--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dnaclust.xml	Thu Sep 06 23:05:22 2012 -0400
@@ -0,0 +1,34 @@
+<?xml version="1.0"?>
+<tool id="dnaclust_1" name="dnaclust">
+  <description>Cluster sequences  into OTUs using DNAclust </description>
+  <command> dnaclust  -s $similarity -i $inputFastaFile > $outputfile </command>
+  <inputs>
+    <param format="fasta" name="inputFastaFile" type="data" label="Fasta input file"/>
+ <param name="similarity" size="10" type="text" value="0.99" label="similarity between center and cluster sequences" />
+
+  </inputs>
+  <outputs>
+
+     <data format="tabular" name="outputfile" />
+  </outputs>
+
+<help>
+
+.. class:: infomark
+
+**TIP**
+
+see the  DNACLUST documentation at http://dnaclust.sourceforge.net/
+
+
+
+Each line will contain the ids of the sequences in each cluster, and the first id of each line is the cluster representative.
+
+Example: To cluster a set of 16S rRNA fragments at 0.98 similarity use:
+./dnaclust file.fasta -l -s 0.98 > clusters
+
+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\
+st cases.
+</help>
+</tool>
+