Mercurial > repos > iuc > hyphy_fade

annotate hyphy_fade.xml @ 35:d593926e5b71 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:37:49 +0000
parents 2246695d4539
children
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1 <tool id="hyphy_fade" name="HyPhy-FADE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>: FUBAR* Approach to Directional Evolution (*Fast
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3 Unconstrained Bayesian Approximation)</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 hyphy fade
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12 --alignment $input_file
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13 @INPUT_TREE@
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14 @branch_options@
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15 --model '$model'
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16 --method '$advanced_options.posteriorEstimationMethod.method'
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17 @posteriorEstimationMethod_cmd@
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18 --grid '$advanced_options.grid_points'
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19 --concentration_parameter '$advanced_options.concentration'
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20 --output '$fade_output'
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21 > fade_stdout.md
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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="branches"/>
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27 <expand macro="substitution" argument="--model"/>
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28 <section name="advanced_options" title="Advanced Options" expanded="false">
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29 <expand macro="conditional_posteriorEstimationMethod" />
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30 <param argument="--grid" name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points" help="The number of grid points." />
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31 <param argument="--concentration_parameter" name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior" help="The concentration parameter of the Dirichlet prior." />
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32 </section>
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33 </inputs>
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34 <outputs>
2
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35 <data name="fade_output" format="hyphy_results.json" />
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36 <data name="fade_md_report" format="markdown" from_work_dir="fade_stdout.md" label="FADE Report (Markdown) for ${tool.name} on ${on_string}" />
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37 </outputs>
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38 <tests>
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39 <test expect_num_outputs="2">
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40 <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
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41 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>
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42 <param name="model" value="WAG"/>
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43 <section name="advanced_options">
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44 <conditional name="posteriorEstimationMethod">
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45 <param name="method" value="Variational-Bayes"/>
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46 </conditional>
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47 <param name="grid_points" value="20"/>
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48 <param name="concentration" value="0.5"/>
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49 </section>
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50 <output name="fade_output">
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51 <assert_contents>
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52 <has_text text="Empiricial Bayes Factor for substitution bias"/>
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53 <has_text text="Substitution history on selected branches"/>
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54 </assert_contents>
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55 </output>
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56 <output name="fade_md_report">
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57 <assert_contents>
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58 <has_text text="FADE analysis summary. Evidence for directional selection evaluated using empirical Bayes factor threshold of 100"/>
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59 </assert_contents>
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60 </output>
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64
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65 FADE : FUBAR Approach to Directional Evolution
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66 ==============================================
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67
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68 What question does this method answer?
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69 --------------------------------------
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70
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71 Which site(s) in an alignment evolve towards to or away from a particular residue.
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72
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73 Recommended Applications
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74 ------------------------
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75
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76 Screen protein sequence alignments where the direction of evolution can be resolved
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77 (via tree rooting, e.g. using an outgroup) to find sites which evolve differently from
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78 a standard protein model (selected by the user), or a gene-average model (GTR) to find
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79 evidence of directional selection.
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80
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81 Brief description
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82 -----------------
1
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83
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84 FADE (FUBAR Approach to Directional Evolution) is a fast method to test whether or not a subset of sites in a protein alignment evolve towards a particular residue along a subset of branches at accelerated rates compared to a reference model. FADE uses a random effects model and latent Dirichlet allocation (LDA)-inspired approximation methods to allocate sites to rate classes.
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85
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86 The intuition behind FADE is to detect directional selection, where amino acid substitutions are consistently biased towards a particular residue type. This can be indicative of adaptation to new functional constraints or environments. By comparing the observed substitution patterns to a null model (e.g., a standard protein substitution model or a gene-average model), FADE identifies sites that exhibit significant directional bias in their evolutionary trajectory.
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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 of protein sequences.
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92 2. A *rooted* 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
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102 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FADE for an example)
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103
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104 Further reading
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105 ---------------
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106
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107 http://hyphy.org/methods/selection-methods/#FADE
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108
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109
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110 Tool options
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111 ------------
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112
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113 ::
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114
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115
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116 --model The baseline substitution model to use
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117 [default] use GTR
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118
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119 --branches Which branches should be tested for selection?
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120 All [default] : test all branches
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121
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122 Internal : test only internal branches (suitable for
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123 intra-host pathogen evolution for example, where terminal branches
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124 may contain polymorphism data)
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125
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126 Leaves: test only terminal (leaf) branches
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127
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128 Unlabeled: if the Newick string is labeled using the {} notation,
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129 test only branches without explicit labels
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130 (see http://hyphy.org/tutorials/phylotree/)
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131
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132 --grid The number of grid points
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133 Smaller : faster
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134 Larger : more precise posterior estimation but slower
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135 default value: 20
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136
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137 --method Inference method to use
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138 Variational-Bayes : 0-th order Variational Bayes approximation; fastest [default]
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139 Metropolis-Hastings : Full Metropolis-Hastings MCMC algorithm; orignal method [slowest]
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140 Collapsed-Gibbs : Collapsed Gibbs sampler [intermediate speed]
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141
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142
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143 --chains How many MCMC chains to run (does not apply to Variational-Bayes)
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144 default value: 5
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145
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146 --chain-length MCMC chain length (does not apply to Variational-Bayes)
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147 default value: 2,000,000
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148
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149 --burn-in MCMC chain burn in (does not apply to Variational-Bayes)
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150 default value: 1,000,000
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151
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152 --samples MCMC samples to draw (does not apply to Variational-Bayes)
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153 default value: 1,000
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154
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155 --concentration_parameter
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156 The concentration parameter of the Dirichlet prior
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157 default value: 0.5
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158
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159 Output
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160 ------
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161
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162 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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163
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164 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FADE for an example)
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165
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166 A Markdown file with a summary of the analysis.
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167
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168 ]]>
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169 </help>
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170 <expand macro="citations">
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171 </expand>
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172 </tool>