Mercurial > repos > iuc > hyphy_fel
view hyphy_fel.xml @ 3:e90f16ec5929 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author | iuc |
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date | Fri, 14 Feb 2020 16:47:30 -0500 |
parents | a8b34daec0d9 |
children | 1b62167f7ab2 |
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<?xml version="1.0"?> <tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy1"> <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 && @HYPHYMPI@ fel --alignment ./fel_input.fa --tree ./fel_input.nhx --code '$gencodeid' --branches '$branches' --srv '$include_srv' --pvalue '$p_value' --output '$fel_output' > '$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" /> </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>