Mercurial > repos > john-mccallum > dnaclust
comparison cut_dnaclust.xml @ 0:84be1fe7e34a draft
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| author | john-mccallum |
|---|---|
| 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="cutClust_1" name="cutClust"> | |
| 3 <description>Remove clusters below a certain depth</description> | |
| 4 <command >cut -f $depth- $inputFile | sed '/^$/d' | sort | uniq > $outputfile</command> | |
| 5 <inputs> | |
| 6 <param format="tabular" name="inputFile" type="data" label="Columnar Input File" help="tabular file of DNAclust clusters" /> | |
| 7 <param name="depth" size="10" type="text" value="50" label="Minimum depth for cutoff" /> | |
| 8 | |
| 9 </inputs> | |
| 10 <outputs> | |
| 11 <data format="tabular" name="outputfile" /> | |
| 12 </outputs> | |
| 13 <help> | |
| 14 .. class:: infomark | |
| 15 | |
| 16 **TIP** | |
| 17 | |
| 18 :: | |
| 19 | |
| 20 This tool simply cuts off columns from the left | |
| 21 e.g. set to 2 to remove singletons, 50 to remove clusters with less than 50 reads | |
| 22 </help> | |
| 23 | |
| 24 | |
| 25 </tool> |