Mercurial > repos > greg > gregs
comparison abyss/abyss.xml @ 4:a188de29f06e
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| author | g2cmnty@test-web1.g2.bx.psu.edu |
|---|---|
| date | Tue, 28 Jun 2011 10:29:09 -0400 |
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| 3:6ad594db0143 | 4:a188de29f06e |
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| 1 <tool id="abyss" name="Abyss" version="1.0.0"> | |
| 2 <description>Assemble short unpaired reads</description> | |
| 3 <command interpreter='bash'>abyss_wrapper.sh $k $infile $outfile</command> | |
| 4 | |
| 5 <inputs> | |
| 6 <param name="infile" type="data" format="fasta|fastq" label="Unpaired read sequences" /> | |
| 7 <param name="k" type="integer" value="41" label="K-mer size" help="Try multiple sizes, starting around 2/3 read length" /> | |
| 8 </inputs> | |
| 9 | |
| 10 <outputs> | |
| 11 <data name="outfile" format="fasta" /> | |
| 12 </outputs> | |
| 13 | |
| 14 <help> | |
| 15 **What it does** | |
| 16 | |
| 17 ABySS is a de novo sequence assembler that is designed for short reads. | |
| 18 | |
| 19 .. image:: http://www.bcgsc.ca/platform/bioinfo/software/abyss/screenshot | |
| 20 | |
| 21 **Reference** | |
| 22 | |
| 23 http://www.bcgsc.ca/platform/bioinfo/software/abyss | |
| 24 </help> | |
| 25 </tool> |