--- a/nucBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/nucBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,40 +1,38 @@
-<tool id="bedtools_nucbed" name="bedtools NucBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_nucbed" name="bedtools NucBed" version="@TOOL_VERSION@">
     <description>profile the nucleotide content of intervals in a FASTA file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools nuc
-        $s
-        $seq
-        #if str($pattern):
-            -pattern '$pattern'
-            $C
-        #end if
-        -fi '$fasta'
-        -bed '$input'
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools nuc
+$s
+$seq
+#if str($pattern):
+    -pattern '$pattern'
+    $C
+#end if
+-fi '$fasta'
+-bed '$input'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param format="fasta" name="fasta" type="data" label="FASTA file"/>
+        <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file"/>
 
-        <param argument="-s" type="boolean" checked="false" truevalue="-s" falsevalue=""
+        <param argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
             label="Profile the sequence according to strand" />
-        <param argument="-seq" type="boolean" checked="false" truevalue="-seq" falsevalue=""
+        <param argument="-seq" type="boolean" truevalue="-seq" falsevalue="" checked="false"
             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=""
+        <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false"
             label="Ignore case when matching -pattern"/>
     </inputs>
     <outputs>
-        <data format="tabular" name="output" />
+        <data name="output" format="tabular" />
     </outputs>
     <tests>
         <test>
@@ -56,14 +54,12 @@
             <output name="output" file="nucBed_result3.bed" ftype="tabular" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Profiles the nucleotide content of intervals in a fasta file.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>