<macros>
    <token name="@BOWTIE2_COMMAND@"><![CDATA[
        #set $pattern = "% overall alignment rate"
        @LN_FILES@
    ]]></token>
    <xml name="bowtie2_form">
        <param name="input" type="data" format="txt" multiple="true" label="Output of Bowtie 2" help="It should contain 'reads; of these:'"/>
    </xml>
    <!-- add here your test files and tests, the more stringent the better -->
    <xml name="bowtie2_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="bowtie2"/>
                    <param name="input" value="bowtie2_1.txt,bowtie2_2.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="bowtie2_se_plot"/>
                    <has_text text="mqc-module-section-bowtie2"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="bowtie2_1_txt"/>
                    <has_n_lines n="3"/>
                    <has_n_columns n="2"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="1"/>
        </test>
    </xml>
</macros>