<tool id="phabox_tree" name="PhaBOX tree" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT">
    <description>Build phylogenetic trees based on marker genes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <xrefs>
        <xref type="bio.tools">phabox</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">phabox</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        phabox2 --task tree
            @GENERAL@
            @TREE@
    ]]></command>
    <inputs>
        <expand macro="general"/>
        <expand macro="tree"/>
    </inputs>
    <outputs>
        <collection name="marker_genes" format="fasta" type="list">
            <discover_datasets pattern="found_marker_(?P&lt;designation&gt;.+)_combined_db.fa" directory="output/final_prediction/tree_supplementary"/>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="dbdir" value="phaboxdb"/>
            <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/>
            <output_collection name="marker_genes" count="2">
                <element name="portal">
                    <assert_contents>
                        <has_text text=">" n="4281"/>
                    </assert_contents>
                </element>
                <element name="terl">
                    <assert_contents>
                        <has_text text=">" n="4672"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Get sequences of specific marker genes that can be used for phylogentic tree construction.

@COMMON_INPUT_DOC@

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