Mercurial > repos > iuc > hyphy_bgm

annotate hyphy_bgm.xml @ 36:e45ec7931bfd draft default tip

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 d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:38:49 +0000
parents d162a1f8e495
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
35
d162a1f8e495 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
1 <tool id="hyphy_bgm" name="HyPhy-BGM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
2 <description>- Detecting coevolving sites via Bayesian graphical models</description>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
3 <macros>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
5 </macros>
33
ac3e2bd6ef2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents: 32
diff changeset
6 <expand macro="bio_tools"/>
0
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
ebf951fda5a3 "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
dd69abea3146 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents: 16
diff changeset
9 @SYMLINK_FILES@
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
10 ENV="TOLERATE_NUMERICAL_ERRORS=1;" @HYPHYMP@ bgm
26
9a4d1613c31d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2dd9bdc695433c217bbb7e11c1c0138245beb801"
iuc
parents: 25
diff changeset
11 --alignment $input_file
25
c28a0ba1b36a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 23
diff changeset
12 @INPUT_TREE@
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
13 --type $datatype.value
0
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
14 #if $datatype.value == "codon":
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
15 --code '$datatype.gencodeid'
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
16 #end if
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
17 #if $datatype.value == "amino-acid":
35
d162a1f8e495 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
18 --baseline_model '$datatype.baseline_model'
0
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
19 #end if
25
c28a0ba1b36a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 23
diff changeset
20 @branch_options@
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
21 --steps '$chain_length'
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
22 --burn-in '$burn_in'
0
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
23 --samples '$samples'
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
24 --max-parents '$parents'
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
25 --min-subs '$min_subs'
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
26 --output '$bgm_output'
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
27 > bgm_stdout.md
25
c28a0ba1b36a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 23
diff changeset
28 @ERRORS@
0
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
29 ]]></command>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
30 <inputs>
23
dd69abea3146 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents: 16
diff changeset
31 <expand macro="inputs" />
0
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
32 <conditional name="datatype">
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
33 <param name="value" type="select" label="Type of data">
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
34 <option value="nucleotide">Nucleotide</option>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
35 <option value="amino-acid">Amino acid</option>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
36 <option value="codon">Codon</option>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
37 </param>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
38 <when value="nucleotide"/>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
39 <when value="amino-acid">
35
d162a1f8e495 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
40 <expand macro="substitution" argument="--baseline_model" />
0
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
41 </when>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
42 <when value="codon">
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
43 <expand macro="gencode" />
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
44 </when>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
45 </conditional>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
46 <expand macro="branches"/>
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
47 <section name="advanced_options" title="Advanced Options" expanded="false">
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
48 <param argument="--steps" name="chain_length" type="integer" value="100000" min="0" max="1000000000" label="Length of MCMC chain" help="The total number of steps in the MCMC simulation."/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
49 <param argument="--burn-in" type="integer" value="10000" min="0" max="1000000000" label="Number of samples to discard for burn-in" help="The initial portion of the MCMC chain is often discarded to allow the simulation to converge to the posterior distribution."/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
50 <param argument="--samples" type="integer" value="100" min="0" max="100000" label="Number of steps to extract from chain sample" help="The number of samples to draw from the MCMC chain after the burn-in period."/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
51 <param argument="--max-parents" name="parents" type="integer" value="1" min="1" max="3" label="Maximum number of parents allowed per node" help="This parameter controls the complexity of the graphical model. It sets the maximum number of other sites that can directly influence a given site."/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
52 <param argument="--min-subs" type="integer" value="1" min="1" max="1000" label="Minimum number of substitutions per site to be included in the analysis" help="Sites with very few substitutions provide little information for detecting co-evolution. This parameter allows you to filter out such low-complexity sites from the analysis."/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
53 </section>
0
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
54 </inputs>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
55 <outputs>
26
9a4d1613c31d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2dd9bdc695433c217bbb7e11c1c0138245beb801"
iuc
parents: 25
diff changeset
56 <data name="bgm_output" format="hyphy_results.json" />
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
57 <data name="bgm_md_report" format="markdown" from_work_dir="bgm_stdout.md" label="BGM Report (Markdown) for ${tool.name} on ${on_string}" />
0
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
58 </outputs>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
59 <tests>
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
60 <test expect_num_outputs="2">
0
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
61 <param name="input_file" ftype="fasta" value="bgm-in1.fa"/>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
62 <param name="input_nhx" ftype="nhx" value="bgm-in1.nhx"/>
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
63 <conditional name="datatype">
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
64 <param name="value" value="codon"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
