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comparison hyphy_bgm.xml @ 35:35723f87964d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
author iuc
date Thu, 02 Mar 2023 15:13:13 +0000
parents 5b6b8b08f1a9
children
comparison
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34:4515f2f64e13 35:35723f87964d
1 <?xml version="1.0"?> 1 <tool id="hyphy_bgm" name="HyPhy-BGM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <tool id="hyphy_bgm" name="HyPhy-BGM" version="@TOOL_VERSION@+galaxy2" profile="19.09">
3 <description>- Detecting coevolving sites via Bayesian graphical models</description> 2 <description>- Detecting coevolving sites via Bayesian graphical models</description>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
7 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
15 --run_type $datatype.value 14 --run_type $datatype.value
16 #if $datatype.value == "codon": 15 #if $datatype.value == "codon":
17 --code '$datatype.gencodeid' 16 --code '$datatype.gencodeid'
18 #end if 17 #end if
19 #if $datatype.value == "protein": 18 #if $datatype.value == "protein":
20 --baseline_model '$datatype.model' 19 --baseline_model '$datatype.baseline_model'
21 #end if 20 #end if
22 @branch_options@ 21 @branch_options@
23 --chain '$chain_length' 22 --chain '$chain_length'
24 --burn_in '$burn_in' 23 --burn_in '$burn_in'
25 --samples '$samples' 24 --samples '$samples'
35 <option value="amino-acid">Amino acid</option> 34 <option value="amino-acid">Amino acid</option>
36 <option value="codon">Codon</option> 35 <option value="codon">Codon</option>
37 </param> 36 </param>
38 <when value="nucleotide"/> 37 <when value="nucleotide"/>
39 <when value="amino-acid"> 38 <when value="amino-acid">
40 <expand macro="substitution" /> 39 <expand macro="substitution" argument="--baseline_model" />
41 </when> 40 </when>
42 <when value="codon"> 41 <when value="codon">
43 <expand macro="gencode" /> 42 <expand macro="gencode" />
44 </when> 43 </when>
45 </conditional> 44 </conditional>
46 <expand macro="branches"/> 45 <expand macro="branches"/>
47 <param name="chain_length" type="integer" value="100000" min="0" max="1000000000" label="Length of MCMC chain"/> 46 <param argument="--chain" 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"/> 47 <param argument="--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"/> 48 <param argument="--samples" type="integer" value="100" min="0" max="100" label="Number of steps to extract from chain sample"/>
50 <param argument="--max-parents" name="parents" type="integer" value="1" min="1" max="3" label="Maximum number of parents allowed per node" /> 49 <param argument="--max-parents" name="parents" type="integer" value="1" min="1" max="3" label="Maximum number of parents allowed per node" />
51 <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" /> 50 <param argument="--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> 51 </inputs>
53 <outputs> 52 <outputs>
54 <data name="bgm_output" format="hyphy_results.json" /> 53 <data name="bgm_output" format="hyphy_results.json" />
55 </outputs> 54 </outputs>
56 <tests> 55 <tests>