--- a/collect.shared.xml	Fri Jun 24 16:26:58 2016 -0400
+++ b/collect.shared.xml	Fri May 19 04:31:36 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 &&
 
@@ -25,6 +28,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
         && rm otu.dat  ## don't want this collected into datacollection
     ]]></command>
     <inputs>
@@ -38,45 +42,19 @@
             </options>
         </param>
         <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none are selected)">
+            <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>
         </param>
         <param name="freq" type="float" value="100" label="freq - indicates when to output your data" help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/>
     </inputs>
@@ -110,12 +88,12 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
-The collect.shared_ command generates collector's curves for calculators_, which describe the similarity between communities or their shared richness. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators
+The collect.shared_ command generates collector's curves for calculators_, which describe the similarity between communities or their shared richness. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators
 
-.. _calculators: http://www.mothur.org/wiki/Calculators
-.. _collect.shared: http://www.mothur.org/wiki/Collect.shared
+.. _calculators: https://www.mothur.org/wiki/Calculators
+.. _collect.shared: https://www.mothur.org/wiki/Collect.shared
 ]]>
     </help>
     <expand macro="citations"/>