<macros>
    <token name="@METAPHLAN_COMMAND@"><![CDATA[
        #set $pattern = "#clade_name\tNCBI_tax_id\trelative_abundance\t"
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, str($identifier) + '.txt')
            ln -s '$file' '$file_path' &&
        #end for
    ]]></token>
    <xml name="metaphlan_form">
        <param name="input" type="data" format="txt" multiple="true" label="Output of MetaPhlAn" help="It should contain '#clade_name\tNCBI_tax_id\trelative_abundance\t'"/>
    </xml>
    <xml name="metaphlan_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="metaphlan"/>
                    <param name="input" value="metaphlan.txt"/>
                </conditional>
            </repeat>
            <param name="title" value="Title of the report"/>
            <param name="comment" value="Commment for the report"/>
            <param name="flat" value="true"/>
            <param name="export" value="true"/>
            <output name="html_report">
                <assert_contents>
                    <has_text text="Title of the report"/>
                    <has_text text="Commment for the report"/>
                    <has_text text="MetaPhlAn"/>
                    <has_text text="Top taxa"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="metaphlan-Moraxella_lacunata"/>
                    <has_text text="metaphlan-Top"/>
                    <has_text text="22.57968"/>
                    <has_text text="100.00001000000002"/>
                    <has_n_lines n="2"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="7"/>
        </test>
    </xml>
</macros>