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<tool id="split_paired_reads" name="Split paired end reads" version="1.0.0">
  <description></description>
  <command interpreter="python">
    split_paired_reads.py $input $output1 $output2
  </command>
    <inputs>
        <param name="input" type="data" format="fastqsanger" label="Your paired-end file" />
    </inputs>
    <outputs>
        <data name="output1" format="fastqsanger"/>
        <data name="output2" format="fastqsanger"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="3.fastqsanger" ftype="fastqsanger"/>
            <output name="output1" file="split_pair_reads_1.fastqsanger" ftype="fastqsanger"/>
            <output name="output2" file="split_pair_reads_2.fastqsanger" ftype="fastqsanger"/>
        </test>
    </tests>
<help>
        
**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.  

-----

**Input formats**

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**

One end::

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

The other end::

    @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
    GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
    +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
    hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
    
</help>
</tool>