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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
author | iuc |
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date | Thu, 17 Jan 2019 04:23:36 -0500 |
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children | 6c3ece5fb602 |
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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" /> <expand macro="version_command" /> <command detect_errors="exit_code"> <![CDATA[ ln -s '$input_file' fel_input.fa && ln -s '$input_nhx' fel_input.nhx && echo $gencodeid > tool_params && echo `pwd`/fel_input.fa >> tool_params && echo `pwd`/fel_input.nhx >> tool_params && echo '$branches' >> tool_params && echo '$include_srv' >> tool_params && echo '$p_value' >> tool_params && @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FEL.bf > '$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="1">Yes (recommended)</option> <option value="2">No</option> </param> </inputs> <outputs> <data name="fel_log" format="txt" /> <data name="fel_output" format="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. ]]> </help> <expand macro="citations"> <citation type="doi">10.1093/molbev/msi105</citation> </expand> </tool>