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comparison macros.xml @ 5:16b4a3869bd5 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 18:12:40 -0500
parents c16dd6b14657
children d55ab4b13106
comparison
equal deleted inserted replaced
4:c16dd6b14657 5:16b4a3869bd5
4 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> 4 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
5 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/> 5 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
6 </xml> 6 </xml>
7 <xml name="substitution"> 7 <xml name="substitution">
8 <param name="model" type="select" label="Substitution model"> 8 <param name="model" type="select" label="Substitution model">
9 <option value="GTR">GTR - General time reversible
10 model</option>
9 <option value="LG">LG - Generalist empirical model from 11 <option value="LG">LG - Generalist empirical model from
10 Le and Gascuel (2008)</option> 12 Le and Gascuel (2008)</option>
11 <option value="HIVBm">HIVBm - Specialist empirical model 13 <option value="HIVBm">HIVBm - Specialist empirical model
12 for between-host HIV sequences</option> 14 for between-host HIV sequences</option>
13 <option value="HIVWm">HIVWm - Specialist empirical model 15 <option value="HIVWm">HIVWm - Specialist empirical model
24 for vertebrate mitochondrial genomes</option> 26 for vertebrate mitochondrial genomes</option>
25 <option value="mtInv">mtInv - Specialist empirical model 27 <option value="mtInv">mtInv - Specialist empirical model
26 for invertebrate mitochondrial genomes</option> 28 for invertebrate mitochondrial genomes</option>
27 <option value="gcpREV">gcpREV - Specialist empirical 29 <option value="gcpREV">gcpREV - Specialist empirical
28 model for green plant chloroplast genomes</option> 30 model for green plant chloroplast genomes</option>
29 <option value="GTR">GTR - General time reversible
30 model</option>
31 </param> 31 </param>
32 </xml> 32 </xml>
33
34 <xml name="conditional_posteriorEstimationMethod">
35 <conditional name="posteriorEstimationMethod">
36 <param argument="--method" type="select" label="Posterior estimation method">
37 <option value="Variational-Bayes">0-th order Variational Bayes approximation</option>
38 <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option>
39 <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option>
40 </param>
41 <when value="Variational-Bayes">
42 </when>
43 <when value="Metropolis-Hastings">
44 <expand macro="mcmc_options" />
45 </when>
46 <when value="Collapsed-Gibbs">
47 <expand macro="mcmc_options" />
48 </when>
49 </conditional>
50 </xml>
51
52 <token name="@posteriorEstimationMethod_cmd@">
53 #if $posteriorEstimationMethod.method != "Variational-Bayes"
54 --chains '$posteriorEstimationMethod.chains'
55 --chain-length '$posteriorEstimationMethod.chain_length'
56 --burn-in '$posteriorEstimationMethod.samples'
57 --samples '$posteriorEstimationMethod.samples_per_chain'
58 #end if
59 </token>
60
61 <xml name="mcmc_options">
62 <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" />
63 <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />
64 <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" />
65 <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" />
66 </xml>
67
33 <xml name="gencode"> 68 <xml name="gencode">
34 <param name="gencodeid" type="select" label="Genetic code"> 69 <param name="gencodeid" type="select" label="Genetic code">
35 <option value="Universal">Universal code</option> 70 <option value="Universal">Universal code</option>
36 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA 71 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA
37 code</option> 72 code</option>
60 <xml name="branches"> 95 <xml name="branches">
61 <param name="branches" type="select" label="Set of branches to test"> 96 <param name="branches" type="select" label="Set of branches to test">
62 <option value="All">All branches</option> 97 <option value="All">All branches</option>
63 <option value="Internal">Internal branches</option> 98 <option value="Internal">Internal branches</option>
64 <option value="Leaves">Leaf branches</option> 99 <option value="Leaves">Leaf branches</option>
65 <option value="'Unlabeled-branches'">Unlabeled 100 <option value="'Unlabeled-branches'">Unlabeled branches</option>
66 branches</option>
67 </param> 101 </param>
68 </xml> 102 </xml>
69 <xml name="citations"> 103 <xml name="citations">
70 <citations> 104 <citations>
71 <citation type="doi">10.1093/bioinformatics/bti079</citation> 105 <citation type="doi">10.1093/molbev/msz197</citation>
72 <yield/> 106 <yield/>
73 </citations> 107 </citations>
74 </xml> 108 </xml>
75 <token name="@VERSION@">2.5.3</token> 109 <token name="@VERSION@">2.5.4</token>
76 <xml name="requirements"> 110 <xml name="requirements">
77 <requirements> 111 <requirements>
78 <requirement type="package" version="@VERSION@"> 112 <requirement type="package" version="@VERSION@">hyphy</requirement>
79 hyphy</requirement>
80 <yield/> 113 <yield/>
81 </requirements> 114 </requirements>
82 </xml> 115 </xml>
83 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> 116 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
84 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which hyphy` && 117 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[
85 export HYPHY_PATH=`dirname \$HYPHY` && 118 export HYPHY=`which hyphy` &&
86 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token> 119 export HYPHY_PATH=`dirname \$HYPHY` &&
87 <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB ]]></token> 120 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>
121 <token name="@HYPHY_INVOCATION@"><![CDATA[
122 @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB
123 ]]></token>
88 </macros> 124 </macros>