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comparison hyphy_slac.xml @ 6:25782236e47e 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 18:13:33 -0500
parents 8522e7cc4fb4
children dc9e52b2d0e1
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5:232bd7cd4639 6:25782236e47e
20 ]]></command> 20 ]]></command>
21 <inputs> 21 <inputs>
22 <expand macro="inputs"/> 22 <expand macro="inputs"/>
23 <expand macro="gencode"/> 23 <expand macro="gencode"/>
24 <expand macro="branches"/> 24 <expand macro="branches"/>
25 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/> 25 <param argument="--pvalue" name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
26 <param name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/> 26 <param argument="--samples" name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/>
27 </inputs> 27 </inputs>
28 <outputs> 28 <outputs>
29 <data name="slac_log" format="txt"/> 29 <data name="slac_log" format="txt"/>
30 <data name="slac_output" format="hyphy_results.json" /> 30 <data name="slac_output" format="hyphy_results.json" />
31 </outputs> 31 </outputs>
35 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> 35 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
36 <output name="slac_output" file="slac-out1.json" compare="sim_size"/> 36 <output name="slac_output" file="slac-out1.json" compare="sim_size"/>
37 </test> 37 </test>
38 </tests> 38 </tests>
39 <help><![CDATA[ 39 <help><![CDATA[
40 SLAC (Single-Likelihood Ancestor Counting) uses a combination of maximum-likelihood and counting approaches to infer nonsynonymous and synonymous substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. SLAC assumes that the selection pressure for each site is constant along the entire phylogeny. 40 SLAC : Single Likelihood Ancestor Counting
41 ==========================================
41 42
42 See the online documentation_ for more information. 43 What question does this method answer?
44 --------------------------------------
43 45
44 .. _documentation: http://hyphy.org/methods/selection-methods/#slac 46 Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection?
45 ]]></help> 47
48 Recommended Applications
49 ------------------------
50
51 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics
52 (or balancing selection), including adaptive immune escape by viruses. As such, SLAC is ideally suited to identify sites under positive selection which
53 represent candidate sites subject to strong selective pressures across the entire phylogeny.
54 SLAC provides legacy functionality as a counting-based method adapted for phylogenetic applications.
55 In general, this method will be the least statistically robust (compared to FEL or FUBAR), but it is the most directly interpretable.
56
57 Brief description
58 -----------------
59
60 SLAC (Single Likelihood Ancestor Counting) uses a maximum likelihood
61 ancestral state reconstruction and minimum path substitution counting to
62 estimate site - level dS and dN, and applies a simple binomial - based
63 test to test if dS differs drom dN. The estimates aggregate information
64 over all branches, so the signal is derived from pervasive
65 diversification or conservation. A subset of branches can be selected
66 for testing as well.
67
68 Input
69 -----
70
71 1. A *FASTA* sequence alignment.
72 2. A phylogenetic tree in the *Newick* format
73
74 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
75
76
77 Output
78 ------
79
80 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
81
82 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/SLAC for an example)
83
84 Further reading
85 ---------------
86
87 http://hyphy.org/methods/selection-methods/#SLAC
88
89
90 Tool options
91 ------------
92 ::
93
94
95 --code Which genetic code to use
96
97 --branches Which branches should be tested for selection?
98 All [default] : test all branches
99
100 Internal : test only internal branches (suitable for
101 intra-host pathogen evolution for example, where terminal branches
102 may contain polymorphism data)
103
104 Leaves: test only terminal (leaf) branches
105
106 Unlabeled: if the Newick string is labeled using the {} notation,
107 test only branches without explicit labels
108 (see http://hyphy.org/tutorials/phylotree/)
109
110 --pvalue The significance level used to determine significance
111
112 --samples Draw this many alternative ancestral state reconstructions
113 to evaluate uncertainty
114
115 ]]>
116 </help>
46 <expand macro="citations"> 117 <expand macro="citations">
47 <citation type="doi">10.1093/molbev/msi105</citation> 118 <citation type="doi">10.1093/molbev/msi105</citation>
48 </expand> 119 </expand>
49 </tool> 120 </tool>