--- a/pcr.seqs.xml	Fri Jun 24 16:44:52 2016 -0400
+++ b/pcr.seqs.xml	Fri May 19 05:26:29 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 "$fasta" fasta.dat &&
         ln -s "$name_in" name_in.dat &&
@@ -48,6 +51,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Sequences" help="sequences must be aligned"/>
@@ -81,8 +85,8 @@
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
-        <data name="pcr_fasta" format="mothur.align" from_work_dir="fasta*.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/>
-        <data name="scrap_fasta" format="mothur.align" from_work_dir="fasta*.scrap.pcr.dat" label="${tool.name} on ${on_string}: pcr.scrap.fasta"/>
+        <data name="pcr_fasta" format="mothur.align" from_work_dir="fasta.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/>
+        <data name="scrap_fasta" format="mothur.align" from_work_dir="fasta.scrap.pcr.dat" label="${tool.name} on ${on_string}: pcr.scrap.fasta"/>
         <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pcr.dat" label="${tool.name} on ${on_string}: tax.summary">
             <filter>taxonomy_in</filter>
         </data>
@@ -105,7 +109,7 @@
             <param name="end" value="0"/>
             <param name="pdiffs" value="0"/>
             <expand macro="logfile-test"/>
-            <ouptut name="pcr_fasta" md5="1e78af5a460572e22ce199e522a70388" ftype="mothur.align"/>
+            <output name="pcr_fasta" md5="4f9c3a835bbba51c64fbf86c8a467d0e" ftype="mothur.align"/>
             <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
         </test>
         <test><!-- test with reference method -->
@@ -116,7 +120,7 @@
             <param name="name_in" value="amazon.align_head.names"/>
             <param name="pdiffs" value="2"/>
             <expand macro="logfile-test"/>
-            <ouptut name="pcr_fasta" md5="1e78af5a460572e22ce199e522a70388" ftype="mothur.align"/>
+            <output name="pcr_fasta" md5="4bef877bd45f47041f3d17dc017f21ea" ftype="mothur.align"/>
             <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
             <output name="name_out" md5="0c58174137c2ecabf7da9ab492ea46fc" ftype="mothur.names"/>
         </test>
@@ -130,7 +134,7 @@
             <param name="start" value="5"/>
             <param name="end" value="50"/>
             <expand macro="logfile-test"/>
-            <ouptut name="pcr_fasta" md5="1e78af5a460572e22ce199e522a70388" ftype="mothur.align"/>
+            <output name="pcr_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
             <output name="scrap_fasta" md5="0b63807f339dfd88cf958f7b069eba02" ftype="mothur.align"/>
             <output name="group_out" md5="301c358e61d38c83cc7382a8a210089a" ftype="mothur.groups"/>
             <output name="name_out" md5="62eb1162557408509c931496071add85" ftype="mothur.names"/>
@@ -143,11 +147,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The pcr.seqs_ command assigns sequences to chosen taxonomy outline.
 
-.. _pcr.seqs: http://www.mothur.org/wiki/Pcr.seqs
+.. _pcr.seqs: https://www.mothur.org/wiki/Pcr.seqs
 
 ]]>
     </help>