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annotate abyss_toolsuite-92636934a189/abyss/abyss.xml @ 0:ce99b6666d1f draft

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author msjeon
date Mon, 11 Jun 2012 14:48:15 -0400
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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 <command interpreter='bash'>abyss_wrapper.sh $k $infile $outfile</command>
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5 <inputs>
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6 <param name="infile" type="data" format="fasta|fastq" label="Unpaired read sequences" />
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7 <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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8 </inputs>
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10 <outputs>
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11 <data name="outfile" format="fasta" />
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12 </outputs>
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13
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14 <help>
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15 **What it does**
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16
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17 ABySS is a de novo sequence assembler that is designed for short reads.
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18
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19 .. image:: http://www.bcgsc.ca/platform/bioinfo/software/abyss/screenshot
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20
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21 **Reference**
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23 http://www.bcgsc.ca/platform/bioinfo/software/abyss
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24 </help>
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25 </tool>