65 <param name="gencodeid" value="Universal"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
66 </conditional>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
67 <output name="bgm_output">
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
68 <assert_contents>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
69 <has_text text="Probability that site 2 is conditionally dependent on site 1"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
70 <has_text text="analysis"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
71 </assert_contents>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
72 </output>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
73 <output name="bgm_md_report">
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
74 <assert_contents>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
75 <has_text text="Analysis Description"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
76 <has_text text="BGM analysis summary on 9 sites each with at least 1 substitutions"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
77 </assert_contents>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
78 </output>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
79 </test>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
80 <test expect_num_outputs="2">
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
81 <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
82 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
83 <conditional name="datatype">
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
84 <param name="value" value="amino-acid"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
85 <param name="baseline_model" value="LG"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
86 </conditional>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
87 <output name="bgm_output">
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
88 <assert_contents>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
89 <has_text text='"samples":100'/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
90 <has_text text="Probability that sites 1 and 2 are not conditionally independent"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
91 </assert_contents>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
92 </output>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
93 <output name="bgm_md_report">
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
94 <assert_contents>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
95 <has_text text="pairs of conditionally dependent sites found"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
96 <has_text text="## BGM analysis summary on 149 sites each with at least 1 substitutions."/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
97 </assert_contents>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
98 </output>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
99 </test>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
100 <test expect_num_outputs="2">
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
101 <param name="input_file" ftype="fasta" value="bgm-in1.fa"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
102 <param name="input_nhx" ftype="nhx" value="bgm-in1.nhx"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
103 <conditional name="datatype">
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
104 <param name="value" value="nucleotide"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
105 </conditional>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
106 <output name="bgm_output">
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
107 <assert_contents>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
108 <has_text text='"samples":100'/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
109 <has_text text="Probability that sites 1 and 2 are not conditionally independent"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
110 </assert_contents>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
111 </output>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
112 <output name="bgm_md_report">
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
113 <assert_contents>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
114 <has_text text=">type => nucleotide"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
115 <has_text text="BGM analysis summary on 24 sites each with at least 1 substitutions"/>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
116 </assert_contents>
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
117 </output>
0
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
118 </test>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
119 </tests>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
120 <help><![CDATA[
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
121
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
122 BGM : Bayesian Graphical Models for Co-evolving Sites
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
123 =====================================================
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
124
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
125 **What does this do?**
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
126
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
127 This tool identifies groups of sites in a sequence alignment that appear to be co-evolving. Co-evolving sites are those that experience substitutions along the same branches of a phylogenetic tree more often than expected by chance. This pattern of correlated substitutions can imply a functional or structural relationship between the sites. For example, a destabilizing mutation at one site might be compensated for by a mutation at another site to preserve the protein's structure or function.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
128
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
129 **How does it work?**
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
130
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
131 BGM employs a Bayesian Graphical Model to uncover these dependencies. The core idea is to represent each site in the alignment as a node in a graph. The algorithm then seeks to find the edges (links) between these nodes that represent statistically significant correlations in substitution patterns.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
132
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
133 The process involves several steps:
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
134
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
135 1. **Ancestral State Reconstruction:** First, the method reconstructs the evolutionary history of the sequences using maximum likelihood. This allows the tool to map substitution events to specific branches of the phylogenetic tree. For coding data, only non-synonymous substitutions (those that change the amino acid) are considered.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
136
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
137 2. **Bayesian Graphical Model:** The joint distribution of these substitution maps is then analyzed using a Bayesian graphical model. This model represents the probability of the observed substitution patterns given a particular network of dependencies between sites.
