Mercurial > repos > iuc > hyphy_fel
view hyphy_fel.xml @ 2:a8b34daec0d9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
author | iuc |
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date | Thu, 13 Feb 2020 15:04:13 -0500 |
parents | 6c3ece5fb602 |
children | e90f16ec5929 |
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<?xml version="1.0"?> <tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy0"> <description>Fixed Effects Likelihood</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '$input_file' fel_input.fa && ln -s '$input_nhx' fel_input.nhx && @HYPHY_INVOCATION@ fel --alignment ./fel_input.fa --tree ./fel_input.nhx --code '$gencodeid' --branches '$branches' --srv '$include_srv' --pvalue '$p_value' > '$fel_log' ]]></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"> <option value="Yes">Yes (recommended)</option> <option value="No">No</option> </param> </inputs> <outputs> <data name="fel_log" format="txt"/> <data name="fel_output" format="hyphy_results.json" from_work_dir="fel_input.fa.FEL.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> </tests> <help><![CDATA[ FEL (Fixed Effects Likelihood) uses a maximum-likelihood (ML) approach to infer nonsynoymous (dN) and synonymous (dS) substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. This method assumes that the selection pressure for each site is constant along the entire phylogeny. See the online documentation_ for more information. .. _documentation: http://hyphy.org/methods/selection-methods/#fel ]]></help> <expand macro="citations"> <citation type="doi">10.1093/molbev/msi105</citation> </expand> </tool>