--- a/nucBed.xml	Wed Jan 10 19:30:53 2018 -0500
+++ b/nucBed.xml	Sun Jan 21 07:17:19 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.1">
     <description>profile the nucleotide content of intervals in a FASTA file</description>
     <macros>
         <import>macros.xml</import>
@@ -8,10 +8,12 @@
     <command>
 <![CDATA[
         bedtools nuc
-        $strand
+        $s
         $seq
-        $pattern
-        $case
+        #if str($pattern):
+            -pattern '$pattern'
+            $C
+        #end if
         -fi '$fasta'
         -bed '$input'
         > '$output'
@@ -21,14 +23,15 @@
         <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
         <param format="fasta" name="fasta" type="data" label="FASTA file"/>
 
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
-            label="Profile the sequence according to strand" help="(-s)"/>
-        <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue=""
-            label="Print the extracted sequence" help="(-seq)"/>
-        <param name="pattern" type="boolean" checked="false" truevalue="-pattern" falsevalue=""
-            label="Report the number of times a user-defined sequence is observed" help="case-sensitive (-pattern)" />
-        <param name="case" type="boolean" checked="false" truevalue="-C" falsevalue=""
-            label="Ignore case when matching -pattern" help="(-C)"/>
+        <param argument="-s" type="boolean" checked="false" truevalue="-s" falsevalue=""
+            label="Profile the sequence according to strand" />
+        <param argument="-seq" type="boolean" checked="false" truevalue="-seq" falsevalue=""
+            label="Print the extracted sequence" />
+        <param argument="-pattern" type="text" label="Report the number of times a user-defined sequence is observed" help="Case-sensitive by default">
+            <validator type="regex" message="Sequence should only contain letters.">^[A-Za-z]*$</validator>
+        </param>
+        <param argument="-C" type="boolean" checked="false" truevalue="-C" falsevalue=""
+            label="Ignore case when matching -pattern"/>
     </inputs>
     <outputs>
         <data format="tabular" name="output" />
@@ -45,6 +48,13 @@
             <param name="seq" value="True" />
             <output name="output" file="nucBed_result2.bed" ftype="tabular" />
         </test>
+        <test>
+            <param name="input" value="nucBed1.bed" ftype="bed" />
+            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
+            <param name="seq" value="True" />
+            <param name="pattern" value="TAC" />
+            <output name="output" file="nucBed_result3.bed" ftype="tabular" />
+        </test>
     </tests>
     <help>
 <![CDATA[