Mercurial > repos > iuc > hyphy_bgm

annotate hyphy_bgm.xml @ 26:d1c977aee228 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2dd9bdc695433c217bbb7e11c1c0138245beb801"
author iuc
date Tue, 18 May 2021 20:09:03 +0000
parents d88bbb287923
children a8ea0db2c606
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
26
d1c977aee228 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2dd9bdc695433c217bbb7e11c1c0138245beb801"
iuc
parents: 25
diff changeset
2 <tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy2" profile="19.09">
0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
3 <description>- Detecting coevolving sites via Bayesian graphical models</description>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
4 <macros>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
5 <import>macros.xml</import>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
6 </macros>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
23
ede53272264e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents: 16
diff changeset
9 @SYMLINK_FILES@
26
d1c977aee228 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2dd9bdc695433c217bbb7e11c1c0138245beb801"
iuc
parents: 25
diff changeset
10 ln -s '$bgm_output' ${input_file}.BGM.json &&
2
f2c6ada85b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents: 1
diff changeset
11 hyphy bgm
26
d1c977aee228 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2dd9bdc695433c217bbb7e11c1c0138245beb801"
iuc
parents: 25
diff changeset
12 --alignment $input_file
25
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 23
diff changeset
13 @INPUT_TREE@
0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
14 --run_type $datatype.value
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
15 #if $datatype.value == "codon":
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
16 --code '$datatype.gencodeid'
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
17 #end if
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
18 #if $datatype.value == "protein":
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
19 --baseline_model '$datatype.model'
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
20 #end if
25
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 23
diff changeset
21 @branch_options@
0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
22 --chain '$chain_length'
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
23 --burn_in '$burn_in'
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
24 --samples '$samples'
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
25 --parents '$parents'
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
26 --min_subs '$min_subs'
25
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 23
diff changeset
27 @ERRORS@
0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
28 ]]></command>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
29 <inputs>
23
ede53272264e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents: 16
diff changeset
30 <expand macro="inputs" />
0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
31 <conditional name="datatype">
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
32 <param name="value" type="select" label="Type of data">
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
33 <option value="nucleotide">Nucleotide</option>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
34 <option value="amino-acid">Amino acid</option>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
35 <option value="codon">Codon</option>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
36 </param>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
37 <when value="nucleotide"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
38 <when value="amino-acid">
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
39 <expand macro="substitution" />
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
40 </when>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
41 <when value="codon">
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
42 <expand macro="gencode" />
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
43 </when>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
44 </conditional>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
45 <expand macro="branches"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
46 <param name="chain_length" type="integer" value="100000" min="0" max="1000000000" label="Length of MCMC chain"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
47 <param name="burn_in" type="integer" value="10000" min="0" max="1000000000" label="Number of samples to discard for burn-in"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
48 <param name="samples" type="integer" value="100" min="0" max="100" label="Number of steps to extract from chain sample"/>
5
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
49 <param argument="--max-parents" name="parents" type="integer" value="1" min="1" max="3" label="Maximum number of parents allowed per node" />
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
50 <param argument="--min-subs" name="min_subs" type="integer" value="1" min="1" max="100000" label="Minimum number of ubstitutions per site to be included in the analysis" />
0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
51 </inputs>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
52 <outputs>
26
d1c977aee228 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2dd9bdc695433c217bbb7e11c1c0138245beb801"
iuc
parents: 25
diff changeset
53 <data name="bgm_output" format="hyphy_results.json" />
0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
54 </outputs>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
55 <tests>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
56 <test>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
57 <param name="input_file" ftype="fasta" value="bgm-in1.fa"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
58 <param name="input_nhx" ftype="nhx" value="bgm-in1.nhx"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
59 <output name="bgm_output" file="bgm-out1.json" compare="sim_size"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
60 </test>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
61 </tests>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
62 <help><![CDATA[
5
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
63
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
64 BGM : Bayesian Graphical Models
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
65 ===============================
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
66
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
67 What does this do?
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
68 ------------------
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
69
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
70 This tools identifies groups of sites in the alignments that experience substitutions along the same branches,
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
71 i.g. *co-evolve*.
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
72
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
73 Brief description
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
74 -----------------
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
75
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
76 GM (Bayesian Graphical Model) uses a maximum likelihood ancestral state
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
77 reconstruction to map substitution (non-synonymous only for coding data)
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
78 events to branches in the phylogeny and then analyzes the joint
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
79 distribution of the substitution map using a Bayesian graphical model
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
80 (network). Next, a Markov chain Monte Carlo analysis is used to generate
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
81 a random sample of network structures from the posterior distribution
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
82 given the data. Each node in the network represents a site in the
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
83 alignment, and links (edges) between nodes indicate high posterior
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
84 support for correlated substitutions at the two sites over time, which
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
85 implies coevolution.
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
86
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
87
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
88 Input
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
89 -----
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
90
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
91 1. A *FASTA* sequence alignment.
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
92 2. A phylogenetic tree in the *Newick* format
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
93
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
94 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
95
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
96 Output
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
97 ------
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
98
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
99 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
100
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
101 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BGM for an example)
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
102
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
103 Further reading
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
104 ---------------
1
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
105
5
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
106 http://hyphy.org/methods/selection-methods/#BGM
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
107
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
108
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
109 Tool options
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
110 ------------
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
111 ::
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
112
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
113 --branches Which branches should be tested for selection?
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
114 All [default] : test all branches
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
115
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
116 Internal : test only internal branches (suitable for
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
117 intra-host pathogen evolution for example, where terminal branches
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
118 may contain polymorphism data)
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
119
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
120 Leaves: test only terminal (leaf) branches
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
121
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
122 Unlabeled: if the Newick string is labeled using the {} notation,
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
123 test only branches without explicit labels
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
124 (see http://hyphy.org/tutorials/phylotree/)
1
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
125
5
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
126 --max-parents The maximum number of parents allowed per node, i.e. how many sites
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
127 can directly influence substitution patterns at another site
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
128 Increasing this number scales complexity nonlinearly
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
129 default value: 1
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
130
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
131 --min-subs The minium number of substitutions per site to include it in the analysis
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
132 Filter low complexity (too few substitution) sites
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
133 default value: 1
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
134
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
135 --chains How many MCMC chains to run (does not apply to Variational-Bayes)
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
136 default value: 5
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
137
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
138 --steps MCMC chain length (does not apply to Variational-Bayes)
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
139 default value: 100,000
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
140
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
141 --burn-in MCMC chain burn in (does not apply to Variational-Bayes)
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
142 default value: 10,000
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
143
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
144 --samples MCMC samples to draw (does not apply to Variational-Bayes)
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
145 default value: 100
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
146
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents: 3
diff changeset
147
0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
148 ]]></help>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
149 <expand macro="citations">
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
150 <citation type="doi">10.1371/journal.pcbi.0030231</citation>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
151 </expand>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
152 </tool>