<tool id="preppereadsforvelet" name="Prepare paired-end reads for use with Velvet (FASTQ)"  version="1.0.0">
	<description>Prepare paired-end reads for use with Velvet</description>
	<command interpreter="python">
	  preppereads.py 
           '$__app__.config.new_file_path'
	   '$input1'
           '$input2'
           '$outpe'
	   '$outsingletons'; exit 0
	</command>
        <inputs>
            <param name="input1" type="data" format="illuminafastq" label="Read 1 of paired-end dataset"/>
            <param name="input2" type="data" format="illuminafastq" label="Read 2 of paired-end dataset"/>
        </inputs>
	<outputs>
                <data format="illuminafastq" name="outpe" label="Merged paired-end reads ready for velvet"/>
		<data format="illuminafastq" name="outsingletons" label="Singleton reads reads for velvet"/>
		
	</outputs>
	<requirements>
	</requirements>
	<help>
**Paired-end reads preparation for velvet**

Velvet requires paired-end reads to be in the same file in an interleaved FASTQ format. This format specifies that read 1 should be followed immediately by read 2. 

This script is useful to ensure reads are in the correct order prior to passing the data to Velvet.

Singleton reads can also be produced if quality trimming or other filtering criteria have removed the read's mate. These can also be passed to Velvet using a second short read channel. 

	</help>
</tool>