Mercurial > repos > iuc > hyphy_bgm
view macros.xml @ 17:ac0b16f873f7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f4e2f03dfd430f3706cba5fe5b7ac69dbe5da509"
author | iuc |
---|---|
date | Thu, 19 Nov 2020 22:07:01 +0000 |
parents | 26ad9a6b1293 |
children | 63b9f220f585 |
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<?xml version="1.0"?> <macros> <xml name="inputs"> <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> <param name="input_nhx" type="data" format="nhx" label="Input newick file"/> </xml> <xml name="substitution"> <param name="model" type="select" label="Substitution model"> <option value="GTR">GTR - General time reversible model</option> <option value="LG">LG - Generalist empirical model from Le and Gascuel (2008)</option> <option value="HIVBm">HIVBm - Specialist empirical model for between-host HIV sequences</option> <option value="HIVWm">HIVWm - Specialist empirical model for within-host HIV sequences</option> <option value="WAG">WAG - Generalist empirical model from Whelan and Goldman (2001)</option> <option value="JTT">JTT - Generalist empirical model from Jones, Taylor, and Thornton (1996)</option> <option value="JC69">JC69 - Generalist empirical model from with equal exchangeability rates</option> <option value="mtMet">mtMet - Specialist empirical model for metazoan mitochondrial genomes</option> <option value="mtVer">mtVer - Specialist empirical model for vertebrate mitochondrial genomes</option> <option value="mtInv">mtInv - Specialist empirical model for invertebrate mitochondrial genomes</option> <option value="gcpREV">gcpREV - Specialist empirical model for green plant chloroplast genomes</option> </param> </xml> <xml name="conditional_posteriorEstimationMethod"> <conditional name="posteriorEstimationMethod"> <param argument="--method" type="select" label="Posterior estimation method"> <option value="Variational-Bayes">0-th order Variational Bayes approximation</option> <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option> <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option> </param> <when value="Variational-Bayes"> </when> <when value="Metropolis-Hastings"> <expand macro="mcmc_options" /> </when> <when value="Collapsed-Gibbs"> <expand macro="mcmc_options" /> </when> </conditional> </xml> <token name="@posteriorEstimationMethod_cmd@"> #if $posteriorEstimationMethod.method != "Variational-Bayes" --chains '$posteriorEstimationMethod.chains' --chain-length '$posteriorEstimationMethod.chain_length' --burn-in '$posteriorEstimationMethod.samples' --samples '$posteriorEstimationMethod.samples_per_chain' #end if </token> <xml name="mcmc_options"> <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" /> <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" /> <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" /> <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" /> </xml> <xml name="gencode"> <param name="gencodeid" type="select" label="Genetic code"> <option value="Universal">Universal code</option> <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA code</option> <option value="Yeast-mtDNA">Yeast mitochondrial DNA code</option> <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> <option value="Invertebrate-mtDNA">Invertebrate mitochondrial DNA code</option> <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and Hexamita Nuclear code</option> <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA code</option> <option value="Euplotid-Nuclear">Euplotid Nuclear code</option> <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear code</option> <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA code</option> <option value="Flatworm-mtDNA">Flatworm mitochondrial DNA code</option> <option value="Blepharisma-Nuclear">Blepharisma Nuclear code</option> </param> </xml> <xml name="branches"> <param name="branches" type="select" label="Set of branches to test"> <option value="All">All branches</option> <option value="Internal">Internal branches</option> <option value="Leaves">Leaf branches</option> <option value="'Unlabeled-branches'">Unlabeled branches</option> </param> </xml> <xml name="citations"> <citations> <citation type="doi">10.1093/molbev/msz197</citation> <yield/> </citations> </xml> <token name="@VERSION@">2.5.23</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">hyphy</requirement> <yield/> </requirements> </xml> <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> <token name="@CATCH_MPIERR@"><![CDATA[ EC=\$? ; if [ \$EC -ne 0 ] ; then cat errors.log.mpinode0 >&2 ; fi ; exit \$EC ]]></token> <token name="@HYPHY_ENVIRONMENT@"><![CDATA[ export HYPHY=`which hyphy` && export HYPHY_PATH=`dirname \$HYPHY` && export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token> <token name="@HYPHY_INVOCATION@"><![CDATA[ @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB ]]></token> </macros>