--- a/align.seqs.xml	Fri Jun 24 17:30:20 2016 -0400
+++ b/align.seqs.xml	Fri May 19 05:01:07 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@
+
         ## enable mothur to find blast
         loc=`which mothur` && ln -s "\${loc%/mothur}"/* . &&
 
@@ -36,6 +39,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | ./mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="candidate" type="data" format="fasta" label="fasta - Candiate Sequences"/>
@@ -98,6 +102,9 @@
         <expand macro="logfile-output"/>
         <data name="out_file" format="mothur.align" from_work_dir="candidate.align" label="${tool.name} on ${on_string}: align"/>
         <data name="report" format="mothur.align.report" from_work_dir="candidate.align.report" label="${tool.name} on ${on_string}: align.report"/>
+        <data name="flip_accnos" format="mothur.accnos" from_work_dir="candidate.flip.accnos" label="${tool.name} on ${on_string}: flip.accnos">
+            <filter>reverse['flip'] == 'yes'</filter>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -149,13 +156,24 @@
             <output name="report" md5="9ec830c9a278e20d8499ba55fef6f501" ftype="mothur.align.report"/>
             <expand macro="logfile-test"/>
         </test>
+        <test><!-- test accno file recovery with flip set to true -->
+            <param name="candidate" value="amazon.fasta"/>
+            <param name="source" value="history"/>
+            <param name="template" value="HMP_MOCK.v35.align"/>
+            <param name="flip" value="yes"/>
+            <param name="threshold" value="0.5"/>
+            <output name="out_file" md5="73b3b1d0c1176ed9731eedbda70b5957" ftype="mothur.align"/>
+            <output name="report" md5="e502a984ffb97026f1d84c9aee616003" ftype="mothur.align.report"/>
+            <output name="flip_accnos" md5="afd8e7629be76baa74451b91423aaa2f" ftype="mothur.accnos"/>
+            <expand macro="logfile-test"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The align.seqs_ command aligns a user-supplied fasta-formatted candidate sequence file to a user-supplied fasta-formatted template_alignment_.
 
@@ -166,8 +184,8 @@
 
 In general the alignment is very fast - we are able to align over 186,000 full-length sequences to the SILVA alignment in less than 3 hrs with a quality as good as the SINA aligner. Furthermore, this rate can be accelerated using multiple processors. While the aligner doesn't explicitly take into account the secondary structure of the 16S rRNA gene, if the template database is based on the secondary structure, then the resulting alignment will at least be implicitly based on the secondary structure.
 
-.. _template_alignment: http://www.mothur.org/wiki/Alignment_database
-.. _align.seqs: http://www.mothur.org/wiki/Align.seqs
+.. _template_alignment: https://www.mothur.org/wiki/Alignment_database
+.. _align.seqs: https://www.mothur.org/wiki/Align.seqs
 
 ]]>
     </help>