Mercurial > repos > john-mccallum > dnaclust
comparison dnaclust.xml @ 0:84be1fe7e34a draft
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| author | john-mccallum |
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| date | Thu, 06 Sep 2012 23:05:22 -0400 |
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| -1:000000000000 | 0:84be1fe7e34a |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="dnaclust_1" name="dnaclust"> | |
| 3 <description>Cluster sequences into OTUs using DNAclust </description> | |
| 4 <command> dnaclust -s $similarity -i $inputFastaFile > $outputfile </command> | |
| 5 <inputs> | |
| 6 <param format="fasta" name="inputFastaFile" type="data" label="Fasta input file"/> | |
| 7 <param name="similarity" size="10" type="text" value="0.99" label="similarity between center and cluster sequences" /> | |
| 8 | |
| 9 </inputs> | |
| 10 <outputs> | |
| 11 | |
| 12 <data format="tabular" name="outputfile" /> | |
| 13 </outputs> | |
| 14 | |
| 15 <help> | |
| 16 | |
| 17 .. class:: infomark | |
| 18 | |
| 19 **TIP** | |
| 20 | |
| 21 see the DNACLUST documentation at http://dnaclust.sourceforge.net/ | |
| 22 | |
| 23 | |
| 24 | |
| 25 Each line will contain the ids of the sequences in each cluster, and the first id of each line is the cluster representative. | |
| 26 | |
| 27 Example: To cluster a set of 16S rRNA fragments at 0.98 similarity use: | |
| 28 ./dnaclust file.fasta -l -s 0.98 > clusters | |
| 29 | |
| 30 You can optionally specify a k-mer length for the filter. The longer k-mers use more memory. Also the filter will be more specific with longer k-mers. The default log_4(median length) should be good for mo\ | |
| 31 st cases. | |
| 32 </help> | |
| 33 </tool> | |
| 34 |