--- a/sub.sample.xml	Fri Jun 24 16:51:17 2016 -0400
+++ b/sub.sample.xml	Thu May 18 18:44:02 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 "$input.otu" input_otu.dat &&
         ln -s "$count" count.dat &&
@@ -61,6 +64,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -139,13 +143,16 @@
         </conditional>
         <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/>
         <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
-        <param name="taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/>
+        <param name="taxonomy" type="data" format="mothur.seq.taxonomy,mothur.ref.taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
         <data name="fasta_out" format_source="otu" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.fasta">
             <filter>input['format'] == 'fasta'</filter>
         </data>
+        <data name="taxonomy_out" format_source="taxonomy" from_work_dir="taxonomy.subsample.dat" label="${tool.name} on ${on_string}: subsample.taxonomy">
+            <filter>taxonomy</filter>
+        </data>
         <collection name="list_out" type="list" label="${tool.name} on ${on_string}: subsample.list">
             <filter>input['format'] == 'list'</filter>
             <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.subsample\.dat" format="mothur.list"/>
@@ -198,14 +205,20 @@
             </output_collection>
             <expand macro="logfile-test"/>
         </test>
-        <test><!-- test with fasta -->
+        <test><!-- test with fasta and taxonomy -->
             <param name="format" value="fasta"/>
             <param name="otu" value="amazon.fasta" ftype="fasta"/>
+            <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
             <output name="fasta_out" ftype="fasta">
                 <assert_contents>
                     <has_text text=">U"/>
                 </assert_contents>
             </output>
+            <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
+                <assert_contents>
+                    <has_line_matching expression="^U[0-9]+\tBacteria.*$"/>
+                </assert_contents>
+            </output>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with fasta and group file and name file -->
@@ -277,15 +290,15 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The sub.sample_ command can be used as a way to normalize your data, or to create a smaller set from your original set. It takes as an input the following file types: fasta, list_, shared_, rabund_ and sabund_ to generate a new file that contains a sampling of your original file.
 
-.. _list: http://www.mothur.org/wiki/List_file
-.. _shared: http://www.mothur.org/wiki/Shared_file
-.. _rabund: http://www.mothur.org/wiki/Rabund_file
-.. _sabund: http://www.mothur.org/wiki/Sabund_file
-.. _sub.sample: http://www.mothur.org/wiki/Sub.sample
+.. _list: https://www.mothur.org/wiki/List_file
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _rabund: https://www.mothur.org/wiki/Rabund_file
+.. _sabund: https://www.mothur.org/wiki/Sabund_file
+.. _sub.sample: https://www.mothur.org/wiki/Sub.sample
 
 ]]>
     </help>