<macros>
    <token name="@PAIRTOOLS_COMMAND@"><![CDATA[
        #set $pattern = "total_single_sided_mapped"
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, str($identifier))
            #if $file_path in $file_paths
                #set $file_path += '_' + str($file_paths.count($file_path))
            #end if
            #set $file_paths += [$file_path]
            grep -Pzq "(?s)(?=.*total_single_sided_mapped\t)(?=.*cis\t)(?=.*trans\t)(?=.*pair_types/)" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
            ln -s '$file' '$file_path'  &&
        #end for
    ]]></token>
    <xml name="pairtools_form">
        <param name="input" type="data" format="tabular" multiple="true" label="Output of Pairtools"/>
    </xml>
    <xml name="pairtools_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="pairtools"/>
                    <param name="input" value="output_dedup_pairs.stats"/>
                </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="output_dedup_pairs"/>
                    <has_text text="Pairs by alignment status"/>
                    <has_text text="Fraction of read pairs by strand orientation"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="pairtools-total"/>
                    <has_text text="pairtools-frac_unmapped"/>
                    <has_text text="0.001992"/>
                    <has_text text="45.88353413654618"/>
                    <has_text text="pairtools-frac_dups"/>
                    <has_text text="0.4518072289156626"/>
                    <has_n_lines n="2"/>
                    <has_n_columns n="8"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="5"/>
        </test>
    </xml>
</macros>