<macros>
    <token name="@BAMTOOLS_COMMAND@"><![CDATA[
        #set $pattern = "Stats for BAM file(s)"
        @LN_FILES@
    ]]></token>
    <xml name="bamtools_form">
        <param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'This file was produced by bcftools stats'"/>
    </xml>
    <xml name="bamtools_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="bamtools"/>
                    <param name="input" value="bamtools.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="bamtools-stats"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="bamtools_txt"/>
                    <has_text text="bamtools-duplicates_pct"/>
                    <has_n_lines n="2"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="1"/>
        </test>
    </xml>
</macros>