<macros>
    <token name="@STAR_COMMAND@"><![CDATA[
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            @CREATE_REPEAT_DIR_2@
            #if str($repeat2.type.type) == "log"
                #for $file in $repeat2.type.input
                    @ESCAPE_IDENTIFIER@
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type.type) == "genecounts"
                #for $file in $repeat2.type.input
                    @ESCAPE_IDENTIFIER@
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab')
                    ln -s '$file' '$file_path' &&
                #end for
            #end if
        #end for
    ]]></token>
    <xml name="star_form">
        <repeat name="output" title="STAR output" min="1">
            <conditional name="type">
                <param name="type" type="select" label="Type of STAR output?">
                    <option value="log">Log</option>
                    <option value="genecounts">Gene counts</option>
                </param>
                <when value="log">
                    <param name="input" type="data" format="txt" label="STAR log output" multiple="true"/>
                </when>
                <when value="genecounts">
                    <param name="input" type="data" format="tabular,tsv" label="STAR gene count output" multiple="true"/>
                </when>
            </conditional>
        </repeat>
    </xml>
    <xml name="star_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="star"/>
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="log"/>
                            <param name="input" value="star_log.txt"/>
                        </conditional>
                    </repeat>
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="genecounts"/>
                            <param name="input" value="star_counts.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="star_alignment_plot"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="STAR_mqc_generalstats_star_uniquely_mapped_percent"/>
                    <has_text text="star_log_txt"/>
                    <has_n_lines n="2"/>
                    <has_n_columns n="7"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="1"/>
        </test>
    </xml>
</macros>