<macros>
    <token name="@VCFTOOLS_COMMAND@"><![CDATA[
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            @CREATE_REPEAT_DIR_2@
            #if str($repeat2.type.type) == "relatedness2"
                #for $file in $repeat2.type.input
                    @ESCAPE_IDENTIFIER@
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "tstv_by_count"
                #for $file in $repeat2.type.input
                    @ESCAPE_IDENTIFIER@
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "tstv_by_qual"
                #for $file in $repeat2.type.input
                    @ESCAPE_IDENTIFIER@
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "tstv_summary"
                #for $file in $repeat2.type.input
                    @ESCAPE_IDENTIFIER@
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary')
                    ln -s '$file' '$file_path' &&
                #end for
            #end if
        #end for
    ]]></token>
    <xml name="vcftools_form">
        <repeat name="output" title="VCFTools output" min="1">
            <conditional name="type">
                <param name="type" type="select" label="Type of VCFTools output?">
                    <option value="relatedness2">relatedness2</option>
                    <option value="tstv_by_count">tstv_by_count</option>
                    <option value="tstv_by_qual">tstv_by_qual</option>
                    <option value="tstv_summary">tstv_summary</option>
                </param>
                <when value="relatedness2">
                    <param name="input" type="data" format="txt" label="VCFTools relatedness2 output" multiple="true"/>
                </when>
                <when value="tstv_by_count">
                    <param name="input" type="data" format="tabular,tsv" label="VCFTools TsTV count output" multiple="true"/>
                </when>
                <when value="tstv_by_qual">
                    <param name="input" type="data" format="tabular" label="VCFTools TsTV qual output" multiple="true"/>
                </when>
                <when value="tstv_summary">
                    <param name="input" type="data" format="txt" label="VCFTools TsTV summary output" multiple="true"/>
                </when>
            </conditional>
        </repeat>
    </xml>
    <xml name="vcftools_test">
        <test expect_num_outputs="2">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="vcftools"/>
                    <repeat name="output">
                        <conditional name="type">
                            <param name="type" value="tstv_by_qual"/>
                            <param name="input" value="vcftools.txt"/>
                        </conditional>
                    </repeat>
                </conditional>
            </repeat>
            <param name="title" value="Title of the report"/>
            <param name="comment" value="Commment for the report"/>
            <output name="html_report">
                <assert_contents>
                    <has_text text="Title of the report"/>
                    <has_text text="Commment for the report"/>
                    <has_text text="cutadapt_trimmed_sequences_plot"/>
                    <has_text text="All-in-one FASTQ preprocessor"/>
                    <has_text text="trimmomatic_plot"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="dataset_33"/>
                    <has_text text="R1_fq"/>
                    <has_text text="result_right"/>
                    <has_text text="25839_merged"/>
                    <has_text text="C2"/>
                    <has_n_lines n="11"/>
                    <has_n_columns n="22"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="29"/>
        </test>
    </xml>
</macros>