Mercurial > repos > iuc > hyphy_fubar
view macros.xml @ 33:55a45d4c31dc draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author | iuc |
---|---|
date | Wed, 30 Mar 2022 00:18:55 +0000 |
parents | 90e57f65ddd9 |
children | 1b893cdead55 |
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<?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">2.5.36</token> <xml name="inputs"> <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" /> <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/> </xml> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">HyPhy</xref> </xrefs> </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="srv"> <conditional name="advanced" label="Advanced options"> <param name="srv_options" type="select" label="Set advanced parameters" help="If these parameters are not set, RELAX will calculate appropriate values at runtime"> <option value="defaults">Calculate</option> <option value="specify">Specify values</option> </param> <when value="defaults" /> <when value="specify"> <param argument="--grid-size" type="integer" value="250" label="Points in the initial distributional guess for likelihood fitting" /> <param argument="--starting-points" type="integer" value="1" label="Initial random guesses to seed rate values optimization" /> <param argument="--syn-rates" type="integer" min="1" max="10" value="3" label="Alpha rate classes to include in the model" /> <param argument="--rates" type="integer" min="2" max="10" value="3" label="Omega rate classes to include in the model" /> <param argument="--srv" type="boolean" truevalue="Yes" falsevalue="No" label="Include synonymous rate variation" /> <param name="save_alternative_model" type="boolean" label="Save alternative model fit" /> </when> </conditional> </xml> <xml name="branches"> <conditional name="branch_cond"> <param name="branch_sel" 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> <option value="specify">Enter a branch label</option> </param> <when value="specify"> <param name="branch_label" type="text" value="Test" optional="false" label="Branch label"> <sanitizer invalid_char=""> <valid initial="default" /> </sanitizer> </param> </when> <when value="All" /> <when value="Internal" /> <when value="Leaves" /> <when value="'Unlabeled-branches'" /> </conditional> </xml> <xml name="citations"> <citations> <citation type="doi">10.1093/molbev/msz197</citation> <yield/> </citations> </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement> <yield/> </requirements> </xml> <xml name="alternative_model_output"> <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json"> <filter>advanced['save_alternative_model']</filter> </data> </xml> <xml name="resample"> <param argument="--resample" type="integer" value="0" min="0" optional="true" label="Perform parametric bootstrap resampling to derive site-level null LRT distributions" help="Warning: This will result in a significantly slower analysis. This parameter specifies the maximum number of replicates per site." /> </xml> <token name="@resample@"><![CDATA[ #if $resample: --resample $resample #end if ]]> </token> <token name="@INPUT_TREE@"><![CDATA[ #if $input_nhx: --tree input.nhx #end if ]]> </token> <token name="@branch_options@"><![CDATA[ #if $branch_cond.branch_sel == 'specify': --branches '$branch_cond.branch_label' #else: --branches $branch_cond.branch_sel #end if ]]> </token> <token name="@advanced_options@"><![CDATA[ #if $advanced.srv_options == 'specify': --grid-size $advanced.grid_size --starting-points $advanced.starting_points --syn-rates $advanced.syn_rates --rates $advanced.rates --srv $advanced.srv #if $advanced.save_alternative_model: --save-fit alternative_model.json #end if #end if ]]></token> <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> <token name="@ERRORS@"><![CDATA[ ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; 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> <token name="@SYMLINK_FILES@"><![CDATA[ #if $input_nhx is not None: ln -s '$input_nhx' input.nhx && #end if ln -s '$input_file' input.$input_file.extension && #set $input_file = 'input.%s' % $input_file.extension ]]></token> </macros>