--- a/find_subsequences.xml	Fri Mar 20 06:21:30 2015 -0400
+++ b/find_subsequences.xml	Fri Apr 10 06:47:42 2015 -0400
@@ -6,14 +6,15 @@
     <command interpreter="python">
     <![CDATA[
         find_subsequences.py
-            --input $input
-            --output $output
+            --input "${input}"
+            --output "${output}"
             --pattern "$pattern_conditional.pattern"
             #if $input.ext == 'fasta':
                 --format 'fasta'
             #else:
                 --format 'fastq'
             #end if
+            --strand '$strand'
     ]]>
     </command>
     <inputs>
@@ -248,6 +249,11 @@
                 </param>
             </when>
         </conditional>
+        <param name="strand" type="select" label="Search pattern on">
+            <option value='both'>both strands</option>
+            <option value='forward'>forward strand</option>
+            <option value='reverse'>reverse strand</option>
+        </param>
     </inputs>
     <outputs>
         <data format="bed" name="output" />
@@ -271,6 +277,20 @@
             <param name="pattern_conditional_select" value="user"/>
             <output name="output" file="find_subsequences_advanced_result1.bed" ftype="bed"/>
         </test>
+        <test>
+            <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/>
+            <param name="pattern" value="atnncg"/>
+            <param name="strand" value="reverse"/>
+            <param name="pattern_conditional_select" value="user"/>
+            <output name="output" file="find_subsequences_advanced_result2.bed" ftype="bed"/>
+        </test>
+        <test>
+            <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/>
+            <param name="pattern" value="atnncg"/>
+            <param name="strand" value="forward"/>
+            <param name="pattern_conditional_select" value="user"/>
+            <output name="output" file="find_subsequences_advanced_result3.bed" ftype="bed"/>
+        </test>
     </tests>
     <help>
 <![CDATA[