Mercurial > repos > iuc > hyphy_absrel
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author | iuc |
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date | Wed, 30 Mar 2022 00:15:54 +0000 |
parents | 3f59ebfbfe3d |
children | 841557158611 |
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<?xml version="1.0"?> <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy2" profile="19.09"> <description>adaptive Branch Site Random Effects Likelihood</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @SYMLINK_FILES@ ln -s '$absrel_output' ${input_file}.aBSREL.json && @HYPHYMPI@ absrel --alignment ./$input_file @INPUT_TREE@ --code '$gencodeid' @branch_options@ --output '$absrel_output' --multiple-hits $multiple_hits $srv @ERRORS@ ]]></command> <inputs> <expand macro="inputs"/> <expand macro="gencode"/> <param name="multiple_hits" type="select" argument="--multiple-hits" label="Include support for multiple nucleotide substitutions"> <option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option> <option value="Double">Include branch-specific rates for double nucleotide substitutions</option> <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option> </param> <param argument="--srv" type="boolean" truevalue="--srv Yes" falsevalue="" label="Include synonymous rate variation" /> <expand macro="branches"/> </inputs> <outputs> <data name="absrel_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"/> <param name="multiple_hits" value="None" /> <output name="absrel_output" file="absrel-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="multiple_hits" value="Double" /> <output name="absrel_output" file="absrel-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="multiple_hits" value="Double" /> <param name="srv" value="--srv Yes" /> <output name="absrel_output" file="absrel-out2.json" compare="sim_size"/> </test> </tests> <help><![CDATA[ aBSREL : Adaptive Branch-Site Random Effects Likelihood ======================================================= What question does this method answer? -------------------------------------- Is some proportion of sites is subject to positive selection along specific branches or lineages of a phylogeny? Recommended Applications ------------------------ 1. Exploratory testing for evidence of lineage-specific positive diversifying selection in small to medium sized alignments (up to 100 sequences). 2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences) Brief description ----------------- aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive random effects branch-site model framework to test whether each branch has evolved under positive selection, using a procedure which infers an optimal number of rate categories per branch. 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). For each tested branch the analysis will infer the appropriate number of selective regimes, and whether or not there is statistical evidence of positive selection on that branch. A custom visualization module for viewing these results is available (see http://vision.hyphy.org/aBSREL for an example) Further reading --------------- http://hyphy.org/methods/selection-methods/#absrel 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/) ]]></help> <expand macro="citations"> <citation type="doi">10.1093/molbev/msv022</citation> </expand> </tool>