Mercurial > repos > iuc > hyphy_fade
comparison hyphy_fade.xml @ 5:16b4a3869bd5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
author | iuc |
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date | Thu, 20 Feb 2020 18:12:40 -0500 |
parents | b959fd359a6b |
children | 7dbcce65a8ff |
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4:c16dd6b14657 | 5:16b4a3869bd5 |
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12 hyphy fade | 12 hyphy fade |
13 --alignment ./fade_input.fa | 13 --alignment ./fade_input.fa |
14 --tree ./fade_input.nhx | 14 --tree ./fade_input.nhx |
15 --branches '$branches' | 15 --branches '$branches' |
16 --model '$model' | 16 --model '$model' |
17 --method '$posteriorEstimationMethod' | 17 --method '$posteriorEstimationMethod.method' |
18 --grid '$grid_points' | 18 --grid '$grid_points' |
19 --concentration_parameter '$concentration' | 19 --concentration_parameter '$concentration' |
20 #if $posteriorEstimationMethod != "Metropolis-Hastings" | 20 @posteriorEstimationMethod_cmd@ |
21 --chains '$mcmc' | |
22 --chain-length '$chain_length' | |
23 --burn-in '$samples' | |
24 --samples '$samples_per_chain' | |
25 #end if | |
26 --output '$fade_output' | 21 --output '$fade_output' |
27 > '$fade_log' | 22 > '$fade_log' |
28 ]]></command> | 23 ]]></command> |
29 <inputs> | 24 <inputs> |
30 <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/> | 25 <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/> |
31 <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/> | 26 <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/> |
32 <expand macro="branches"/> | 27 <expand macro="branches"/> |
33 <expand macro="substitution" /> | 28 <expand macro="substitution"/> |
29 <expand macro="branches"/> | |
30 <expand macro="conditional_posteriorEstimationMethod" /> | |
34 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/> | 31 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/> |
35 <param name="mcmc" type="integer" value="5" min="2" max="20" label="Number of MCMC chains"/> | |
36 <param name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain"/> | |
37 <param name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in"/> | |
38 <param name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain"/> | |
39 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/> | 32 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/> |
40 <expand macro="branches"/> | |
41 <param name="posteriorEstimationMethod" type="select" label="Posterior estimation method"> | |
42 <option value="Variational-Bayes">Metropolis-Hastings - Full | |
43 Metropolis-Hastings MCMC algorithm (slowest, original 2013 | |
44 paper implementation)</option> | |
45 <option value="Collapsed-Gibbs">Collapsed Gibbs - Collapsed Gibbs sampler | |
46 (intermediate speed)</option> | |
47 <option value="Metropolis-Hastings">Variational Bayes - 0-th order Variational | |
48 Bayes approximations (fastest, recommended default)</option> | |
49 </param> | |
50 </inputs> | 33 </inputs> |
51 <outputs> | 34 <outputs> |
52 <data name="fade_log" format="txt"/> | 35 <data name="fade_log" format="txt"/> |
53 <data name="fade_output" format="hyphy_results.json" /> | 36 <data name="fade_output" format="hyphy_results.json" /> |
54 </outputs> | 37 </outputs> |
58 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/> | 41 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/> |
59 <output name="fade_output" file="fade-out1.json" compare="sim_size"/> | 42 <output name="fade_output" file="fade-out1.json" compare="sim_size"/> |
60 </test> | 43 </test> |
61 </tests> | 44 </tests> |
62 <help><![CDATA[ | 45 <help><![CDATA[ |
63 FADE (FUBAR Approach to Directional Evolution) uses the same underlying algorithmic advances as impletented in FUBAR to apply Baysian MCMC accounting of parameter uncertiantiy to detect sites evolving under directional evolution in protien alignments. | |
64 | 46 |
