<macros>
    <token name="@BUSCO_COMMAND@"><![CDATA[
        ## Searches for files "short_summary_[samplename].txt"
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier))
            ln -s '$file' '$file_path' &&
        #end for
    ]]></token>
    <xml name="busco_form">
        <param name="input" type="data" format="txt" multiple="true" label="Output of BUSCO"/>
    </xml>
    <!-- add here your test files and tests, the more stringent the better -->
    <xml name="busco_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="busco"/>
                    <param name="input" value="busco.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="busco-lineage-fungi_odb9"/>
                </assert_contents>
            </output>
            <!-- Not sure why this is empty 
            <output name="stats">
                <assert_contents>
                    <has_text text="R1_fq"/>
                    <has_text text="result_right"/>
                    <has_text text="25839_merged"/>
                    <has_text text="C2"/>
                    <has_n_lines n="11"/>
                    <has_n_columns n="22"/>
                </assert_contents>
            </output>
            -->
            <output_collection name="plots" type="list" count="1"/>
        </test>
    </xml>
</macros>