<tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>on joined paired end reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <edam_topics>
        <edam_topic>topic_0622</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_3359</edam_operation>
    </edam_operations>
    <expand macro="requirements"/>
    <command><![CDATA[
gx-fastq-paired-end-splitter '$input1_file' '${input1_file.extension[len('fastq'):]}' '$pairs.forward' '$pairs.reverse'
    ]]></command>
    <inputs>
        <param name="input1_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" />
    </inputs>
    <outputs>
        <collection name="pairs" format_source="input1_file" type="paired" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" />
            <output_collection name="pairs">
                <element name="forward" value="split_pair_reads_1.fastqsanger" ftype="fastqsanger"/>
                <element name="reverse" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Splits a single fastq dataset representing paired-end run into two datasets (one for each end). This tool works only for datasets where both ends have **the same** length.

Sequence identifiers will have /1 or /2 appended for the split forward and reverse reads, respectively.

-----

**Input format**

A multiple-fastq file, for example::

    @HWI-EAS91_1_30788AAXX:7:21:1542:1758
    GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
    +HWI-EAS91_1_30788AAXX:7:21:1542:1758
    hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR

-----

**Outputs**

Forward Read::

    @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
    GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
    +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
    hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh

Reverse Read::

    @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
    GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
    +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
    hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btq281</citation>
    </citations>
</tool>