<?xml version="1.0"?>
<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy1" profile="19.09">
    <description>adaptive Branch Site Random Effects Likelihood</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <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
        @ERRORS@
        ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
        <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>
        <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>
    </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>