<macros>
    <token name="@FEATURECOUNTS_COMMAND@"><![CDATA[
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_prefix = os.path.join($software_dir, str($identifier))
            if grep -qw Status '$file'; then
                ln -s '$file' '${file_prefix}.summary';
            else
                echo -e 'Status\t${identifier}' > '${file_prefix}.summary';
                cat '$file' >> '${file_prefix}.summary';
            fi &&
        #end for
    ]]></token>
    <xml name="featurecounts_form">
        <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of FeatureCounts"/>
    </xml>
    <!-- add here your test files and tests, the more stringent the better -->
    <xml name="featurecounts_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="featureCounts"/>
                    <param name="input" value="featureCounts.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="featureCounts_assignment_plot"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="featureCounts_mqc_generalstats_featurecounts_Assigned"/>
                    <has_text text="accepted_hits"/>
                    <has_text text="TopHat"/>
                    <has_text text="featureCounts_mqc_generalstats_featurecounts_percent_assigned"/>
                    <has_n_lines n="7"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="1"/>
        </test>
    </xml>
</macros>