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1 <?xml version="1.0"?>
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2 <tool id="dnaclust_1" name="dnaclust">
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3 <description>Cluster sequences into OTUs using DNAclust </description>
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4 <command> dnaclust -s $similarity -i $inputFastaFile > $outputfile </command>
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5 <inputs>
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6 <param format="fasta" name="inputFastaFile" type="data" label="Fasta input file"/>
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7 <param name="similarity" size="10" type="text" value="0.99" label="similarity between center and cluster sequences" />
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8
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9 </inputs>
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10 <outputs>
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11
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12 <data format="tabular" name="outputfile" />
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13 </outputs>
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14
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15 <help>
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16
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17 .. class:: infomark
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18
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19 **TIP**
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20
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21 see the DNACLUST documentation at http://dnaclust.sourceforge.net/
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22
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23
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24
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25 Each line will contain the ids of the sequences in each cluster, and the first id of each line is the cluster representative.
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26
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27 Example: To cluster a set of 16S rRNA fragments at 0.98 similarity use:
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28 ./dnaclust file.fasta -l -s 0.98 > clusters
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29
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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\
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31 st cases.
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32 </help>
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33 </tool>
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34
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