<?xml version="1.0"?>
<tool id="rapidnj" name="Join neighbors" version="@VERSION@">
    <description>rapidly with RapidNJ</description>
    <macros>
        <token name="@VERSION@">2.3.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="v@VERSION@">rapidnj</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $alignments.is_of_type('fasta'):
            #set $input_format = 'fa'
        #else if $alignments.is_of_type('stockholm'):
            #set $input_format = 'sth'
        #else:
            #set $input_format = 'pd'
        #end if
        ln -s '$alignments' input_file.$input_format &&
        rapidnj '$alignments'
            --input-format $input_format
            --output-format $output_format
            --evolution-model $evolution_model
            --cores \${GALAXY_SLOTS:-1}
            #if $bootstrap:
                --bootstrap $bootstrap
            #end if
            --alignment-type $alignment_type
            $no_negative_length
            > '$distances'
        ]]>
    </command>
    <inputs>
        <param name="alignments" type="data" format="phylip,fasta,stockholm" label="Input to construct or reconstruct trees" />
        <param argument="--output-format" name="output_format" type="select" label="Output format">
            <option value="t">Phylogenetic tree in newick format</option>
            <option value="m">Distance matrix</option>
        </param>
        <param argument="--evolution-model" name="evolution_model" type="select" label="Evolution model" help="Specifies which sequence evolution method to use when computing distance estimates from multiple alignments, using Kimura's model by default.">
            <option value="kim">Kimura</option>
            <option value="jc">Jukes-Cantor</option>
        </param>
        <param argument="--bootstrap" type="integer" optional="true" label="Samples to use for computing bootstrap" help="The output tree will be annotated with bootstrap values" />
        <param argument="--alignment-type" name="alignment_type" type="select" label="Input alignment type">
            <option value="p">Protein</option>
            <option value="d">DNA</option>
        </param>
        <param argument="--no-negative-length" name="no_negative_length" type="boolean" truevalue="--no-negative-length" falsevalue="" label="Adjust for negative branch lengths." />
    </inputs>
    <outputs>
        <data name="distances" format="nhx" label="${tool.name} on ${on_string}: Calculated distances">
            <change_format>
                <when input="output_format" value="m" format="tabular" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="alignments" value="rapidnj-in1.fa" />
            <param name="output_format" value="t" />
            <output name="distances" ftype="nhx" value="rapidnj-out1.nhx" />
        </test>
        <test>
            <param name="alignments" value="rapidnj-in2.fa" />
            <param name="output_format" value="t" />
            <output name="distances" ftype="nhx" value="rapidnj-out2.nhx" />
        </test>
    </tests>
    <help><![CDATA[
============
RapidNJ
============

Especially useful for large datasets where maximum-likelihood based phylogenetic inference becomes intractable, RapidNJ reduces the computing time of canonical neighbour-joining for phylogenetic tree inference. RapidNJ accepts either matrices in phylip format or alignments in stockholm or FASTA format. 
        ]]>
    </help>
    <citations>
        <citation type="doi">doi:10.1007/978-3-540-87361-7_10</citation>
    </citations>
</tool>