Mercurial > repos > iuc > hyphy_bgm
comparison macros.xml @ 5:823a5afee916 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
| author | iuc |
|---|---|
| date | Thu, 20 Feb 2020 18:09:03 -0500 |
| parents | f276acfde263 |
| children | 1647c9f95dc7 |
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| 4:f276acfde263 | 5:823a5afee916 |
|---|---|
| 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> |