<macros>
    <token name="@FREYJA_COMMAND@"><![CDATA[
        #set $pattern = "summarized\t\["
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, str($identifier) + '.tsv')
            ln -s '$file' '$file_path' &&
        #end for
    ]]></token>
    <xml name="freyja_form">
        <param name="input" type="data" format="tsv" multiple="true" label="Output of Freyja" help="It should contain 'summarized\t['"/>
    </xml>
    <xml name="freyja_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="freyja"/>
                    <param name="input" value="freyja.tsv"/>
                </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="Freyja Summary"/>
                    <has_text text="Top lineage"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="freyja-Top_lineage_freyja"/>
                    <has_text text="freyja-Top_lineage_freyja_percentage"/>
                    <has_text text="A"/>
                    <has_text text="57.89470000000878"/>
                    <has_n_lines n="2"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="1"/>
        </test>
    </xml>
</macros>