--- a/summary.shared.xml	Fri Jun 24 16:52:13 2016 -0400
+++ b/summary.shared.xml	Thu May 18 18:36:00 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 "$otu" otu.dat &&
 
@@ -37,6 +40,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
@@ -49,46 +53,19 @@
             </options>
         </param>
         <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
+            <expand macro="calc-common"/>
+            <!-- set default option(s) -->
             <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
             <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
             <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
-            <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
             <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
             <option value="jest" selected="true">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" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
             <option value="sorest" selected="true">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" selected="true">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" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
             <option value="thetan" selected="true">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>
         <param name="all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/>
         <param name="distance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="distance - Output a distance file for each calculator at each label"/>
@@ -113,14 +90,13 @@
         <data name="summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: shared.summary"/>
         <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist">
             <filter>distance</filter>
-            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.dist" format="mothur.dist">
-                <!-- doesn't seem to work for collection elements yet
-                <change_format>
-                    <when input="output" value="lt" format="mothur.lower.dist"/>
-                    <when input="output" value="square" format="mothur.square.dist"/>
-                </change_format>
-                -->
-            </discover_datasets>
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.dist" format="mothur.dist" />
+            <!-- doesn't seem to work for collection elements yet
+            <change_format>
+                <when input="output" value="lt" format="mothur.lower.dist"/>
+                <when input="output" value="square" format="mothur.square.dist"/>
+            </change_format>
+            -->
         </collection>
     </outputs>
     <tests>
@@ -176,13 +152,13 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
-The summary.shared_ command produce a summary file that has the calculator value for each line in the OTU data of the shared_ file and for all possible comparisons between the different groups in the group_ file.  This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators
+The summary.shared_ command produce a summary file that has the calculator value for each line in the OTU data of the shared_ file and for all possible comparisons between the different groups in the group_ file.  This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators
 
-.. _shared: http://www.mothur.org/wiki/Shared_file
-.. _group: http://www.mothur.org/wiki/Group_file
-.. _summary.shared: http://www.mothur.org/wiki/Summary.shared
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _summary.shared: https://www.mothur.org/wiki/Summary.shared
 ]]>
     </help>
     <expand macro="citations"/>