--- a/macros.xml	Fri Jun 24 16:33:26 2016 -0400
+++ b/macros.xml	Thu May 18 18:09:47 2017 -0400
@@ -7,7 +7,14 @@
     <xml name="version_command">
         <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command>
     </xml>
+    <xml name="stdio">
+        <stdio>
+            <regex match="\[ERROR\]" source="stdout" level="fatal"/>
+            <exit_code range="1:" level="fatal"/>
+        </stdio>
+    </xml>
     <token name="@WRAPPER_VERSION@">1.36.1</token>
+    <token name="@SHELL_OPTIONS@">set -o pipefail;</token>
     <token name="@MOTHUR_OVERVIEW@">
 <![CDATA[
 
@@ -16,7 +23,7 @@
 Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team
 in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.
 
-.. _Mothur-Wiki: http://www.mothur.org/wiki/Main_Page
+.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page
 
 ]]>
     </token>
@@ -25,8 +32,54 @@
             <filter type="data_meta" ref="otu" key="labels"/>
         </options>
     </xml>
+    <xml name="calc-common">
+        <!-- you can set defaults in tool xml by repeating those options again after macro expand, overriding first -->
+        <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
+        <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
+        <option value="canberra">canberra - Community Structure Similarity</option>
+        <option value="gower">gower - Community Structure Similarity</option>
+        <option value="hamming">hamming - Community Membership Similarity</option>
+        <option value="hellinger">hellinger - Community Structure Similarity</option>
+        <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
+        <option value="jclass">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="jsd">jsd</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="manhattan">manhattan - Community Structure 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="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
+        <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
+        <option value="odum">odum - Community Structure Similarity</option>
+        <option value="rjsd">rjsd</option>
+        <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</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>
+        <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="soergel">soergel - Community Structure Similarity</option>
+        <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson 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="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="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
+        <option value="thetayc">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
+        <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
+        <yield/>
+    </xml>
     <xml name="logfile-output">
-        <data name="logfile" format="txt" from_work_dir="mothur.*.logfile" label="${tool.name} on ${on_string}: logfile"/>
+        <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/>
     </xml>
     <xml name="logfile-test">
         <output name="logfile" ftype="txt">