annotate hyphy_fel.xml @ 15:d968c5dddfeb draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit adf0f20535bd585663c291f8f15137a7ba947949"
author iuc
date Fri, 21 Aug 2020 15:21:40 -0400
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy0">
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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 </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 '$input_file' fel_input.fa &&
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10 ln -s '$input_nhx' fel_input.nhx &&
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11 @HYPHYMPI@ fel
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12 --alignment ./fel_input.fa
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13 --tree ./fel_input.nhx
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14 --code '$gencodeid'
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15 --branches '$branches'
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16 --srv '$include_srv'
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17 --pvalue '$p_value'
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18 --output '$fel_output'
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19 > '$fel_log'
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20 ;
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21 @CATCH_MPIERR@
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22 ]]></command>
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23 <inputs>
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24 <expand macro="inputs"/>
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25 <expand macro="gencode"/>
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26 <expand macro="branches"/>
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27 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/>
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28 <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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29 <option value="Yes">Yes (recommended)</option>
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30 <option value="No">No</option>
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31 </param>
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32 </inputs>
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33 <outputs>
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34 <data name="fel_log" format="txt"/>
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35 <data name="fel_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="absrel-in1.fa"/>
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40 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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41 <output name="fel_output" file="fel-out1.json" compare="sim_size"/>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 FEL : Fixed effects likelihood
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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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50
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51 Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection?
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52
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53 Recommended Applications
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54 ------------------------
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55
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56 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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57 (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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58 represent candidate sites subject to strong selective pressures across the entire phylogeny.
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59
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60 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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61
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62 Brief description
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63 -----------------
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64
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65 FEL (Fixed Effects Likelihood) estimates site-wise synonymous (alpha)
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66 and non-synonymous rates (beta), and uses a likelihood ratio test to
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67 determine if beta != alpha at a site. The estimates aggregate
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68 information over all branches, so the signal is derived from pervasive
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69 diversification or conservation. A subset of branches can be selected
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70 for testing as well, in which case an additional (nuisance) parameter
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71 will be inferred -- the non-synonymous rate on branches NOT selected for
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72 testing.
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73
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75 Input
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76 -----
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77
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78 1. A *FASTA* sequence alignment.
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79 2. A phylogenetic tree in the *Newick* format
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80
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81 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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82
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83
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84 Output
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85 ------
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86
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87 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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88 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FEL for an example)
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89
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90 Further reading
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91 ---------------
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92
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93 http://hyphy.org/methods/selection-methods/#FEL
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94
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95
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96 Tool options
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97 ------------
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98
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99 ::
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100
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101 --code Which genetic code to use
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102
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103 --branches Which branches should be tested for selection?
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104 All [default] : test all branches
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105
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106 Internal : test only internal branches (suitable for
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107 intra-host pathogen evolution for example, where terminal branches
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108 may contain polymorphism data)
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109
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110 Leaves: test only terminal (leaf) branches
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111
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112 Unlabeled: if the Newick string is labeled using the {} notation,
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113 test only branches without explicit labels
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114 (see http://hyphy.org/tutorials/phylotree/)
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115
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116 --pvalue The significance level used to determine significance
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117
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118 --srv Include site-to-site synonymous rate variation?
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119 Yes [default] or No
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120
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121
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122
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123
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124 ]]>
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125
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126 </help>
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127
0
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128 <expand macro="citations">
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129 <citation type="doi">10.1093/molbev/msi105</citation>
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130 </expand>
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131 </tool>