<tool id="qiime_make_phylogeny" name="Make phylogeny" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="8.2.9">raxml</requirement>
        <requirement type="package" version="2.1">clustalw</requirement>
        <requirement type="package" version="3.8.1551">muscle</requirement>
        <requirement type="package" version="1.0.9">clearcut</requirement>
    </expand>
    <version_command>make_phylogeny.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        make_phylogeny.py
            --input_fp '$input_fp'
            --result_fp '$result_fp'
            --tree_method '$tree_method'
            --log_fp '$log_fp'
            --root_method '$root_method'
    ]]></command>
    <inputs>
        <param argument="--input_fp" type="data" format="fasta" label="Input fasta alignment"/>
        <param argument="--tree_method" type="select" label="Method for tree building">
            <option value="clustalw">ClustalW</option>
            <option value="raxml_v730">raxml_v730</option>
            <option value="muscle">muscle</option>
            <option value="fasttree" selected="true">fasttree</option>
            <option value="clearcut">clearcut</option>
        </param>
        <param argument="--root_method" type="select" label="Method for choosing root of phylo tree">
            <option value="midpoint">Midpoint</option>
            <option value="tree_method_default" selected="true">Default method of tree method</option>
        </param>
    </inputs>
    <outputs>
        <data name="result_fp" format="nhx" label="${tool.name} on ${on_string}: Tree"/>
        <data name="log_fp" format="txt" label="${tool.name} on ${on_string}: Log"/>
    </outputs>
    <tests>
        <test>
            <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
            <param name="tree_method" value="fasttree"/>
            <param name="root_method" value="tree_method_default" />
            <output name="result_fp" file="make_phylogeny/fasttree_tree_method_default.tre"/>
            <output name="log_fp">
                <assert_contents>
                    <has_text text="Method:fasttree"/>
                    <has_text text="CogentTreeBuilder parameters:"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
            <param name="tree_method" value="raxml_v730"/>
            <param name="root_method" value="tree_method_default" />
            <output name="result_fp" ftype="nhx" >
                <assert_contents>
                    <has_text text="seq_20"/>
                    <has_text text="seq_46"/>
                    <has_text text="seq_11"/>
                </assert_contents>
            </output>
	    <output name="log_fp">
                <assert_contents>
                    <has_text text="Method:raxml_v730"/>
                    <has_text text="CogentTreeBuilder parameters:"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
            <param name="tree_method" value="muscle"/>
            <param name="root_method" value="tree_method_default" />
            <output name="result_fp" file="make_phylogeny/muscle.tre"/>
            <output name="log_fp">
                <assert_contents>
                    <has_text text="Method:muscle"/>
                    <has_text text="CogentTreeBuilder parameters:"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
            <param name="tree_method" value="clustalw"/>
            <param name="root_method" value="tree_method_default" />
            <output name="result_fp" file="make_phylogeny/clustalw.tre"/>
            <output name="log_fp">
                <assert_contents>
                    <has_text text="Method:clustalw"/>
                    <has_text text="CogentTreeBuilder parameters:"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
            <param name="tree_method" value="clearcut"/>
            <param name="root_method" value="tree_method_default" />
            <output name="result_fp" ftype="nhx" >
                <assert_contents>
                    <has_text text="seq_20"/>
                    <has_text text="seq_46"/>
                    <has_text text="seq_11"/>
                </assert_contents>
            </output>
            <output name="log_fp">
                <assert_contents>
                    <has_text text="Method:clearcut"/>
                    <has_text text="CogentTreeBuilder parameters:"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
            <param name="tree_method" value="fasttree"/>
            <param name="root_method" value="midpoint" />
            <output name="result_fp" file="make_phylogeny/fasttree_midpoint.tre"/>
            <output name="log_fp">
                <assert_contents>
                    <has_text text="Method:fasttree"/>
                    <has_text text="CogentTreeBuilder parameters:"/>
                </assert_contents>
            </output>
        </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>