Mercurial > repos > iuc > hyphy_bgm

comparison hyphy_bgm.xml @ 0:bf97cacc1a55 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:23:09 -0400
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children cdfa1afd7cb0
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-1:000000000000 0:bf97cacc1a55
1 <?xml version="1.0"?>
2 <tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy0">
3 <description>- Detecting coevolving sites via Bayesian graphical models</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_file' bgm_input.fa &&
10 ln -s '$input_nhx' bgm_input.nhx &&
11 @HYPHY_INVOCATION@ bgm
12 --alignment ./bgm_input.fa
13 --tree ./bgm_input.nhx
14 --run_type $datatype.value
15 #if $datatype.value == "codon":
16 --code '$datatype.gencodeid'
17 #end if
18 #if $datatype.value == "protein":
19 --baseline_model '$datatype.model'
20 #end if
21 --branches '$branches'
22 --chain '$chain_length'
23 --burn_in '$burn_in'
24 --samples '$samples'
25 --parents '$parents'
26 --min_subs '$min_subs'
27 > '$bgm_log'
28 ]]></command>
29 <inputs>
30 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
31 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
32 <conditional name="datatype">
33 <param name="value" type="select" label="Type of data">
34 <option value="nucleotide">Nucleotide</option>
35 <option value="amino-acid">Amino acid</option>
36 <option value="codon">Codon</option>
37 </param>
38 <when value="nucleotide"/>
39 <when value="amino-acid">
40 <expand macro="substitution" />
41 </when>
42 <when value="codon">
43 <expand macro="gencode" />
44 </when>
45 </conditional>
46 <expand macro="branches"/>
47 <param name="chain_length" type="integer" value="100000" min="0" max="1000000000" label="Length of MCMC chain"/>
48 <param name="burn_in" type="integer" value="10000" min="0" max="1000000000" label="Number of samples to discard for burn-in"/>
49 <param name="samples" type="integer" value="100" min="0" max="100" label="Number of steps to extract from chain sample"/>
50 <param name="parents" type="integer" value="1" min="1" max="3" label="Maximum number of parents allowed per node"/>
51 <param name="min_subs" type="integer" value="1" min="1" max="100000" label="Minimum number of ubstitutions per site to be included in the analysis"/>
52 </inputs>
53 <outputs>
54 <data name="bgm_log" format="txt"/>
55 <data name="bgm_output" format="hyphy_results.json" from_work_dir="bgm_input.fa.BGM.json"/>
56 </outputs>
57 <tests>
58 <test>
59 <param name="input_file" ftype="fasta" value="bgm-in1.fa"/>
60 <param name="input_nhx" ftype="nhx" value="bgm-in1.nhx"/>
61 <output name="bgm_output" file="bgm-out1.json" compare="sim_size"/>
62 </test>
63 </tests>
64 <help><![CDATA[
65 The Bayesian Graphical Model (BGM) method is a tool for detecting coevolutionary interactions between amino acid positions in a protein.
66 ]]></help>
67 <expand macro="citations">
68 <citation type="doi">10.1371/journal.pcbi.0030231</citation>
69 </expand>
70 </tool>