<tool id="interleave" name="interleave fastqs" version="0.1.0">
    <description>takes two fastq or fastq.gz files and interleaves them</description>
    <requirements>
        <requirement type="package" version="4.0.2">mira4_assembler</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        interleave-fastqgz-MITOBIM.py
        	$fastq1 $fastq2 > $output1
    ]]></command>
    <inputs>
        <param type="data" name="fastq1" format="fastqsanger,fastq" 
        	   label="Paire end forward read" />
        <param type="data" name="fastq2" format="fastqsanger,fastq" 
        	   label="Paire end reverse read" />
    </inputs>
    <outputs>
        <data name="output1" format="fastqsanger" />
    </outputs>

    <help><![CDATA[
        
This script takes two fastq or fastq.gz files and interleaves them

Usage:
    interleave-fastqgz-MITOBIM.py fastq1 fastq2 > out.fastq

    ]]></help>

</tool>