Mercurial > repos > iuc > hyphy_busted

annotate hyphy_busted.xml @ 9:cb5ff3a1d7c6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
author iuc
date Wed, 22 Apr 2020 16:06:07 +0000
parents 51548f9a253f
children 4f0942146044
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3e7799d80897 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0">
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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>
3e7799d80897 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$input_file' busted_input.fa &&
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10 ln -s '$input_nhx' busted_input.nhx &&
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11 hyphy busted
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12 --alignment ./busted_input.fa
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13 --tree ./busted_input.nhx
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14 --code $gencodeid
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15 --branches '$branches'
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16 --output '$busted_output'
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17 > '$busted_log'
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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 </inputs>
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24 <outputs>
1
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25 <data name="busted_log" format="txt"/>
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26 <data name="busted_output" format="hyphy_results.json" />
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27 </outputs>
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28 <tests>
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29 <test>
1
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30 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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31 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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32 <output name="busted_output" file="busted-out1.json" compare="sim_size"/>
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33 </test>
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34 </tests>
1
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35 <help><![CDATA[
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36
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37 BUSTED : Bayesian UnresTricted Test of Episodic Diversification
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38 ===============================================================
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39
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40 What question does this method answer?
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41 --------------------------------------
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42
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43 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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44 either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)?
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45 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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46 If a priori information about lineages of interest is available (e.g., due to migration, change in the environment, etc.),
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47 then BUSTED can be restricted to test for selection only on a subset of tree lineages, potentially boosting power.
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48
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49 Recommended Applications
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50 ------------------------
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51
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52 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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53 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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54
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55 Brief description
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56 -----------------
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57
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58 BUSTED (branch-site unrestricted statistical test of episodic
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59 diversification) uses a random effects branch-site model fitted jointly
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60 to all or a subset of tree branches in order to test for alignment-wide
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61 evidence of episodic diversifying selection. Assuming there is evidence
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62 of positive selection (i.e. there is an omega > 1), BUSTED will also
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63 perform a quick evidence-ratio style analysis to explore which
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64 individual sites may have been subject to selection.
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65
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67 Input
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68 -----
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69
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70 1. A *FASTA* sequence alignment.
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71 2. A phylogenetic tree in the *Newick* format
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72
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73 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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74
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76 Output
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77 ------
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78
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79 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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80
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81 For each tested branch the analysis will infer the appropriate number of selective regimes,
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82 and whether or not there is statistical evidence of positive selection on that branch.
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83
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84 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BUSTED for an example)
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85
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86 Further reading
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87 ---------------
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88
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89 http://hyphy.org/methods/selection-methods/#busted
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90
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91
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92 Tool options
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93 ------------
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94 ::
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95
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96
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97 --code Which genetic code to use
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98
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99 --branches Which branches should be tested for selection?
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100 All [default] : test all branches
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101
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102 Internal : test only internal branches (suitable for
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103 intra-host pathogen evolution for example, where terminal branches
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104 may contain polymorphism data)
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105
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106 Leaves: test only terminal (leaf) branches
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107
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108 Unlabeled: if the Newick string is labeled using the {} notation,
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109 test only branches without explicit labels
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110 (see http://hyphy.org/tutorials/phylotree/)
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111 ]]>
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112 </help>
0
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113 <expand macro="citations">
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114 <citation type="doi">10.1093/molbev/msv035</citation>
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115 </expand>
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116 </tool>