<tool id="qiime_make_phylogeny" name="Make phylogeny" version="1.9.1">

    <description></description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />

    <version_command><![CDATA[
        make_phylogeny.py --version
    ]]>
    </version_command>

    <stdio></stdio>

    <command>
<![CDATA[  
        make_phylogeny.py 
            -i $input_fp
            -o $result_fp
            -t $tree_method
            -l $log_fp
            -r $root_method
    ]]>
    </command>

    <inputs>
        <param name="input_fp" type="data" format="fasta" 
            label="Input fasta alignment" help="(-i/--input_fp)"/>

        <param name="tree_method" type="select" 
            label="Method for tree building" help="(-t/--tree_method)">
            <option value="clustalw">ClustalW</option>
            <option value="raxml_v730">raxml_v730</option>
            <option value="muscle">muscle</option>
            <option value="fasttree" selected="true">fasttree</option>
            <option value="clearcut">clearcut</option>
        </param>

        <param name="root_method" type="select" 
            label="Method for choosing root of phylo tree" help="(-r/--root_method)">
            <option value="midpoint">Midpoint</option>
            <option value="tree_method_default" selected="true">Default method of tree method</option>
        </param>

    </inputs>

    <outputs>
        <data format="txt" name="result_fp" 
            label="${tool.name} on ${on_string}: Tree"/>
        <data format="txt" name="log_fp" 
            label="${tool.name} on ${on_string}: Log"/>
    </outputs>

    <tests>
        <test>
        </test>
    </tests>

    <help><![CDATA[
**What it does**

This tool produces a tree from a multiple sequence alignment. Trees are constructed with a set of sequences representative of the OTUs

More information about this tool is available on 
`QIIME documentation <http://qiime.org/scripts/make_phylogeny.html>`_.
    ]]>
    </help>

    <citations>
        <expand macro="citations" />
    </citations>
</tool>