--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/classify.tree.xml	Fri May 19 05:05:16 2017 -0400
@@ -0,0 +1,82 @@
+<tool profile="16.07" id="mothur_classify_tree" name="Classify.tree" version="@WRAPPER_VERSION@.0">
+    <description>Get a consensus taxonomy for each node on a tree</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 "$tree" tree.dat &&
+        ln -s "$name" name.dat &&
+        ln -s "$group" group.dat &&
+        ln -s "$taxonomy" taxonomy.dat &&
+
+        echo 'classify.tree(
+            tree=tree.dat,
+            #if $name
+                name=name.dat,
+            #end if
+            #if $group:
+                group=group.dat,
+            #end if
+            taxonomy=taxonomy.dat
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="taxonomy" type="data" format="mothur.ref.taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
+        <param name="tree" type="data" format="txt" label="tree - Sequences to filter"/>
+        <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file"/>
+        <param name="group" type="data" format="group" optional="true" label="group - Sequences Group reference"/>
+        <param name="cutoff" type="integer" value="51" min="51" max="100" optional="true" label="cutoff - consensus confidence threshold" help="The default is 51, meaning 51%. Cutoff cannot be below 51"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_tree" format="txt" from_work_dir="tree.*taxonomy.tre" label="${tool.name} on ${on_string}: taxonomy.tre"/>
+        <data name="summary" format="tabular" from_work_dir="tree.*taxonomy.summary" label="${tool.name} on ${on_string}: taxonomy.summary"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.ref.taxonomy"/>
+            <param name="tree" value="treetest.tre" ftype="txt"/>
+            <output name="out_tree" md5="cd2d3275d225ee8ba5df004a9885f50c" ftype="txt"/>
+            <output name="summary" md5="78dfe4198793f7ee5632c5b88b6bc295" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+
+**Command Documentation**
+
+The classify.tree_ command is used to get a consensus taxonomy for each node on a tree.
+Input is a taxonomy_ and a tree_ with optional name_ or group_ reference.
+The output is a tree_ and a summary..
+
+  TreeNode  NumRep  Taxonomy
+  243   2   Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
+  244   3   Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
+  245   4   Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
+  ...
+
+
+.. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
+.. _tree: http://evolution.genetics.washington.edu/phylip/newicktree.html
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _classify.tree: https://www.mothur.org/wiki/Classify.tree
+
+v.1.25.0: Trivial upgrade to Mothur 1.33
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>