<tool id="get_pairs" name="Separate paired and unpaired reads" version="0.3" >
	<!-- author : lecorguille@sb-roscoff.fr -->
	<!-- date : 20-11-12 -->
	<!-- adapted by abretaud -->

	<description>from two fastq files</description>

    <requirements>
        <requirement type="package" version="3.6">python</requirement>
    </requirements>

	<command><![CDATA[
        #if $library.type == 'paired':
            python '$__tool_directory__/get_pairs.py' '$library.input_left' '$library.input_right'
        #else if $library.type == 'paired_collection'
            python '$__tool_directory__/get_pairs.py' '$library.input.forward' '$library.input.reverse'
        #end if
	]]></command>

	<inputs>
        <conditional name="library">
            <param name="type" type="select" label="Input type">
                <option value="paired" selected="true">Independent datasets</option>
                <option value="paired_collection">Paired-end collection</option>
            </param>

            <when value="paired">
				<param name="input_left" type="data" format="fastqsanger" label="Forward reads" />
				<param name="input_right" type="data" format="fastqsanger" label="Reverse reads" />
            </when>

            <when value="paired_collection">
                <param name="input" format="fastqsanger" type="data_collection" collection_type="paired" label="Paired collection" />
            </when>

        </conditional>
	</inputs>

	<outputs>
		<data format="fastqsanger" name="left_paired" from_work_dir="left.paired.fastq" label="${tool.name} on ${on_string}: paired forward" />
		<data format="fastqsanger" name="right_paired" from_work_dir="right.paired.fastq" label="${tool.name} on ${on_string}: paired reverse" />
		<data format="fastqsanger" name="left_unpaired" from_work_dir="left.unpaired.fastq" label="${tool.name} on ${on_string}: unpaired forward" />
		<data format="fastqsanger" name="right_unpaired" from_work_dir="right.unpaired.fastq" label="${tool.name} on ${on_string}: unpaired reverse" />
	</outputs>
    <tests>
        <test>
            <conditional name="library">
                <param name="input_left" value="r1.fastq" />
                <param name="input_right" value="r2.fastq" />
            </conditional>
            <output name="left_paired" file="r1_paired.fastq" />
            <output name="right_paired" file="r2_paired.fastq" />
            <output name="left_unpaired" file="r1_unpaired.fastq" />
            <output name="right_unpaired" file="r2_unpaired.fastq" />
        </test>
        <test>
            <conditional name="library">
                <param name="type" value="paired_collection" />
                <param name="input">
                    <collection type="paired">
                        <element name="forward" ftype="fastq" value="r1.fastq" />
                        <element name="reverse" ftype="fastq" value="r2.fastq" />
                    </collection>
                </param>
            </conditional>
            <output name="left_paired" file="r1_paired.fastq" />
            <output name="right_paired" file="r2_paired.fastq" />
            <output name="left_unpaired" file="r1_unpaired.fastq" />
            <output name="right_unpaired" file="r2_unpaired.fastq" />
        </test>
    </tests>

    <help><![CDATA[
        A tool to separate paired and unpaired reads from fastq datasets.
    ]]></help>
    <citations>
    </citations>
</tool>