<macros>
    <token name="@DIAMOND_COMMAND@"><![CDATA[
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, 'diamond.log')
            ln -s '$file' '$file_path' &&
        #end for
    ]]></token>
    <xml name="diamond_form">
        <param name="input" type="data" format="txt" multiple="true" label="Log output of DIAMOND"/>
    </xml>
    <xml name="diamond_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="diamond"/>
                    <param name="input" value="diamond.log"/>
                </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="DIAMOND"/>
                    <has_text text="Queries aligned"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="Sample"/>
                    <has_text text="diamond_0"/>
                    <has_text text="diamond-queries_aligned"/>
                    <has_text text="1"/>
                    <has_n_lines n="2"/>
                    <has_n_columns n="2"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="0"/>
        </test>
    </xml>
</macros>