<?xml version="1.0"?>
<tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy1" profile="19.09">
    <description>Single Likelihood Ancestor Counting</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        hyphy slac
            --alignment ./$input_file
            @INPUT_TREE@
            --code '$gencodeid'
            @branch_options@
            --samples '$number_of_samples'
            --pvalue '$p_value'
            --output '$slac_output'
        @ERRORS@
    ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <expand macro="branches"/>
        <param argument="--pvalue" name="p_value" type="float" value=".1" min="0" max="1" label="P-value"  />
        <param argument="--samples" name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/>
    </inputs>
    <outputs>
        <data name="slac_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="slac_output" file="slac-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
SLAC : Single Likelihood Ancestor Counting
==========================================

What question does this method answer?
--------------------------------------

Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection?

Recommended Applications
------------------------

The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics
(or balancing selection), including adaptive immune escape by viruses. As such, SLAC is ideally suited to identify sites under positive selection which
represent candidate sites subject to strong selective pressures across the entire phylogeny.
SLAC provides legacy functionality as a counting-based method adapted for phylogenetic applications.
In general, this method will be the least statistically robust (compared to FEL or FUBAR), but it is the most directly interpretable.

Brief description
-----------------

SLAC (Single Likelihood Ancestor Counting) uses a maximum likelihood
ancestral state reconstruction and minimum path substitution counting to
estimate site - level dS and dN, and applies a simple binomial - based
test to test if dS differs drom dN. The estimates aggregate information
over all branches, so the signal is derived from pervasive
diversification or conservation. A subset of branches can be selected
for testing as well.

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).

A custom visualization module for viewing these results is available (see http://vision.hyphy.org/SLAC for an example)

Further reading
---------------

http://hyphy.org/methods/selection-methods/#SLAC


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/)

     --pvalue           The significance level used to determine significance

     --samples          Draw this many alternative ancestral state reconstructions
                        to evaluate uncertainty

  ]]>
  </help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msi105</citation>
    </expand>
</tool>