annotate progressivemauve.xml @ 2:faa752f96ab9 draft default tip

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1 <tool id="progressivemauve" name="progressiveMauve" version="19.1.0.0" profile="16.04">
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2 <description>constructs multiple genome alignments</description>
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3 <macros>
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4 <import>macros.xml</import>
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5
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6 </macros>
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7 <requirements>
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8 <requirement type="package">progressivemauve</requirement>
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9 </requirements>
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10 <command detect_errors="aggressive"><![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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15
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16 progressiveMauve
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17 ## Input Options
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18
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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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24
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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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28
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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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32
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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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36
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37 '$collinear'
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38 --scoring-scheme='$scoring_scheme'
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39 '$no_weight_scaling'
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40
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41 --max-breakpoint-distance-scale='$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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45
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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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49
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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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53
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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" label="Select sequences to align" help="in fasta format"/>
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94 <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="True" help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)"/>
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95 <param type="integer" label="Island gap size" value="20" name="island_gap_size" help="Alignment gaps above this size in nucleotides are considered to be islands (--island-gap-size)"/>
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96 <param type="boolean" truevalue="--disable-backbone" falsevalue="" name="disable_backbone" label="Disable backbone" help="Disable backbone detection (--disable-backbone)"/>
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97 <param type="boolean" truevalue="True" falsevalue="" name="output_guide_tree" label="Output Guide Tree" help="Write out the guide tree used for alignment to a file (--output-guide-tree)"/>
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98 <param type="boolean" truevalue="True" falsevalue="" name="output_backbone" label="Output Backbone" help="Write out the backbone to a file (--backbone-output)"/>
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99 <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" name="mums" help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs) (--mums)"/>
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100 <param type="integer" label="Seed weight" name="seed_weight" value="0" optional="True" help="Use the specified seed weight for calculating initial anchors (--seed-weight)"/>
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101 <param type="data" format="tabular" label="Match Input" name="match_input" optional="True" help="Use specified match file instead of searching for matches (--match-input)"/>
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102 <!--<param type="file" label="input-id-matrix" help="An identity matrix describing similarity among all pairs of input sequences/alignments (- -input-id-matrix)" />-->
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103 <param type="integer" label="Max gapped aligner length" value="0" optional="True" name="max_gapped_aligner_length" help="Maximum number of base pairs to attempt aligning with the gapped aligner (--max-gapped-aligner-length)"/>
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104 <param type="data" format="nhx" label="input-guide-tree" optional="True" name="input_guide_tree" help="A phylogenetic guide tree in Newick format that describes the order in which sequences will be aligned (--input-guide-tree)"/>
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105 <param type="boolean" truevalue="--collinear" falsevalue="" label="Collinear inputs" name="collinear" help="Assume that input sequences are collinear--they have no rearrangements (--collinear)"/>
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106 <param type="select" label="Scoring scheme" name="scoring_scheme" help="Selects the anchoring score function. (--scoring-scheme)">
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107 <option value="sp" selected="True">Extant sum-of-pairs (sp)</option>
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108 <option value="ancestral_sp">Sum-of-pairs + Ancestral (ancestral_sp)</option>
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109 <option value="ancestral">Ancestral (ancestral)</option>
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110 </param>
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111 <param type="boolean" truevalue="--no-weight-scaling" falsevalue="" label="No weight scaling" name="no_weight_scaling" help="Don't scale LCB weights by conservation distance and breakpoint distance (--no-weight-scaling)"/>
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112 <param type="float" min="0" max="1" label="max-breakpoint-distance-scale" value="0.5" name="max_breakpoint_distance_scale" help="Set the maximum weight scaling by breakpoint distance. (--max-breakpoint-distance-scale)"/>
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113 <param type="float" min="0" max="1" label="conservation-distance-scale" value="0.5" name="conservation_distance_scale" help="Scale conservation distances by this amount. (--conservation-distance-scale)"/>
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114 <param type="boolean" truevalue="--skip-refinement" falsevalue="" label="Skip refinement" name="skip_refinement" help="Do not perform iterative refinement (--skip-refinement)"/>
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115 <param type="boolean" truevalue="--skip-gapped-alignment" falsevalue="" label="Skip gapped alignment" name="skip_gapped_alignment" help="Do not perform gapped alignment (--skip-gapped-alignment)"/>
