Mercurial > repos > iuc > hyphy_fel

annotate hyphy_fel.xml @ 24:9bec2688cd72 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 10:15:30 +0000
parents 1329c96bd214
children 5a67e5b055e0
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy0" profile="19.09">
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3 <description>Fixed Effects Likelihood</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <token name="@OPERATION@">FEL</token>
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7 <token name="@operation@">fel</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@ fel
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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 '$branches'
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19 --srv '$include_srv'
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20 --pvalue '$p_value'
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21 --output '$fel_output'
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22 > '$fel_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"/>
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31 <param name="include_srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site">
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32 <option value="Yes">Yes (recommended)</option>
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33 <option value="No">No</option>
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34 </param>
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35 </inputs>
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36 <outputs>
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37 <data name="fel_log" format="txt"/>
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38 <data name="fel_output" format="hyphy_results.json" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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43 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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44 <output name="fel_output" file="fel-out1.json" compare="sim_size"/>
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45 </test>
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46 </tests>
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47 <help><![CDATA[
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48 FEL : Fixed effects likelihood
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49 ==============================
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50
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51 What question does this method answer?
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52 --------------------------------------
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53
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54 Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, 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. As such, FEL is ideally suited to identify sites under positive selection which
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61 represent candidate sites subject to strong selective pressures across the entire phylogeny.
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62
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63 FEL is our recommended method for analyzing small-to-medium size datasets when one wishes only to study pervasive selection at individual sites.
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64
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65 Brief description
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66 -----------------
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67
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68 FEL (Fixed Effects Likelihood) estimates site-wise synonymous (alpha)
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69 and non-synonymous rates (beta), and uses a likelihood ratio test to
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70 determine if beta != alpha at a site. The estimates aggregate
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71 information over all branches, so the signal is derived from pervasive
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72 diversification or conservation. A subset of branches can be selected
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73 for testing as well, in which case an additional (nuisance) parameter
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74 will be inferred -- the non-synonymous rate on branches NOT selected for
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75 testing.
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78 Input
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79 -----
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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 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FEL for an example)
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92
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93 Further reading
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94 ---------------
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95
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96 http://hyphy.org/methods/selection-methods/#FEL
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97
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98
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99 Tool options
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100 ------------
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101
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102 ::
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103
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104 --code Which genetic code to use
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105
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106 --branches Which branches should be tested for selection?
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107 All [default] : test all branches
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108
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109 Internal : test only internal branches (suitable for
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110 intra-host pathogen evolution for example, where terminal branches
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111 may contain polymorphism data)
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112
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113 Leaves: test only terminal (leaf) branches
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114
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115 Unlabeled: if the Newick string is labeled using the {} notation,
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116 test only branches without explicit labels
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117 (see http://hyphy.org/tutorials/phylotree/)
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118
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119 --pvalue The significance level used to determine significance
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120
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121 --srv Include site-to-site synonymous rate variation?
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122 Yes [default] or No
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123
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124
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125
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126
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127 ]]>
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128
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129 </help>
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130
0
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131 <expand macro="citations">
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132 <citation type="doi">10.1093/molbev/msi105</citation>
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133 </expand>
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134 </tool>