--- a/classify.tree.xml	Fri Sep 08 14:42:44 2017 -0400
+++ b/classify.tree.xml	Tue Mar 20 22:11:18 2018 -0400
@@ -7,34 +7,36 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@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 &&
+## 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
+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="mothur.groups" 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"/>
+        <param argument="taxonomy" type="data" format="mothur.ref.taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
+        <param argument="tree" type="data" format="txt" label="tree - Sequences to filter"/>
+        <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file"/>
+        <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Group reference"/>
+        <param argument="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"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -47,11 +49,11 @@
             <param name="tree" value="treetest.tre" ftype="txt"/>
             <output name="out_tree" md5="cd2d3275d225ee8ba5df004a9885f50c" ftype="txt"/>
             <output name="summary" md5="78dfe4198793f7ee5632c5b88b6bc295" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -76,7 +78,7 @@
 .. _classify.tree: https://www.mothur.org/wiki/Classify.tree
 
 v.1.25.0: Trivial upgrade to Mothur 1.33
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>