--- a/complementBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/complementBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,24 +1,22 @@
-<tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@">
     <description>Extract intervals not represented by an interval file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        complementBed
-        -i "$input"
-        -g @GENOME_FILE@
-        > "$output"
-]]>
-    </command>
+    <command><![CDATA[
+complementBed
+-i '$input'
+-g @GENOME_FILE@
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="input_conditional_genome_file" />
     </inputs>
     <outputs>
-        <data format_source="input" name="output" metadata_source="input" label="Complement of ${input.name}"/>
+        <data name="output" format_source="input" metadata_source="input" label="Complement of ${input.name}"/>
     </outputs>
     <tests>
         <test>
@@ -28,8 +26,7 @@
             <output name="output" file="complementBed_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input @STD_BEDTOOLS_INPUT_LABEL@ file.
@@ -37,7 +34,6 @@
 .. image:: $PATH_TO_IMAGES/complement-glyph.png
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>