple
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351 alignments. The count is normalized to a similarity value between 0 and 1 by
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352 dividing by the average size of gx and gy. The similarity value is subtracted
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353 from 1 to arrive at a distance estimate. Neighbor joining is then applied to
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354 the matrix of distance estimates to yield a guide tree topology. Note that the
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355 guide tree is not intended to be a phylogeny indicative of the genealogy of
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356 input genomes. It is merely a computational crutch for progressive genome
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357 alignment. Also note that alignments are later refined independently of a
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358 single guide tree toplogy to avoid biasing later phylogenetic inference.
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359
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360 Computing a pairwise breakpoint distance matrix
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361 -----------------------------------------------
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362
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363 Prior to alignment, progressiveMauve attempts to compute a conservative
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364 estimate of the number of rearrangement breakpoints among any pair of genomes.
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365 For each pair of genomes, pairwise alignments are created from the
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366 local-multiple alignments and the pairwise alignments are subjected to greedy
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367 breakpoint elimination. The breakpoint penalty used for greedy breakpoint
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368 elimination is set high for closely related genomes and scaled downward
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369 according to the estimate of genomic content distance. Because the breakpoint
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370 penalty is high, the resulting set of locally collinear blocks represent
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371 robustly supported segmental homology, and a conservative estimate of the
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372 breakpoint distance can be made on this basis. The conservative estimate of
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373 breakpoint distance is used later during progressive alignment to scale
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374 breakpoint penalties.
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375
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376 Progressive genome alignment
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377 ----------------------------
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378
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379 A genome alignment is progressively built up according to the guide tree. At
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380 each step of the progressive genome alignment, alignment anchors are selected
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381 from the initial set of local multiple alignments. Anchors are selected so that
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382 they maximize a Sum-of-pairs scoring scheme which applies a penalty for
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383 predicting breakpoints among any pair of genomes. Because rates of genomic
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384 rearrangement are highly variable, especially in some bacterial pathogens, some
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385 genomes may be expected to exhibit greater rearrangement than others. As such,
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386 a single choice of scoring penalty is unlikely to yield accurate alignments for
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387 all genomes. To cope with this phenomenon, progressiveMauve scales the
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388 breakpoint penalty according to the expected level of sequence divergence and
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389 the number of well-supported genomic rearrangements among the pair of input
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390 genomes. These scaling values are taken from the distance matrices computed
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391 earlier in the algorithm.
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392
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393 Anchored alignment
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394 ------------------
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395
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396 Once anchors have been computed at a node in the guide tree, a global alignment
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397 is computed on the basis of the anchors. Given a set of anchors among two
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398 genomes, a genome and an alignment, or a pair of alignments, a modified MUSCLE
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399 global alignment algorithm is applied to compute an anchored profile-profile
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400 alignment. MUSCLE is then used to perform tree-independent iterative refinement
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401 on the global genome alignment.
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402
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403 Rejecting alignment of unrelated sequence
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404 -----------------------------------------
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405
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406 Although we compute a global alignment among sequences, genomes often contain
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407 lineage-specific sequence and are thus not globally related. The global
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408 alignment will often contain forced alignment of unrelated sequence. A simple
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409 hidden Markov model structure is used to detect forced alignment of unrelated
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410 sequence, which are then removed from the alignment.
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411
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412 Strengths of the progressiveMauve algorithm
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413 -------------------------------------------
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414
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415 - It can be applied to a much larger number of genomes than the original Mauve
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416 algorithm
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417 - It can align more divergent genomes than the original algorithm. Genomes
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418 with as little as 50% nucleotide identity can be alignable
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419 - Manual adjustment of the alignment scoring parameters is usually not
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420 necessary
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421 - It aligns the pan-genome, e.g. regions conserved among subsets of the input
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422 genomes
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423 - It is more accurate than the previous Mauve algorithm
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424
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425 Notes on Reproducibility
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426 ------------------------
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427
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428 The command line programme progressiveMauve seems to behave differently when::
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429
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430 --max-breakpoint-distance-scale=0.5 --conservation-distance-scale=0.5
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431
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432 are passed to the tool, compared to when those options are not passed. This
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433 means that if you wish to precisely replicate the results you see in Galaxy at
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434 the command line, you'll need to pass these flags with their "default" values.
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435
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436 @ATTRIBUTION@
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437 ]]></help>
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438 <expand macro="citation" />
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439 </tool>