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1 <tool id="abyss" name="Abyss" version="1.0.0">
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2 <description>Assemble short unpaired reads</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
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10 ABYSS -k$k $infile -o $outfile
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11 ]]>
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12 </command>
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13
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14 <inputs>
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15 <param name="infile" type="data" format="fasta|fastq" label="Unpaired read sequences" />
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16 <param name="k" type="integer" value="41" label="K-mer size" help="Try multiple sizes, starting around 2/3 read length" />
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17 </inputs>
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18
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19 <outputs>
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20 <data name="outfile" format="fasta" />
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21 </outputs>
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22
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23 <help>
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24 **What it does**
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25
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26 ABySS is a de novo sequence assembler that is designed for short reads.
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27
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28 .. image:: http://www.bcgsc.ca/platform/bioinfo/software/abyss/screenshot
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29
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30 **Reference**
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31
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32 http://www.bcgsc.ca/platform/bioinfo/software/abyss
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33 </help>
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34 </tool>
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