Mercurial > repos > iuc > hyphy_fel

annotate hyphy_fel.xml @ 33:b3f852331afe draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Tue, 29 Mar 2022 23:51:17 +0000
parents 5827e3607f8c
children a822a4869772
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_fel" name="HyPhy-FEL" version="@TOOL_VERSION@+galaxy1" 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 </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@ fel
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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 --srv '$include_srv'
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17 --pvalue '$p_value'
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18 @resample@
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19 --precision $precision
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20 $ci
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21 --output '$fel_output'
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22 @ERRORS@
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23 ]]></command>
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24 <inputs>
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25 <expand macro="inputs"/>
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26 <expand macro="gencode"/>
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27 <expand macro="branches"/>
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28 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/>
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29 <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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30 <option value="Yes">Yes (recommended)</option>
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31 <option value="No">No</option>
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32 </param>
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33 <param argument="--ci" type="boolean" truevalue="--ci Yes" falsevalue="" label="Compute profile likelihood confidence intervals for each variable site" />
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34 <expand macro="resample"/>
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35 <param argument="--precision" type="select" label="Optimization precision for preliminary fits">
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36 <option value="standard">Standard</option>
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37 <option value="reduced">Reduced for faster fitting</option>
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <data name="fel_output" format="hyphy_results.json" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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46 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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47 <output name="fel_output" file="fel-out1.json" compare="sim_size"/>
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48 </test>
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49 <test>
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50 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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51 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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52 <param name="ci" value="true" />
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53 <param name="precision" value="reduced" />
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54 <output name="fel_output" file="fel-out1.json" compare="sim_size"/>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58 FEL : Fixed effects likelihood
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59 ==============================
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60
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61 What question does this method answer?
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62 --------------------------------------
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63
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64 Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection?
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65
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66 Recommended Applications
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67 ------------------------
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68
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69 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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70 (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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71 represent candidate sites subject to strong selective pressures across the entire phylogeny.
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72
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73 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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74
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75 Brief description
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76 -----------------
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77
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78 FEL (Fixed Effects Likelihood) estimates site-wise synonymous (alpha)
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79 and non-synonymous rates (beta), and uses a likelihood ratio test to
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80 determine if beta != alpha at a site. The estimates aggregate
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81 information over all branches, so the signal is derived from pervasive
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82 diversification or conservation. A subset of branches can be selected
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83 for testing as well, in which case an additional (nuisance) parameter
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84 will be inferred -- the non-synonymous rate on branches NOT selected for
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85 testing.
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86
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87
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88 Input
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89 -----
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90
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91 1. A *FASTA* sequence alignment.
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92 2. A phylogenetic tree in the *Newick* format
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93
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94 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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95
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96
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97 Output
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98 ------
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99
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100 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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101 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FEL for an example)
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102
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103 Further reading
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104 ---------------
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105
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106 http://hyphy.org/methods/selection-methods/#FEL
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107
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108
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109 Tool options
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110 ------------
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111
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112 ::
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113
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114 --code Which genetic code to use
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115
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116 --branches Which branches should be tested for selection?
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117 All [default] : test all branches
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118
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119 Internal : test only internal branches (suitable for
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120 intra-host pathogen evolution for example, where terminal branches
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121 may contain polymorphism data)
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122
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123 Leaves: test only terminal (leaf) branches
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124
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125 Unlabeled: if the Newick string is labeled using the {} notation,
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126 test only branches without explicit labels
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127 (see http://hyphy.org/tutorials/phylotree/)
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128
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129 --pvalue The significance level used to determine significance
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130
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131 --srv Include site-to-site synonymous rate variation?
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132 Yes [default] or No
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134
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135
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136
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137 ]]>
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138
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139 </help>
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140
0
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141 <expand macro="citations">
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142 <citation type="doi">10.1093/molbev/msi105</citation>
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143 </expand>
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144 </tool>