Mercurial > repos > iuc > abyss
comparison abyss.xml @ 4:c8a188ea46d5 draft
Uploaded
| author | iuc |
|---|---|
| date | Wed, 29 Apr 2015 12:07:23 -0400 |
| parents | 1d0f1274d999 |
| children | bb97dd7d11d5 |
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| 3:9975f2d010a5 | 4:c8a188ea46d5 |
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| 1 <tool id="abyss" name="Abyss" version="1.0.0"> | |
| 2 <description>Assemble short unpaired reads</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 ABYSS -k$k $infile -o $outfile | |
| 11 ]]> | |
| 12 </command> | |
| 13 | |
| 14 <inputs> | |
| 15 <param name="infile" type="data" format="fasta|fastq" label="Unpaired read sequences" /> | |
| 16 <param name="k" type="integer" value="41" label="K-mer size" help="Try multiple sizes, starting around 2/3 read length" /> | |
| 17 </inputs> | |
| 18 | |
| 19 <outputs> | |
| 20 <data name="outfile" format="fasta" /> | |
| 21 </outputs> | |
| 22 | |
| 23 <help> | |
| 24 **What it does** | |
| 25 | |
| 26 ABySS is a de novo sequence assembler that is designed for short reads. | |
| 27 | |
| 28 .. image:: http://www.bcgsc.ca/platform/bioinfo/software/abyss/screenshot | |
| 29 | |
| 30 **Reference** | |
| 31 | |
| 32 http://www.bcgsc.ca/platform/bioinfo/software/abyss | |
| 33 </help> | |
| 34 </tool> |