Mercurial > repos > iuc > hyphy_busted

annotate hyphy_busted.xml @ 30:d538129f4fe5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:55:26 +0000
parents 62f9b7fc4054
children 0494d850a4d6
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy1" profile="19.09">
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3 <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
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4 <expand macro="bio_tools"/>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @SYMLINK_FILES@
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11 hyphy busted
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12 --alignment ./$input_file
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13 @INPUT_TREE@
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14 --code $gencodeid
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15 @branch_options@
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16 --output '$busted_output'
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17 @advanced_options@
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18 @ERRORS@
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19 ]]></command>
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20 <inputs>
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21 <expand macro="inputs"/>
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22 <expand macro="gencode"/>
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23 <expand macro="branches"/>
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24 <expand macro="srv"/>
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25 </inputs>
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26 <outputs>
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27 <data name="busted_output" format="hyphy_results.json" />
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28 <expand macro="alternative_model_output" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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33 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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34 <output name="busted_output" file="busted-out1.json" compare="sim_size"/>
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35 </test>
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36 <test>
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37 <param name="input_file" ftype="nex" value="busted-in2.nex"/>
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38 <param name="branches" value="specify" />
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39 <param name="branch_label" value="B_US_90_WEAU160" />
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40 <param name="srv_options" value="specify" />
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41 <param name="save_alternative_model" value="true" />
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42 <output name="busted_output" file="busted-out2-1.json" compare="sim_size"/>
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43 <output name="alternative_model" file="busted-out2-2.json" compare="sim_size"/>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47
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48 BUSTED : Bayesian UnresTricted Test of Episodic Diversification
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49 ===============================================================
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50
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51 What question does this method answer?
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52 --------------------------------------
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53
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54 Is there evidence that some sites in the alignment have been subject to positive diversifying selection,
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55 either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)?
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56 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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57 If a priori information about lineages of interest is available (e.g., due to migration, change in the environment, etc.),
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58 then BUSTED can be restricted to test for selection only on a subset of tree lineages, potentially boosting power.
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59
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60 Recommended Applications
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61 ------------------------
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62
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63 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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64 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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66 Brief description
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67 -----------------
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69 BUSTED (branch-site unrestricted statistical test of episodic
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70 diversification) uses a random effects branch-site model fitted jointly
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71 to all or a subset of tree branches in order to test for alignment-wide
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72 evidence of episodic diversifying selection. Assuming there is evidence
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73 of positive selection (i.e. there is an omega > 1), BUSTED will also
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74 perform a quick evidence-ratio style analysis to explore which
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75 individual sites may have been subject to selection.
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78 Input
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79 -----
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80
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81 1. A *FASTA* sequence alignment.
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82 2. A phylogenetic tree in the *Newick* format
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83
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84 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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85
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86
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87 Output
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88 ------
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89
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90 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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91
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92 For each tested branch the analysis will infer the appropriate number of selective regimes,
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93 and whether or not there is statistical evidence of positive selection on that branch.
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94
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95 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BUSTED for an example)
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96
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97 Further reading
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98 ---------------
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99
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100 http://hyphy.org/methods/selection-methods/#busted
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101
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102
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103 Tool options
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104 ------------
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105 ::
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106
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107
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108 --code Which genetic code to use
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109
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110 --branches Which branches should be tested for selection?
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111 All [default] : test all branches
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112
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113 Internal : test only internal branches (suitable for
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114 intra-host pathogen evolution for example, where terminal branches
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115 may contain polymorphism data)
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116
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117 Leaves: test only terminal (leaf) branches
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118
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119 Unlabeled: if the Newick string is labeled using the {} notation,
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120 test only branches without explicit labels
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121 (see http://hyphy.org/tutorials/phylotree/)
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122 ]]>
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123 </help>
0
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124 <expand macro="citations">
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125 <citation type="doi">10.1093/molbev/msv035</citation>
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126 </expand>
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127 </tool>