<tool id="abyss" name="Abyss" version="1.0.0">
<description>Assemble short unpaired reads</description>
<command interpreter='bash'>abyss_wrapper.sh $k $infile $outfile</command>

<inputs>
    <param name="infile" type="data" format="fasta|fastq" label="Unpaired read sequences" />
    <param name="k" type="integer" value="41" label="K-mer size" help="Try multiple sizes, starting around 2/3 read length" />
</inputs>

<outputs>
    <data name="outfile" format="fasta" />
</outputs>

<help>
**What it does**

ABySS is a de novo sequence assembler that is designed for short reads.

.. image:: http://www.bcgsc.ca/platform/bioinfo/software/abyss/screenshot

**Reference**

http://www.bcgsc.ca/platform/bioinfo/software/abyss
</help>
</tool>