Mercurial > repos > iuc > hyphy_meme

annotate hyphy_meme.xml @ 31:cdbb233119cb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
author iuc
date Sat, 27 Nov 2021 11:26:48 +0000
parents 45a2366d777e
children 5d8389d684bf
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@TOOL_VERSION@+galaxy2" profile="19.09">
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3 <description>Mixed Effects Model of Evolution</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 @HYPHYMPI@ meme
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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 --pvalue '$p_value'
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17 --output '$meme_output'
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18 --full-model '$full_model'
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19 @ERRORS@
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20 ]]></command>
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21 <inputs>
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22 <expand macro="inputs"/>
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23 <expand macro="gencode"/>
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24 <expand macro="branches"/>
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25 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
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26 <param argument="--full-model" type="boolean" truevalue="Yes" falsevalue="No" label="Perform branch length re-optimization under the full codon model" />
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27 </inputs>
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28 <outputs>
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29 <data name="meme_output" format="hyphy_results.json" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
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34 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>
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35 <conditional name="branch_cond">
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36 <param name="branch_sel" value="All"/>
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37 </conditional>
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38 <param name="p_value" value="0.1"/>
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39 <output name="meme_output" file="meme-out1.json" compare="sim_size" delta="25000"/>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 MEME: Mixed Effects Model of Evolution
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44 ======================================
8
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45
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46 What question does this method answer?
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47 --------------------------------------
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48
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49 Which site(s) in a gene are subject to pervasive or *episodic*, i.e. only on a
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50 single lineage or subset of lineages, diversifying selection?
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51
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52 Recommended Applications
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53 ------------------------
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54
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55 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics
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56 (or balancing selection), including adaptive immune escape by viruses.
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57 MEME is ideally suited to identify sites under positive selection which
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58 represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny.
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59
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60 MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection.
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61 MEME is therefore our recommended method if maximum power is desired.
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62
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63
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64 Brief description
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65 -----------------
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66
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67 MEME (Mixed Effects Model of Evolution) estimates a site-wise synonymous
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68 (alpha) and a two-category mixture of non-synonymous (beta-, with
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69 proportion p-, and beta+ with proportion [1-p-]) rates, and uses a
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70 likelihood ratio test to determine if beta+ > &alpha; at a site. The
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71 estimates aggregate information over a proportion of branches at a site,
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72 so the signal is derived from episodic diversification, which is a
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73 combination of strength of selection [effect size] and the proportion of
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74 the tree affected. A subset of branches can be selected for testing as
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75 well, in which case an additional (nuisance) parameter will be inferred
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76 -- the non-synonymous rate on branches NOT selected for testing.
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77
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78 Input
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79 -----
1
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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 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/MEME for an example)
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93
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94 Further reading
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95 ---------------
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96
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97 http://hyphy.org/methods/selection-methods/#MEME
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98
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99
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100 Tool options
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101 ------------
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102 ::
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103
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104
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105 --code Which genetic code to use
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106
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107 --branches Which branches should be tested for selection?
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108 All [default] : test all branches
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109
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110 Internal : test only internal branches (suitable for
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111 intra-host pathogen evolution for example, where terminal branches
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112 may contain polymorphism data)
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113
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114 Leaves: test only terminal (leaf) branches
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115
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116 Unlabeled: if the Newick string is labeled using the {} notation,
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117 test only branches without explicit labels
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118 (see http://hyphy.org/tutorials/phylotree/)
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119
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120 --pvalue The significance level used to determine significance
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121
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122
0
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123 ]]></help>
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124 <expand macro="citations">
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125 <citation type="doi">10.1371/journal.pgen.1002764</citation>
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126 </expand>
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127 </tool>