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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d
author | iuc |
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date | Thu, 18 Aug 2022 13:53:29 +0000 |
parents | 8a6ef85b934d |
children | ec783806a5c3 |
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<?xml version="1.0"?> <tool id="hyphy_fel" name="HyPhy-FEL" version="@TOOL_VERSION@+galaxy1" profile="19.09"> <description>Fixed Effects Likelihood</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @SYMLINK_FILES@ @HYPHYMPI@ fel --alignment ./$input_file @INPUT_TREE@ --code '$gencodeid' @branch_options@ --srv '$include_srv' --pvalue '$p_value' @resample@ --precision $precision $ci --output '$fel_output' @ERRORS@ ]]></command> <inputs> <expand macro="inputs"/> <expand macro="gencode"/> <expand macro="branches"/> <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/> <param name="include_srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site"> <option value="Yes">Yes (recommended)</option> <option value="No">No</option> </param> <param argument="--ci" type="boolean" truevalue="--ci Yes" falsevalue="" label="Compute profile likelihood confidence intervals for each variable site" /> <expand macro="resample"/> <param argument="--precision" type="select" label="Optimization precision for preliminary fits"> <option value="standard">Standard</option> <option value="reduced">Reduced for faster fitting</option> </param> </inputs> <outputs> <data name="fel_output" format="hyphy_results.json" /> </outputs> <tests> <test> <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> <output name="fel_output" file="fel-out1.json" compare="sim_size"/> </test> <test> <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> <param name="ci" value="true" /> <param name="precision" value="reduced" /> <output name="fel_output" file="fel-out1.json" compare="sim_size"/> </test> </tests> <help><![CDATA[ FEL : Fixed effects likelihood ============================== What question does this method answer? -------------------------------------- Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection? Recommended Applications ------------------------ The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics (or balancing selection), including adaptive immune escape by viruses. As such, FEL is ideally suited to identify sites under positive selection which represent candidate sites subject to strong selective pressures across the entire phylogeny. FEL is our recommended method for analyzing small-to-medium size datasets when one wishes only to study pervasive selection at individual sites. Brief description ----------------- FEL (Fixed Effects Likelihood) estimates site-wise synonymous (alpha) and non-synonymous rates (beta), and uses a likelihood ratio test to determine if beta != alpha at a site. The estimates aggregate information over all branches, so the signal is derived from pervasive diversification or conservation. A subset of branches can be selected for testing as well, in which case an additional (nuisance) parameter will be inferred -- the non-synonymous rate on branches NOT selected for testing. Input ----- 1. A *FASTA* sequence alignment. 2. A phylogenetic tree in the *Newick* format Note: the names of sequences in the alignment must match the names of the sequences in the tree. Output ------ A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FEL for an example) Further reading --------------- http://hyphy.org/methods/selection-methods/#FEL Tool options ------------ :: --code Which genetic code to use --branches Which branches should be tested for selection? All [default] : test all branches Internal : test only internal branches (suitable for intra-host pathogen evolution for example, where terminal branches may contain polymorphism data) Leaves: test only terminal (leaf) branches Unlabeled: if the Newick string is labeled using the {} notation, test only branches without explicit labels (see http://hyphy.org/tutorials/phylotree/) --pvalue The significance level used to determine significance --srv Include site-to-site synonymous rate variation? Yes [default] or No ]]> </help> <expand macro="citations"> <citation type="doi">10.1093/molbev/msi105</citation> </expand> </tool>