--- a/unique.seqs.xml	Tue Sep 05 16:26:37 2017 -0400
+++ b/unique.seqs.xml	Wed Feb 14 10:07:44 2018 -0500
@@ -7,42 +7,48 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$names" names.dat &&
-        ln -s "$fasta" fasta.dat &&
+## create symlinks to input datasets
+ln -s '$names' names.dat &&
+ln -s '$fasta' fasta.dat &&
 
-        echo 'unique.seqs(
-            #if $names.is_of_type('mothur.names'):
-                name=names.dat,
-            #elif $names.is_of_type('mothur.count_table'):
-                count=names.dat,
-            #end if
-            fasta=fasta.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'unique.seqs(
+    #if $names.is_of_type('mothur.names'):
+        name=names.dat,
+    #elif $names.is_of_type('mothur.count_table'):
+        count=names.dat,
+    #end if
+    fasta=fasta.dat,
+    format=$format
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
         <param name="names" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Names"/>
+        <param name="format" type="select" label="output format">
+            <option value="count" selected="true"> Count table </option>
+            <option value="name"> Name file </option>
+        </param>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
         <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/>
         <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${tool.name} on ${on_string}: names">
-            <filter>names.ext != "mothur.count_table"</filter>
+            <filter> format == "name" </filter>
         </data>
         <data name="out_count" format="mothur.count_table" from_work_dir="fasta*.count_table" label="${tool.name} on ${on_string}: count_table">
-            <filter>names and names.ext == "mothur.count_table"</filter>
+            <filter> format == "count" </filter>
         </data>
     </outputs>
     <tests>
         <test><!-- test with names file -->
             <param name="fasta" value="amazon.fasta"/>
             <param name="names" value="amazon1.names" ftype="mothur.names"/>
+            <param name="format" value="name"/>
             <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
             <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
             <expand macro="logfile-test"/>
@@ -56,13 +62,13 @@
         </test>
         <test><!-- test wth fasta only -->
             <param name="fasta" value="amazon.fasta"/>
+            <param name="format" value="name"/>
             <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
             <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -73,7 +79,6 @@
 .. _name: https://www.mothur.org/wiki/Name_file
 .. _unique.seqs: https://www.mothur.org/wiki/Unique.seqs
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>