--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/otu.hierarchy.xml	Fri May 19 06:00:15 2017 -0400
@@ -0,0 +1,65 @@
+<tool profile="16.07" id="mothur_otu_hierarchy" name="Otu.hierarchy" version="@WRAPPER_VERSION@.0">
+    <description>Relate OTUs at different distances</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 "$otu" otu.dat &&
+
+        echo 'otu.hierarchy(
+            list=otu.dat,
+            label=$label1-$label2,
+            output=$output
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
+        <param name="label1" type="select" label="label - OTU Label 1">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="label2" type="select" label="label - OTU Label 2" help="Must be different than Label 1">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="output" type="select" optional="true" label="output - display the names of the sequences in the otus or the otu numbers">
+            <option value="name" selected="true">OTU sequence names</option>
+            <option value="number">OTU numbers</option>
+        </param>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="hierarchy" format="tabular" from_work_dir="otu*.hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <param name="label1" value="0.05"/>
+            <param name="label2" value="0.03"/>
+            <output name="hierarchy" file="amazon.an.0.03.-.0.05.otu.hierarchy" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The otu.hierarchy_ command relates OTUs from a list_ at different distances.
+
+.. _list: https://www.mothur.org/wiki/List_file
+.. _otu.hierarchy: https://www.mothur.org/wiki/Otu.hierarchy
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>