--- a/seq.error.xml	Fri Jun 24 16:49:43 2016 -0400
+++ b/seq.error.xml	Thu May 18 18:09:32 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 "$fasta_in" fasta_in.dat &&
         ln -s "$name_in" name_in.dat &&
@@ -33,13 +36,19 @@
             #if $count:
                 count=count.dat,
             #end if
+            #if $fasta_in.is_of_type('mothur.align')
+                aligned=T,
+            #else
+                aligned=F,
+            #end if
             processors='\${GALAXY_SLOTS:-8}'
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
-        <param name="fasta_in" type="data" format="mothur.align" label="fasta - Candidate Sequences" help="sequences must be aligned"/>
+        <param name="fasta_in" type="data" format="mothur.align,fasta" label="fasta - Candidate Sequences" help="sequences must be aligned"/>
         <conditional name="alignment">
             <param name="source" type="select" label="Select Reference Template from" help="">
                 <option value="ref">Cached Reference</option>
@@ -51,7 +60,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="template" type="data" format="mothur.align" label="reference - Reference to align with" help=""/>
+                <param name="template" type="data" format="mothur.align,fasta" label="reference - Reference to align with" help=""/>
             </when>
         </conditional>
         <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
@@ -66,22 +75,9 @@
             </when>
             <when value="no"/>
         </conditional>
-        <param name="count" type="data" format="mothur.count_table" optional="true" label="The count parameter allows you to provide a count file associated with your fasta file, so you can include the redundant sequences in your error analysis"/>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count table"/>
         <param name="threshold" type="float" value="" min="0" max="1" optional="true" label="threshold - error rate at which to report (default 1.)"/>
         <param name="ignorechimeras" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ignorechimeras - "/>
-        <param name="output_sel" type="select" multiple="true" display="checkboxes" label="Outputs as history datasets">
-            <option value="summary">error.summary</option>
-            <option value="seq">error.seq</option>
-            <option value="seq_forward">error.seq.forward</option>
-            <option value="seq_reverse">error.seq.reverse</option>
-            <option value="chimera">error.chimera</option>
-            <option value="count">error.count</option>
-            <option value="matrix">error.matrix</option>
-            <option value="quality">error.quality</option>
-            <option value="qual_forward">error.qual.forward</option>
-            <option value="qual_reverse">error.qual.reverse</option>
-            <option value="ref_query">error.ref-query</option>
-        </param>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -162,13 +158,13 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The seq.error_ command evaluates error rate for sequences by comparing to the fasta-formatted template_alignment_.
-This is demonstrated in http://www.mothur.org/wiki/Schloss_SOP#Error_analysis
+This is demonstrated in https://www.mothur.org/wiki/Schloss_SOP#Error_analysis
 
-.. _template_alignment: http://www.mothur.org/wiki/Alignment_database
-.. _seq.error: http://www.mothur.org/wiki/Seq.error
+.. _template_alignment: https://www.mothur.org/wiki/Alignment_database
+.. _seq.error: https://www.mothur.org/wiki/Seq.error
 
 ]]>
     </help>