--- a/windowBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/windowBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,74 +1,71 @@
-<tool id="bedtools_windowbed" name="bedtools WindowBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_windowbed" name="bedtools WindowBed" version="@TOOL_VERSION@">
     <description>find overlapping intervals within a window around an interval</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools window
-        #if $inputA.is_of_type('bam'):
-            -abam '$inputA'
-        #else:
-            -a '$inputA'
-        #end if
-        -b '$inputB'
-        $bed
-        $strandB
-        #if $addition.addition_select == 'window':
-            -w $addition.w
-        #elif $addition.addition_select == 'lr':
-            -l $addition.l
-            -r $addition.r
-        #end if
-        $original
-        $number
-        $nooverlaps
-        $header
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools window
+#if $inputA.is_of_type('bam'):
+    -abam '$inputA'
+#else:
+    -a '$inputA'
+#end if
+-b '$inputB'
+$bed
+$strandB
+#if $addition.addition_select == 'window':
+    -w $addition.w
+#elif $addition.addition_select == 'lr':
+    -l $addition.l
+    -r $addition.r
+#end if
+$original
+$number
+$nooverlaps
+$header
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param name="bed" type="boolean" checked="false" truevalue="-bed" falsevalue=""
-            label="When using BAM input, write output as BED. The default is to write output in BAM when using a bam file"
-            help="(-bed)" />
+        <param name="inputA" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
+        <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
+            label="When using BAM input, write output as BED. The default is to write output in BAM when using a BAM file" />
         <conditional name="addition">
             <param name="addition_select" type="select" label="Choose what you want to do">
                 <option value="window">Add Base pairs for **both** upstream and downstream of each entry in A when searching for overlaps in B</option>
                 <option value="lr">Add Base pairs **separately** for upstream and downstream of each entry in A when searching for overlaps in B</option>
             </param>
             <when value="window">
-                <param name="w" type="integer" value="1000" label="Base pairs to add upstream and downstream" />
+                <param argument="-w" type="integer" value="1000" label="Base pairs to add upstream and downstream" />
             </when>
             <when value="lr">
-                <param name="l" type="integer" value="1000"
+                <param argument="-l" type="integer" value="1000"
                     label="Base pairs added upstream (left) of each entry in A when searching for overlaps in B"
-                    help="Allows one to create assymetrical “windows”. Default is 1000bp. (-l)" />
-                <param name="r" type="integer" value="1000"
+                    help="Allows one to create assymetrical “windows”. Default is 1000bp." />
+                <param argument="-r" type="integer" value="1000"
                     label="Base pairs added downstream (right) of each entry in A when searching for overlaps in B"
-                    help="Allows one to create assymetrical “windows”. Default is 1000bp. (-r)" />
+                    help="Allows one to create assymetrical “windows”. Default is 1000bp." />
             </when>
         </conditional>
         <param name="strandB" type="select" label="Calculation based on strandedness?">
-            <option value="" selected="True">Report any hit in B</option>
+            <option value="" selected="true">Report any hit in B</option>
             <option value="-sm">Only report hits in B that overlap A on the **same** strand</option>
             <option value="-Sm">Only report hits in B that overlap A on the **opposite** strand</option>
         </param>
-        <param name="original" type="boolean" checked="false" truevalue="-u" falsevalue=""
+        <param name="original" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false"
             label="Write original A entry once if any overlaps found in B"
-            help="In other words, just report the fact at least one overlap was found in B. (-u)" />
-        <param name="number" type="boolean" checked="false" truevalue="-c" falsevalue=""
+            help="In other words, just report the fact at least one overlap was found in B" />
+        <param name="number" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
             label="For each entry in A, report the number of hits in B"
-            help="Reports 0 for A entries that have no overlap with B (-c)" />
-        <param name="nooverlaps" type="boolean" checked="false" truevalue="-v" falsevalue=""
-            label="Only report those entries in A that have no overlaps with B" help="(-v)" />
+            help="Reports 0 for A entries that have no overlap with B" />
+        <param name="nooverlaps" argument="-v" type="boolean" truevalue="-v" falsevalue="" checked="false"
+            label="Only report those entries in A that have no overlaps with B" />
         <expand macro="print_header" />
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
+        <data name="output" format_source="inputA" metadata_source="inputA" />
     </outputs>
     <tests>
         <test>
@@ -92,8 +89,7 @@
             <output name="output" file="windowBed_result2.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Similar to bedtools intersect, window searches for overlapping features in A and B. However, window adds a specified number (1000, by default) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are “near” features in A to be detected.
@@ -101,7 +97,6 @@
 .. image:: $PATH_TO_IMAGES/window-glyph.png
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>