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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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34:2246695d4539 35:d593926e5b71
11 hyphy fade 11 hyphy fade
12 --alignment $input_file 12 --alignment $input_file
13 @INPUT_TREE@ 13 @INPUT_TREE@
14 @branch_options@ 14 @branch_options@
15 --model '$model' 15 --model '$model'
16 --method '$posteriorEstimationMethod.method' 16 --method '$advanced_options.posteriorEstimationMethod.method'
17 --grid '$grid_points'
18 --concentration_parameter '$concentration'
19 @posteriorEstimationMethod_cmd@ 17 @posteriorEstimationMethod_cmd@
18 --grid '$advanced_options.grid_points'
19 --concentration_parameter '$advanced_options.concentration'
20 --output '$fade_output' 20 --output '$fade_output'
21 > fade_stdout.md
21 @ERRORS@ 22 @ERRORS@
22 ]]></command> 23 ]]></command>
23 <inputs> 24 <inputs>
24 <expand macro="inputs"/> 25 <expand macro="inputs"/>
25 <expand macro="branches"/> 26 <expand macro="branches"/>
26 <expand macro="substitution" argument="--model"/> 27 <expand macro="substitution" argument="--model"/>
27 <expand macro="conditional_posteriorEstimationMethod" /> 28 <section name="advanced_options" title="Advanced Options" expanded="false">
28 <param argument="--grid" name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/> 29 <expand macro="conditional_posteriorEstimationMethod" />
29 <param argument="--concentration_parameter" name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/> 30 <param argument="--grid" name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points" help="The number of grid points." />
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." />
32 </section>
30 </inputs> 33 </inputs>
31 <outputs> 34 <outputs>
32 <data name="fade_output" format="hyphy_results.json" /> 35 <data name="fade_output" format="hyphy_results.json" />
36 <data name="fade_md_report" format="markdown" from_work_dir="fade_stdout.md" label="FADE Report (Markdown) for ${tool.name} on ${on_string}" />
33 </outputs> 37 </outputs>
34 <tests> 38 <tests>
35 <test> 39 <test expect_num_outputs="2">
36 <param name="input_file" ftype="fasta" value="fade-in1.fa"/> 40 <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
37 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/> 41 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>
38 <output name="fade_output" file="fade-out1.json" compare="sim_size"/> 42 <param name="model" value="WAG"/>
43 <section name="advanced_options">
44 <conditional name="posteriorEstimationMethod">
45 <param name="method" value="Variational-Bayes"/>
46 </conditional>
47 <param name="grid_points" value="20"/>
48 <param name="concentration" value="0.5"/>
49 </section>
50 <output name="fade_output">
51 <assert_contents>
52 <has_text text="Empiricial Bayes Factor for substitution bias"/>
53 <has_text text="Substitution history on selected branches"/>
54 </assert_contents>
55 </output>
56 <output name="fade_md_report">
57 <assert_contents>
58 <has_text text="FADE analysis summary. Evidence for directional selection evaluated using empirical Bayes factor threshold of 100"/>
59 </assert_contents>
60 </output>
39 </test> 61 </test>
40 </tests> 62 </tests>
41 <help><![CDATA[ 63 <help><![CDATA[
42 64
43 FADE : FUBAR Approach to Directional Evolution 65 FADE : FUBAR Approach to Directional Evolution
57 evidence of directional selection. 79 evidence of directional selection.
58 80
59 Brief description 81 Brief description
60 ----------------- 82 -----------------
61 83
62 FFADE (FUBAR Approach to Directional Evolution) is a fast method to test 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.
63 whether or not a subset of sites in a protein alignment evolve towards a 85
64 particular residue along a subset of branches at accelerated rates 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.
65 compared to reference model. FADE uses a random effects model and latent
66 Dirichlet allocation (LDA) - inspired approximation methods to allocate
67 sites to rate classes.
68 87
69 Input 88 Input
70 ----- 89 -----
71 90
72 1. A *FASTA* sequence alignment of protein sequences. 91 1. A *FASTA* sequence alignment of protein sequences.
135 154
136 --concentration_parameter 155 --concentration_parameter
137 The concentration parameter of the Dirichlet prior 156 The concentration parameter of the Dirichlet prior
138 default value: 0.5 157 default value: 0.5
139 158
159 Output
160 ------
140 161
162 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
141 163
142 ]]> 164 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FADE for an example)
165
166 A Markdown file with a summary of the analysis.
167
168 ]]>
143 </help> 169 </help>
144 <expand macro="citations"> 170 <expand macro="citations">
145 </expand> 171 </expand>
146 </tool> 172 </tool>