--- a/remove.groups.xml	Fri Jun 24 16:46:44 2016 -0400
+++ b/remove.groups.xml	Thu May 18 18:24:21 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
         #if $groupnames.source == "other":
             ln -s "$groupnames.group_in" groupnames_group_in.dat &&
@@ -43,6 +46,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="groupnames">
@@ -57,7 +61,7 @@
                         <filter type="data_meta" ref="group_in" key="groups"/>
                     </options>
                 </param>
-                <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
+                <param name="fasta_in" type="data" format="mothur.align,fasta" optional="true" label="fasta - Fasta Sequences"/>
                 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
                 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
                 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
@@ -75,23 +79,26 @@
     <outputs>
         <expand macro="logfile-output"/>
         <data name="fasta_out" format_source="fasta_in" from_work_dir="groupnames_fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
-            <filter>groupname['source'] == 'other' and fasta_in</filter>
+            <filter>groupnames['source'] == 'other' and groupnames['fasta_in']</filter>
         </data>
         <data name="group_out" format="mothur.groups" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
-            <filter>groupname['source'] == 'other' and group_in</filter>
+            <filter>groupnames['source'] == 'other' and groupnames['group_in'].ext == 'mothur.groups'</filter>
+        </data>
+        <data name="count_out" format="mothur.count_table" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.count_table">
+            <filter>groupnames['source'] == 'other' and groupnames['group_in'].ext == 'mothur.count_table'</filter>
         </data>
         <data name="name_out" format="mothur.names" from_work_dir="groupnames_name_in*.pick.*" label="${tool.name} on ${on_string}: pick.names">
-            <filter>groupname['source'] == 'other' and name_in</filter>
+            <filter>groupnames['source'] == 'other' and groupnames['name_in']</filter>
         </data>
         <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="groupnames_taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
-            <filter>groupname['source'] == 'other' and taxonomy_in</filter>
+            <filter>groupnames['source'] == 'other' and groupnames['taxonomy_in']</filter>
         </data>
         <collection name="list_out" type="list" label="${tool.name} on ${on_string}: pick.list">
-            <filter>groupname['source'] == 'other' and list_in</filter>
+            <filter>groupnames['source'] == 'other' and groupnames['list_in']</filter>
             <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/>
         </collection>
         <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: pick.shared">
-            <filter>groupname['source'] == 'shared'</filter>
+            <filter>groupnames['source'] == 'shared'</filter>
             <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
         </collection>
     </outputs>
@@ -127,15 +134,15 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The remove.groups_ command removes sequences from a specific group or set of groups from the following file types: fasta, name_, group_, list_, taxonomy_.
 
-.. _name: http://www.mothur.org/wiki/Name_file
-.. _group: http://www.mothur.org/wiki/Group_file
-.. _list: http://www.mothur.org/wiki/List_file
-.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
-.. _remove.groups: http://www.mothur.org/wiki/Remove.groups
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _list: https://www.mothur.org/wiki/List_file
+.. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
+.. _remove.groups: https://www.mothur.org/wiki/Remove.groups
 
 ]]>
     </help>