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116 <param type="integer" label="BP dist estimate min score" name="bp_dist_estimate_min_score" value="0" optional="True" help="Minimum LCB score for estimating pairwise breakpoint distance (--bp-dist-estimate-min-score)"/>
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117 <param type="integer" label="Gap open" name="gap_open" value="0" optional="True" help="Gap open penalty (--gap-open)"/>
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118 <param type="select" label="Repeat penalty" name="repeat_penalty" help="Sets whether the repeat scores go negative or go to zero for highly repetitive sequences. (--repeat-penalty)">
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119 <option value="negative" selected="True">Negative</option>
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120 <option value="zero">Zero</option>
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121 </param>
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122 <param type="integer" label="Gap extend" name="gap_extend" value="0" optional="True" help="Gap extend penalty (--gap-extend)"/>
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123 <!--<param type="data" label="Substitution matrix" -->
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124 <!--help="Nucleotide substitution matrix in NCBI format (- -substitution-matrix)" />-->
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125 <param type="integer" label="Weight" name="weight" value="0" optional="True" help="Minimum pairwise LCB score (--weight)"/>
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126 <param type="integer" label="Min scaled penalty" name="min_scaled_penalty" value="0" optional="True" help="Minimum breakpoint penalty after scaling the penalty by expected divergence (--min-scaled-penalty)"/>
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127 <param type="float" label="HMM p go homologous" name="hmm_p_go_homologous" min="0" max="1" value="0.00001" help="Probability of transitioning from the unrelated to the homologous state (--hmm-p-go-homologous)"/>
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128 <param type="float" label="HMM p go unrelated" name="hmm_p_go_unrelated" min="0" max="1" value="0.000000001" help="Probability of transitioning from the homologous to the unrelated state (--hmm-p-go-unrelated)"/>
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129 <param type="float" label="HMM identity" name="hmm_identity" min="0" max="1" value="0.7" help="Expected level of sequence identity among pairs of sequences(--hmm-identity)"/>
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130 <param type="boolean" truevalue="--seed-family" falsevalue="" label="Seed family" name="seed_family" help="Use a family of spaced seeds to improve sensitivity (--seed-family)"/>
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131 <param type="boolean" truevalue="--solid-seeds" falsevalue="" label="Solid seeds" name="solid_seeds" help="Use solid seeds. Do not permit substitutions in anchor matches. (--solid-seeds)"/>
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132 <param type="boolean" truevalue="--coding-seeds" falsevalue="" label="Coding seeds" name="coding_seeds" help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy. (--coding-seeds)"/>
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133 <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" name="no_recursion" help="Disable recursive anchor search (--no-recursion)"/>
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134 </inputs>
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135 <outputs>
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136 <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}">
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137 <change_format>
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138 <when input="mums" value="--mums" format="tabular"/>
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139 </change_format>
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140 </data>
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141 <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree">
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142 <filter>output_guide_tree</filter>
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143 </data>
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144 <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone">
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145 <filter>output_backbone</filter>
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146 </data>
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147 </outputs>
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148 <tests>
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149 <test>
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150 <param name="sequences" value="phagey.fa,karma.fa"/>
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151 <output name="output" file="1.xmfa" lines_diff="20"/>
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152 </test>
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153 <test>
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154 <param name="sequences" value="merged.fa"/>
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155 <output name="output" file="2.xmfa" lines_diff="20"/>
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156 </test>
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157 <test>
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158 <param name="sequences" value="merged.fa"/>
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159 <param name="output_guide_tree" value="True"/>
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160 <output name="output" file="3.xmfa" lines_diff="20"/>
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161 <output name="output_guide_tree_file" file="3.nhx"/>
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162 </test>
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163 <test>
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164 <param name="sequences" value="merged.fa"/>
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165 <param name="mums" value="True"/>
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166 <output name="output" file="4.mums" compare="sim_size" delta="1000"/>
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167 </test>
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168 <test>
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169 <param name="sequences" value="merged.fa"/>
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170 <param name="match_input" value="4.mums"/>
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171 <output name="output" file="5.xmfa" lines_diff="24"/>
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172 </test>
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173 </tests>
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174 <help><![CDATA[
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175 What it does
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176 ============
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177
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178 Mauve is a system for efficiently constructing multiple genome alignments in
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179 the presence of large-scale evolutionary events such as rearrangement and
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180 inversion. Multiple genome alignment provides a basis for research into
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181 comparative genomics and the study of evolutionary dynamics. Aligning whole
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182 genomes is a fundamentally different problem than aligning short sequences.
