Mercurial > repos > iuc > hyphy_meme

annotate hyphy_meme.xml @ 32:5d8389d684bf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Wed, 30 Mar 2022 00:22:00 +0000
parents cdbb233119cb
children 5fd8dc04d6af
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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 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools"/>
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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 --resample $resample
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18 --output '$meme_output'
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19 --full-model '$full_model'
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20 @ERRORS@
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21 ]]></command>
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22 <inputs>
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23 <expand macro="inputs"/>
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24 <expand macro="gencode"/>
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25 <expand macro="branches"/>
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26 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
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27 <expand macro="resample"/>
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28 <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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29 </inputs>
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30 <outputs>
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31 <data name="meme_output" format="hyphy_results.json" />
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
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36 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>
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37 <conditional name="branch_cond">
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38 <param name="branch_sel" value="All"/>
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39 </conditional>
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40 <param name="p_value" value="0.1"/>
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41 <output name="meme_output" file="meme-out1.json" compare="sim_size" delta="25000"/>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
5
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45 MEME: Mixed Effects Model of Evolution
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46 ======================================
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47
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48 What question does this method answer?
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49 --------------------------------------
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51 Which site(s) in a gene are subject to pervasive or *episodic*, i.e. only on a
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52 single lineage or subset of lineages, diversifying selection?
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53
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54 Recommended Applications
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55 ------------------------
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56
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57 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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58 (or balancing selection), including adaptive immune escape by viruses.
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59 MEME is ideally suited to identify sites under positive selection which
5
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60 represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny.
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61
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62 MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection.
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63 MEME is therefore our recommended method if maximum power is desired.
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64
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65
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66 Brief description
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67 -----------------
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68
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69 MEME (Mixed Effects Model of Evolution) estimates a site-wise synonymous
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70 (alpha) and a two-category mixture of non-synonymous (beta-, with
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71 proportion p-, and beta+ with proportion [1-p-]) rates, and uses a
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72 likelihood ratio test to determine if beta+ > &alpha; at a site. The
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73 estimates aggregate information over a proportion of branches at a site,
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74 so the signal is derived from episodic diversification, which is a
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75 combination of strength of selection [effect size] and the proportion of
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76 the tree affected. A subset of branches can be selected for testing as
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77 well, in which case an additional (nuisance) parameter will be inferred
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78 -- the non-synonymous rate on branches NOT selected for testing.
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79
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80 Input
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81 -----
1
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82
5
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83 1. A *FASTA* sequence alignment.
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84 2. A phylogenetic tree in the *Newick* format
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85
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86 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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87
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88
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89 Output
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90 ------
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91
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92 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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93
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94 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/MEME for an example)
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95
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96 Further reading
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97 ---------------
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98
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99 http://hyphy.org/methods/selection-methods/#MEME
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100
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101
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102 Tool options
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103 ------------
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104 ::
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105
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106
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107 --code Which genetic code to use
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108
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109 --branches Which branches should be tested for selection?
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110 All [default] : test all branches
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111
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112 Internal : test only internal branches (suitable for
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113 intra-host pathogen evolution for example, where terminal branches
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114 may contain polymorphism data)
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115
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116 Leaves: test only terminal (leaf) branches
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117
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118 Unlabeled: if the Newick string is labeled using the {} notation,
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119 test only branches without explicit labels
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120 (see http://hyphy.org/tutorials/phylotree/)
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121
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122 --pvalue The significance level used to determine significance
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123
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124
0
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125 ]]></help>
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126 <expand macro="citations">
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127 <citation type="doi">10.1371/journal.pgen.1002764</citation>
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128 </expand>
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129 </tool>