--- a/tree.shared.xml	Fri Jun 24 16:53:03 2016 -0400
+++ b/tree.shared.xml	Fri May 19 04:33:57 2017 -0400
@@ -4,8 +4,11 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <expand macro="version_command"/>
-    <command detect_errors="aggressive"><![CDATA[
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
         ## create symlinks to input datasets
         ln -s "$input.dist" input_dist.dat &&
         #if not $input.source == "shared":
@@ -49,6 +52,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -63,7 +67,7 @@
                 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
             </when>
             <when value="phylip">
-                <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+                <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
                 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
             </when>
             <when value="shared">
@@ -96,46 +100,10 @@
             </when>
         </conditional>
         <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
-            <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
-            <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
-            <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
-            <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
+            <expand macro="calc-common"/>
+            <!-- set default option(s) -->
             <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
-            <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
-            <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
-            <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
-            <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
-            <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
-            <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
-            <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
-            <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
-            <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
-            <option value="hamming">hamming - Community Membership Similarity -</option>
-            <option value="memchi2">memchi2 - Community Membership Similarity -</option>
-            <option value="memchord">memchord - Community Membership Similarity -</option>
-            <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
-            <option value="mempearson">mempearson - Community Membership Similarity -</option>
-            <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
-            <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
-            <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
-            <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
-            <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
             <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
-            <option value="canberra">canberra - Community Structure Similarity -</option>
-            <option value="gower">gower - Community Structure Similarity -</option>
-            <option value="hellinger">hellinger - Community Structure Similarity -</option>
-            <option value="manhattan">manhattan - Community Structure Similarity -</option>
-            <option value="odum">odum - Community Structure Similarity -</option>
-            <option value="soergel">soergel - Community Structure Similarity -</option>
-            <option value="spearman">spearman - Community Structure Similarity -</option>
-            <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
-            <option value="structchi2">structchi2 - Community Structure Similarity -</option>
-            <option value="structchord">structchord - Community Structure Similarity -</option>
-            <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
-            <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
-            <option value="structpearson">structpearson - Community Structure Similarity -</option>
-            <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
-            <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
         </param>
     </inputs>
     <outputs>
@@ -189,11 +157,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
-The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators
+The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators
 
-.. _tree.shared: http://www.mothur.org/wiki/Tree.shared
+.. _tree.shared: https://www.mothur.org/wiki/Tree.shared
 
 ]]>
     </help>