Mercurial > repos > iuc > hyphy_meme

annotate hyphy_meme.xml @ 24:efdd06f7f857 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e22821f51ae326b3696a9456cbc44f9982512a52"
author iuc
date Tue, 20 Apr 2021 19:48:07 +0000
parents 2f07f5b4e47b
children e0763df98352
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy1" profile="19.09">
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3 <description>Mixed Effects Model of Evolution</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <token name="@OPERATION@">MEME</token>
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7 <token name="@operation@">meme</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 @HYPHYMPI@ meme
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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 '$branches'
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19 --pvalue '$p_value'
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20 --output '$meme_output'
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21 --full-model '$full_model'
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22 > '$meme_log'
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23 ;
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24 @CATCH_ERROR@
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25 ]]></command>
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26 <inputs>
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27 <expand macro="inputs"/>
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28 <expand macro="gencode"/>
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29 <expand macro="branches"/>
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30 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
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31 <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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32 </inputs>
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33 <outputs>
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34 <data name="meme_log" format="txt"/>
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35 <data name="meme_output" format="hyphy_results.json" />
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
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40 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>
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41 <param name="branches" value="All"/>
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42 <param name="p_value" value="0.1"/>
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43 <output name="meme_output" file="meme-out1.json" compare="sim_size" delta="25000"/>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47 MEME: Mixed Effects Model of Evolution
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48 ======================================
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49
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50 What question does this method answer?
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51 --------------------------------------
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52
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53 Which site(s) in a gene are subject to pervasive or *episodic*, i.e. only on a
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54 single lineage or subset of lineages, diversifying selection?
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55
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56 Recommended Applications
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57 ------------------------
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58
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59 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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60 (or balancing selection), including adaptive immune escape by viruses.
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61 MEME is ideally suited to identify sites under positive selection which
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62 represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny.
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63
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64 MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection.
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65 MEME is therefore our recommended method if maximum power is desired.
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66
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67
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68 Brief description
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69 -----------------
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70
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71 MEME (Mixed Effects Model of Evolution) estimates a site-wise synonymous
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72 (alpha) and a two-category mixture of non-synonymous (beta-, with
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73 proportion p-, and beta+ with proportion [1-p-]) rates, and uses a
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74 likelihood ratio test to determine if beta+ > &alpha; at a site. The
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75 estimates aggregate information over a proportion of branches at a site,
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76 so the signal is derived from episodic diversification, which is a
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77 combination of strength of selection [effect size] and the proportion of
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78 the tree affected. A subset of branches can be selected for testing as
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79 well, in which case an additional (nuisance) parameter will be inferred
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80 -- the non-synonymous rate on branches NOT selected for testing.
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81
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82 Input
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83 -----
1
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84
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85 1. A *FASTA* sequence alignment.
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86 2. A phylogenetic tree in the *Newick* format
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87
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88 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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89
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90
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91 Output
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92 ------
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93
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94 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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95
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96 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/MEME for an example)
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97
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98 Further reading
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99 ---------------
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100
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101 http://hyphy.org/methods/selection-methods/#MEME
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102
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103
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104 Tool options
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105 ------------
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106 ::
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107
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108
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109 --code Which genetic code to use
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110
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111 --branches Which branches should be tested for selection?
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112 All [default] : test all branches
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113
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114 Internal : test only internal branches (suitable for
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115 intra-host pathogen evolution for example, where terminal branches
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116 may contain polymorphism data)
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117
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118 Leaves: test only terminal (leaf) branches
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119
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120 Unlabeled: if the Newick string is labeled using the {} notation,
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121 test only branches without explicit labels
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122 (see http://hyphy.org/tutorials/phylotree/)
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123
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124 --pvalue The significance level used to determine significance
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125
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126
0
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127 ]]></help>
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128 <expand macro="citations">
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129 <citation type="doi">10.1371/journal.pgen.1002764</citation>
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130 </expand>
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131 </tool>