Mercurial > repos > iuc > hyphy_busted

annotate hyphy_busted.xml @ 23:5dafd26110c6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author iuc
date Tue, 20 Apr 2021 10:19:35 +0000
parents 4f0942146044
children 62f9b7fc4054
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0" profile="19.09">
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3 <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <token name="@OPERATION@">BUSTED</token>
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7 <token name="@operation@">busted</token>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <command detect_errors="exit_code"><![CDATA[
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11 @SYMLINK_FILES@
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12 hyphy busted
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13 --alignment ./$input_file
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14 #if $input_nhx:
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15 --tree ./input.nhx
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16 #end if
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17 --code $gencodeid
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18 --branches '$branches'
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19 --output '$busted_output'
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20 > '$busted_log' ;
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21 @CATCH_ERROR@
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22 ]]></command>
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23 <inputs>
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24 <expand macro="inputs"/>
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25 <expand macro="gencode"/>
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26 <expand macro="branches"/>
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27 </inputs>
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28 <outputs>
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29 <data name="busted_log" format="txt"/>
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30 <data name="busted_output" format="hyphy_results.json" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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35 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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36 <output name="busted_output" file="busted-out1.json" compare="sim_size"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40
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41 BUSTED : Bayesian UnresTricted Test of Episodic Diversification
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42 ===============================================================
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43
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44 What question does this method answer?
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45 --------------------------------------
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46
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47 Is there evidence that some sites in the alignment have been subject to positive diversifying selection,
cb5ff3a1d7c6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
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48 either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)?
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49 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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50 If a priori information about lineages of interest is available (e.g., due to migration, change in the environment, etc.),
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51 then BUSTED can be restricted to test for selection only on a subset of tree lineages, potentially boosting power.
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52
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53 Recommended Applications
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54 ------------------------
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55
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56 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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57 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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58
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59 Brief description
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60 -----------------
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61
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62 BUSTED (branch-site unrestricted statistical test of episodic
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63 diversification) uses a random effects branch-site model fitted jointly
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64 to all or a subset of tree branches in order to test for alignment-wide
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65 evidence of episodic diversifying selection. Assuming there is evidence
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66 of positive selection (i.e. there is an omega > 1), BUSTED will also
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67 perform a quick evidence-ratio style analysis to explore which
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68 individual sites may have been subject to selection.
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69
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71 Input
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72 -----
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73
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74 1. A *FASTA* sequence alignment.
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75 2. A phylogenetic tree in the *Newick* format
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76
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77 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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78
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80 Output
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81 ------
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82
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83 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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84
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85 For each tested branch the analysis will infer the appropriate number of selective regimes,
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86 and whether or not there is statistical evidence of positive selection on that branch.
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87
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88 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BUSTED for an example)
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89
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90 Further reading
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91 ---------------
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92
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93 http://hyphy.org/methods/selection-methods/#busted
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94
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95
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96 Tool options
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97 ------------
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98 ::
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99
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100
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101 --code Which genetic code to use
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102
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103 --branches Which branches should be tested for selection?
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104 All [default] : test all branches
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105
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106 Internal : test only internal branches (suitable for
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107 intra-host pathogen evolution for example, where terminal branches
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108 may contain polymorphism data)
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109
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110 Leaves: test only terminal (leaf) branches
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111
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112 Unlabeled: if the Newick string is labeled using the {} notation,
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113 test only branches without explicit labels
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114 (see http://hyphy.org/tutorials/phylotree/)
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115 ]]>
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116 </help>
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117 <expand macro="citations">
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118 <citation type="doi">10.1093/molbev/msv035</citation>
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119 </expand>
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120 </tool>