<macros>
    <token name="@SAMTOOLS_COMMAND@"><![CDATA[
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            @CREATE_REPEAT_DIR_2@
            #if str($repeat2.type.type) == "stats"
                #set $pattern = "This file was produced by samtools stats"
                @LN_3_FILES@
            #elif str($repeat2.type.type) == "flagstat"
                #set $pattern = "in total (QC-passed reads + QC-failed reads)"
                @LN_3_FILES@
            #elif str($repeat2.type.type) == "idxstats"
                #for $file in $repeat2.type.input
                    @ESCAPE_IDENTIFIER@
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type.type) == "rmdup"
                #set $pattern = "[bam_rmdup"
                @LN_3_FILES@
            #end if
        #end for
    ]]></token>
    <xml name="samtools_form">
        <repeat name="output" title="Samtools output" min="1">
            <conditional name="type">
                <param name="type" type="select" label="Type of Samtools output?">
                    <option value="stats">stats</option>
                    <option value="flagstat">flagstat</option>
                    <option value="idxstats">idxstats</option>
                    <option value="rmdup">rmdup</option>
                </param>
                <when value="stats">
                    <param name="input" type="data" format="txt" multiple="true" label="Samtools stats output" help="It should contain 'This file was produced by samtools stats'"/>
                </when>
                <when value="flagstat">
                    <param name="input" type="data" format="txt" multiple="true" label="Samtools flagstat output" help="It should contain 'in total (QC-passed reads + QC-failed reads)'"/>
                </when>
                <when value="idxstats">
                    <param name="input" type="data" format="txt" multiple="true" label="Samtools idxstats output"/>
                </when>
                <when value="rmdup">
                    <param name="input" type="data" format="txt" multiple="true" label="Samtools rmdup output" help="It should contain '[bam_rmdup'"/>
                </when>
            </conditional>
        </repeat>
    </xml>
    <!-- add here your test files and tests, the more stringent the better -->
    <xml name="samtools_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="samtools"/>
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="stats"/>
                            <param name="input" value="samtools_stats.txt"/>
                        </conditional>
                    </repeat>
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="flagstat"/>
                            <param name="input" value="samtools_flagstat.txt"/>
                        </conditional>
                    </repeat>
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="idxstats"/>
                            <param name="input" value="samtools_idxstats.txt"/>
                        </conditional>
                    </repeat>
                </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="samtools-flagstat-dp"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="samtools_flagstat_txt"/>
                    <has_text text="mapped_passed"/>
                    <has_text text="stats_mqc_generalstats_samtools_stats_error_rate"/>
                    <has_text text="samtools_stats_txt"/>
                    <has_n_lines n="3"/>
                    <has_n_columns n="11"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="5"/>
        </test>
    </xml>
</macros>