65 See the online documentation_ for more information. | 47 FADE : FUBAR Approach to Directional Evolution |
48 ============================================== | |
66 | 49 |
67 .. _documentation: http://hyphy.org/methods/selection-methods/#fade | 50 What question does this method answer? |
68 ]]></help> | 51 -------------------------------------- |
52 | |
53 Which site(s) in an alignment evolve towards to or away from a particular residue. | |
54 | |
55 Recommended Applications | |
56 ------------------------ | |
57 | |
58 Screen protein sequence alignments where the direction of evolution can be resolved | |
59 (via tree rooting, e.g. using an outgroup) to find sites which evolve differently from | |
60 a standard protein model (selected by the user), or a gene-average model (GTR) to find | |
61 evidence of directional selection. | |
62 | |
63 Brief description | |
64 ----------------- | |
65 | |
66 FFADE (FUBAR Approach to Directional Evolution) is a fast method to test | |
67 whether or not a subset of sites in a protein alignment evolve towards a | |
68 particular residue along a subset of branches at accelerated rates | |
69 compared to reference model. FADE uses a random effects model and latent | |
70 Dirichlet allocation (LDA) - inspired approximation methods to allocate | |
71 sites to rate classes. | |
72 | |
73 Input | |
74 ----- | |
75 | |
76 1. A *FASTA* sequence alignment of protein sequences. | |
77 2. A *rooted* phylogenetic tree in the *Newick* format | |
78 | |
79 Note: the names of sequences in the alignment must match the names of the sequences in the tree. | |
80 | |
81 | |
82 Output | |
83 ------ | |
84 | |
85 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). | |
86 | |
87 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FADE for an example) | |
88 | |
89 Further reading | |
90 --------------- | |
91 | |
92 http://hyphy.org/methods/selection-methods/#FADE | |
93 | |
94 | |
95 Tool options | |
96 ------------ | |
97 | |
98 :: | |
99 | |
100 | |
101 --model The baseline substitution model to use | |
102 [default] use GTR | |
103 | |
104 --branches Which branches should be tested for selection? | |
105 All [default] : test all branches | |
106 | |
107 Internal : test only internal branches (suitable for | |
108 intra-host pathogen evolution for example, where terminal branches | |
109 may contain polymorphism data) | |
110 | |
111 Leaves: test only terminal (leaf) branches | |
112 | |
113 Unlabeled: if the Newick string is labeled using the {} notation, | |
114 test only branches without explicit labels | |
115 (see http://hyphy.org/tutorials/phylotree/) | |
116 | |
117 --grid The number of grid points | |
118 Smaller : faster | |
119 Larger : more precise posterior estimation but slower | |
120 default value: 20 | |
121 | |
122 --method Inference method to use | |
123 Variational-Bayes : 0-th order Variational Bayes approximation; fastest [default] | |
124 Metropolis-Hastings : Full Metropolis-Hastings MCMC algorithm; orignal method [slowest] | |
125 Collapsed-Gibbs : Collapsed Gibbs sampler [intermediate speed] | |
126 | |
127 | |
128 --chains How many MCMC chains to run (does not apply to Variational-Bayes) | |
129 default value: 5 | |
130 | |
131 --chain-length MCMC chain length (does not apply to Variational-Bayes) | |
132 default value: 2,000,000 | |
133 | |
134 --burn-in MCMC chain burn in (does not apply to Variational-Bayes) | |
135 default value: 1,000,000 | |
136 | |
137 --samples MCMC samples to draw (does not apply to Variational-Bayes) | |
138 default value: 1,000 | |
139 | |
140 --concentration_parameter | |
141 The concentration parameter of the Dirichlet prior | |
142 default value: 0.5 | |
143 | |
144 | |
145 | |
146 ]]> | |
147 </help> | |
69 <expand macro="citations"> | 148 <expand macro="citations"> |
70 <citation type="doi">10.1093/molbev/msv022</citation> | |
71 </expand> | 149 </expand> |
72 </tool> | 150 </tool> |