--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/unique.seqs.xml	Fri May 19 05:51:37 2017 -0400
@@ -0,0 +1,79 @@
+<tool profile="16.07" id="mothur_unique_seqs" name="Unique.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Return unique sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## 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 $names.is_of_type('mothur.count_table'):
+                count=names.dat,
+            #end if
+            fasta=fasta.dat
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
+        <param name="names" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Names"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/>
+        <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${tool.name} on ${on_string}: names">
+            <filter>names.ext != "mothur.count_table"</filter>
+        </data>
+        <data name="out_count" format="mothur.count_table" from_work_dir="fasta*.count_table" label="${tool.name} on ${on_string}: count_table">
+            <filter>names and names.ext == "mothur.count_table"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test><!-- test with names file -->
+            <param name="fasta" value="amazon.fasta"/>
+            <param name="names" value="amazon1.names" ftype="mothur.names"/>
+            <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>
+        <test><!-- test with count file -->
+            <param name="fasta" value="amazon.unique.fasta"/>
+            <param name="names" value="amazon.count_table" ftype="mothur.count_table"/>
+            <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
+            <output name="out_count" md5="2024cbb895f79346606ab196dd130639" ftype="mothur.count_table"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test wth fasta only -->
+            <param name="fasta" value="amazon.fasta"/>
+            <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[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The unique.seqs_ command returns only the unique sequences found in a fasta-formatted sequence file and a name_ file that indicates those sequences that are identical to the reference sequence.
+
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _unique.seqs: https://www.mothur.org/wiki/Unique.seqs
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>