--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.classic.xml	Fri May 19 05:04:17 2017 -0400
@@ -0,0 +1,94 @@
+<tool profile="16.07" id="mothur_cluster_classic" name="Cluster.classic" version="@WRAPPER_VERSION@.0">
+    <description>Assign sequences to OTUs (Dotur implementation)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$dist" dist.dat &&
+        ln -s "$name" name.dat &&
+        ln -s "$count" count.dat &&
+
+        echo 'cluster.classic(
+            phylip=dist.dat,
+            #if $name:
+                name=name.dat,
+            #end if
+            #if $count:
+                count=count.dat,
+            #end if
+            method=$method,
+            #if $cutoff:
+                cutoff=$cutoff,
+            #end if
+            hard=$hard,
+            precision=$precision,
+            sim=$sim
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix" help="format must be mothur.lower.dist or mothur.square.dist"/>
+        <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+        <param name="method" type="select" label="method - Select a Clustering Method" help="">
+            <option value="furthest">Furthest neighbor</option>
+            <option value="nearest">Nearest neighbor</option>
+            <option value="average" selected="true">Average neighbor</option>
+            <option value="weighted">Weighted</option>
+        </param>
+        <param name="cutoff" type="float" value="" min="0" optional="true" label="cutoff - Distance Cutoff threshold" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
+        <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
+        <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
+            <option value="10">.1</option>
+            <option value="100" selected="true">.01</option>
+            <option value="1000">.001</option>
+            <option value="10000">.0001</option>
+            <option value="100000">.00001</option>
+            <option value="1000000">.000001</option>
+        </param>
+        <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="rabund" format="mothur.rabund" from_work_dir="dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
+        <data name="sabund" format="mothur.sabund" from_work_dir="dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
+        <data name="otulist" format="mothur.list" from_work_dir="dist*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
+    </outputs>
+    <tests>
+        <test><!-- test with phylip and default params-->
+            <param name="dist" value="env.dist"/>
+            <output name="rabund" md5="b7f4b5ee46b2c4f5221d487e24dca9db" ftype="mothur.rabund"/>
+            <output name="sabund" md5="ac2df77e39a106fa65fae3d2132bc4ea" ftype="mothur.sabund"/>
+            <output name="otulist" ftype="mothur.list">
+                <assert_contents>
+                    <has_text text="group"/>
+                    <has_text text="unique"/>
+                    <has_line_matching expression="^label\tnumOtus\tOtu01\tOtu02\tOtu03\tOtu04\tOtu05\tOtu06\tOtu07\tOtu08\tOtu09\tOtu10\tOtu11\tOtu12\tOtu13\tOtu14\tOtu15\tOtu16\tOtu17\tOtu18\tOtu19\tOtu20\tOtu21\tOtu22\tOtu23\tOtu24$"/>
+                </assert_contents>
+            </output>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The cluster.classic_ command assign sequences to OTUs (Operational Taxonomy Unit).
+
+.. _cluster.classic: https://www.mothur.org/wiki/Cluster.classic
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>