<macros>
    <token name="@QUALIMAP_COMMAND@"><![CDATA[
        #for $file in $repeat.software_cond.input
            #if re.search("genome_results", str($file.element_identifier))
                sample="\$(grep 'bam file = ' $file | sed 's/bam file = //g' | sed 's: ::g')" &&
                dir_name="$software_dir/\${sample}" &&
                mkdir -p \${dir_name} &&
                filepath_1="\${dir_name}/genome_results.txt" &&
                ln -sf '$file' \${filepath_1} &&
            #elif re.search("coverage_histogram", str($file.element_identifier))
                nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
                mkdir -p \${nested_dir_name} &&
                filepath_2="\${nested_dir_name}/coverage_histogram.txt" &&
                ln -sf '$file' \${filepath_2} &&
            #elif re.search("gc-content_distribution", str($file.element_identifier))
                nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
                mkdir -p \${nested_dir_name} &&
                filepath_3="\${nested_dir_name}/mapped_reads_gc-content_distribution.txt" &&
                ln -sf '$file' \${filepath_3} &&
            #else
                #pass
            #end if
        #end for
    ]]></token>
    <xml name="qualimap_form">
        <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report"/>
    </xml>
    <!-- add here your test files and tests, the more stringent the better -->
    <xml name="qualimap_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="qualimap"/>
                    <param name="input" value="genome_results.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="qualimap"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="BamQC_mqc_generalstats_qualimap_bamqc_mean_coverage"/>
                    <has_text text="BamQC_mqc_generalstats_qualimap_bamqc_mapped_reads"/>
                    <has_text text="BamQC_mqc_generalstats_qualimap_bamqc_total_reads"/>
                    <has_text text="x_bam"/>
                    <has_text text="0.98"/>
                    <has_n_lines n="2"/>
                    <has_n_columns n="6"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="0"/>
        </test>
    </xml>
</macros>