Mercurial > repos > iuc > hyphy_busted

annotate hyphy_busted.xml @ 34:966f51476bd7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
author iuc
date Thu, 02 Mar 2023 15:07:52 +0000
parents 5013ac978803
children 3169a46cd44c
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1 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 @SYMLINK_FILES@
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10 hyphy busted
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11 --alignment ./$input_file
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12 @INPUT_TREE@
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13 --code $gencodeid
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14 @branch_options@
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15 --output '$busted_output'
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16 @advanced_options@
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17 @ERRORS@
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18 ]]></command>
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19 <inputs>
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20 <expand macro="inputs"/>
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21 <expand macro="gencode"/>
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22 <expand macro="branches"/>
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23 <expand macro="srv"/>
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24 </inputs>
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25 <outputs>
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26 <data name="busted_output" format="hyphy_results.json" />
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27 <expand macro="alternative_model_output" />
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28 </outputs>
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29 <tests>
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30 <test>
1
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31 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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32 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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33 <output name="busted_output">
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34 <assert_contents>
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35 <has_size value="113683" delta="2000"/>
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36 <has_text text="substitutions"/>
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37 <has_text text="test results"/>
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38 </assert_contents>
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39 </output>
0
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40 </test>
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41 <test>
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42 <param name="input_file" ftype="nex" value="busted-in2.nex"/>
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43 <conditional name="branch_cond">
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44 <param name="branch_sel" value="specify"/>
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45 <param name="branch_label" value="B_US_90_WEAU160_BRANCH" />
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46 </conditional>
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47 <param name="srv_options" value="specify" />
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48 <param name="save_alternative_model" value="true" />
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49 <output name="busted_output">
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50 <assert_contents>
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51 <has_size value="112119" delta="2000"/>
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52 <has_text text="substitutions"/>
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53 <has_text text="test results"/>
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54 </assert_contents>
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55 </output>
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56 <output name="alternative_model">
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57 <assert_contents>
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58 <has_size value="333928" delta="2000"/>
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59 <has_text text="END;"/>
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60 </assert_contents>
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61 </output>
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62 </test>
0
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63 </tests>
1
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64 <help><![CDATA[
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65
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66 BUSTED : Bayesian UnresTricted Test of Episodic Diversification
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67 ===============================================================
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68
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69 What question does this method answer?
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70 --------------------------------------
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71
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72 Is there evidence that some sites in the alignment have been subject to positive diversifying selection,
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73 either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)?
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74 In other words, BUSTED asks whether a given gene has been subject to positive, diversifying selection at any site, at any time.
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75 If a priori information about lineages of interest is available (e.g., due to migration, change in the environment, etc.),
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76 then BUSTED can be restricted to test for selection only on a subset of tree lineages, potentially boosting power.
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77
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78 Recommended Applications
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79 ------------------------
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80
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81 1. Annotating a collection of alignments with a binary attribute: has this alignment been subject to positive diversifying selection (yes/no)?
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82 2. Testing small or low-divergence alignments (i.e. ~30 sequences) for evidence of positive diversifying selection, where neither branch nor site level methods have sufficient power.
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83
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84 Brief description
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85 -----------------
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86
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87 BUSTED (branch-site unrestricted statistical test of episodic
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88 diversification) uses a random effects branch-site model fitted jointly
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89 to all or a subset of tree branches in order to test for alignment-wide
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90 evidence of episodic diversifying selection. Assuming there is evidence
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91 of positive selection (i.e. there is an omega > 1), BUSTED will also
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92 perform a quick evidence-ratio style analysis to explore which
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93 individual sites may have been subject to selection.
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94
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95
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96 Input
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97 -----
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98
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99 1. A *FASTA* sequence alignment.
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100 2. A phylogenetic tree in the *Newick* format
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101
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102 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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103
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104
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105 Output
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106 ------
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107
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108 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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109
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110 For each tested branch the analysis will infer the appropriate number of selective regimes,
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111 and whether or not there is statistical evidence of positive selection on that branch.
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112
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113 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BUSTED for an example)
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114
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115 Further reading
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116 ---------------
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117
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118 http://hyphy.org/methods/selection-methods/#busted
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119
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120
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121 Tool options
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122 ------------
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123 ::
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124
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125
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126 --code Which genetic code to use
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127
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128 --branches Which branches should be tested for selection?
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129 All [default] : test all branches
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130
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131 Internal : test only internal branches (suitable for
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132 intra-host pathogen evolution for example, where terminal branches
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133 may contain polymorphism data)
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134
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135 Leaves: test only terminal (leaf) branches
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136
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137 Unlabeled: if the Newick string is labeled using the {} notation,
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138 test only branches without explicit labels
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139 (see http://hyphy.org/tutorials/phylotree/)
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140 ]]>
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141 </help>
0
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142 <expand macro="citations">
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143 <citation type="doi">10.1093/molbev/msv035</citation>
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144 </expand>
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145 </tool>