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comparison hyphy_fade.xml @ 5:16b4a3869bd5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
author iuc
date Thu, 20 Feb 2020 18:12:40 -0500
parents b959fd359a6b
children 7dbcce65a8ff
comparison
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4:c16dd6b14657 5:16b4a3869bd5
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>