view abyss.xml @ 2:08452f5bf934 draft

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<tool id="abyss" name="Abyss" version="1.0.0">
    <description>Assemble short unpaired reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
ABYSS -k$k $infile -o $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>