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
138
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
139 3. **MCMC Sampling:** To explore the vast space of possible network structures, BGM uses a Markov Chain Monte Carlo (MCMC) analysis. This method generates a random sample of network structures from the posterior distribution, meaning it finds the networks that are most likely given the data.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
140
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
141 4. **Identifying Co-evolving Sites:** The links (edges) that appear most frequently in the sampled networks are the ones with the highest posterior support. These links connect the sites that are most likely to be co-evolving.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
142
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
143 **Input**
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
144
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
145 * A multiple sequence alignment in FASTA or NEXUS format.
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
146 * A phylogenetic tree in Newick format. The names of the sequences in the alignment must match the names of the tips in the tree.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
147
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
148 **Output**
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
149
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
150 * **JSON file:** A JSON file containing the detailed results of the analysis, including the posterior probabilities of the links between sites. (See http://hyphy.org/resources/json-fields.pdf for a description of the fields).
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
151 * **Markdown report:** A summary report in Markdown format.
1
3f67160aaafd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
152
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
153 A custom visualization module for viewing BGM results is available at http://vision.hyphy.org/BGM.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
154
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
155 **Tool Options**
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
156
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
157 * **Type of data:** The type of sequence data in the alignment file.
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
158 * `nucleotide`: For DNA or RNA sequences.
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
159 * `amino-acid`: For protein sequences.
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
160 * `codon`: For coding DNA sequences. This is the default.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
161
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
162 * **Genetic code:** If using codon data, the genetic code to use for translation.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
163
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
164 * **Substitution model:** If using amino-acid data, the substitution model to use.
1
3f67160aaafd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
165
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
166 * **Set of branches to test:** The set of branches in the phylogeny to consider for the analysis.
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
167 * `All branches`: (Default) Use all branches in the tree.
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
168 * `Internal branches`: Use only the internal branches. This can be useful for studying pathogen evolution within a host, for example, where terminal branches might represent polymorphism rather than fixed differences.
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
169 * `Leaf branches`: Use only the terminal (leaf) branches.
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
170 * `Unlabeled branches`: If the Newick tree is annotated with labels, use only the branches that do not have a label.
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
171 * `Custom`: Specify a custom set of branches by providing a label.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
172
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
173 * **Length of MCMC chain:** The total number of steps in the MCMC simulation. A longer chain will explore the space of possible networks more thoroughly but will take longer to run.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
174
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
175 * **Number of samples to discard for burn-in:** The initial portion of the MCMC chain is often discarded to allow the simulation to converge to the posterior distribution. This parameter specifies the number of initial samples to discard.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
176
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
177 * **Number of steps to extract from chain sample:** The number of samples to draw from the MCMC chain after the burn-in period. These samples are used to estimate the posterior probabilities of the links.
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
178
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
179 * **Maximum number of parents allowed per node:** This parameter controls the complexity of the graphical model. It sets the maximum number of other sites that can directly influence a given site. Increasing this number can reveal more complex dependency networks but also significantly increases the computational complexity.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
180
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
181 * **Minimum number of substitutions per site:** Sites with very few substitutions provide little information for detecting co-evolution. This parameter allows you to filter out such low-complexity sites from the analysis.
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
182
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
183 **Further Reading**
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
184
36
e45ec7931bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
185 For more information, please see the HyPhy documentation: http://hyphy.org/methods/selection-methods/#BGM
5
45a0eca3ef44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 3
diff changeset
186
0
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
187 ]]></help>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
188 <expand macro="citations">
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
189 <citation type="doi">10.1371/journal.pcbi.0030231</citation>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
190 </expand>
ebf951fda5a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
191 </tool>