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183
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184 Mauve has been developed with the idea that a multiple genome aligner should
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185 require only modest computational resources. It employs algorithmic techniques
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186 that scale well in the amount of sequence being aligned. For example, a pair of
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187 Y. pestis genomes can be aligned in under a minute, while a group of 9
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188 divergent Enterobacterial genomes can be aligned in a few hours.
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189
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190
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191 Example Usage
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192 =============
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193
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194 +-----------------------------------+-------------+
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195 | Usage | Notes |
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196 +===================================+=============+
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197 | Align genomes |Simply |
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198 | |select as |
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199 | |many fasta |
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200 | |files with |
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201 | |one or more |
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202 | |sequences as |
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203 | |necessary |
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204 +-----------------------------------+-------------+
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205 | Align genomes but also save |Use the |
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206 | the guide tree and produce a |**Output |
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207 | backbone file |Guide Tree** |
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208 | |and **Output |
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209 | |Backbone** |
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210 | |options |
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211 +-----------------------------------+-------------+
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212 | Align genomes, but do not |Use the |
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213 | detect forced alignment of |**Disable |
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214 | unrelated sequences |backbone** |
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215 | |option |
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216 +-----------------------------------+-------------+
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217 | Detect forced alignment of |Use the |
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218 | unrelated sequence in the |**Apply |
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219 | alignment produced |Backbone** |
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220 | in previous example, use |option and |
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221 | custom Homology HMM transition |specify the |
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222 | parameters. |XMFA file |
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223 | |produced |
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224 | |in the |
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225 | |previous |
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226 | |example |
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227 +-----------------------------------+-------------+
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228 | Compute ungapped |Use the |
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229 | local-multiple alignments among |**MUMs** |
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230 | the input sequences |option |
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231 +-----------------------------------+-------------+
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232 | Compute an alignment of the |Set the |
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233 | same genomes, using previously |**Match |
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234 | computed local-multiple |Input** to |
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235 | alignments |the tabular |
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236 | |MUMs file |
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237 | |produced in |
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238 | |the previous |
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239 | |example |
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240 +-----------------------------------+-------------+
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241 | Set a minimum scaled |Use the |
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242 | breakpoint penalty to cope with |**Min Scaled |
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243 | the case where most genomes |Penalty** and|
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244 | are aligned correctly, but manual |set to a |
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245 | inspection reveals that |value like |
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246 | a divergent genome has too |5000 |
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247 | many predicted rearrangements. | |
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248 +-----------------------------------+-------------+
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249 | Globally align a set of |Use the |
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250 | collinear virus |**Colinear**,|
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251 | genomes, using seed families |**Seed |
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252 | to improve anchoring sensitivity |Family** |
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253 | in regions below 70% sequence |options |
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254 | identity. | |
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255 +-----------------------------------+-------------+
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256
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257 ]]></help>
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258 <citations>
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259 <expand macro="citation/progressive_mauve"/>
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260 <expand macro="citation/mijalisrasche"/>
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261 </citations>
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262 </tool>