view hyphy_absrel.xml @ 3:fb40b0928cad draft

"planemo upload for repository commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author iuc
date Fri, 14 Feb 2020 16:44:41 -0500
parents de93e1fbdc31
children 181f5b9f139f
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<?xml version="1.0"?>
<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy1">
    <description>adaptive Branch Site Random Effects Likelihood</description>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' absrel_input.fa &&
        ln -s '$input_nhx' absrel_input.nhx &&
        @HYPHYMPI@ absrel
            --alignment ./absrel_input.fa
            --tree ./absrel_input.nhx
            --code '$gencodeid'
            --branches '$branches'
            --output '$absrel_output'
            #if $log:
                > '$absrel_log'
            #end if
        <expand macro="inputs"/>
        <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
        <expand macro="gencode"/>
        <expand macro="branches"/>
        <data name="absrel_log" format="txt">
        <data name="absrel_output" format="hyphy_results.json" />
            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
            <param name="log" value="false"/>
            <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
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.

See the online documentation_ for more information.

.. _documentation:
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msv022</citation>