--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annotateBed.xml	Tue Nov 04 01:45:04 2014 -0500
@@ -0,0 +1,66 @@
+<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        bedtools annotate
+        -i $inputA
+        -files 
+        #for $bed in $names.beds:
+            $bed.input
+        #end for
+
+        #if $names.names_select == 'yes':
+            -names
+            #for $bed in $names.beds:
+                $bed.inputName
+            #end for
+        #end if
+        $strand
+        $counts
+        $both
+        &gt; $output
+    </command>
+    <inputs>
+        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" />
+        <!-- Additional files, if the user needs more -->
+         <conditional name="names">
+            <param name="names_select" type="select" label="Specify names for each file">
+                <option value="no" selected="True">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <repeat name="beds" title="Add BED files and names" >
+                    <param name="input" format="bed" type="data" label="BED file" />
+                    <param name="inputName" type="text" label="Name of the file" />
+                </repeat>
+            </when>
+            <when value="no">
+                <repeat name="beds" title="Add BED files" >
+                    <param name="input" format="bed" type="data" label="BED file" />
+                </repeat>
+            </when>
+        </conditional>
+        
+        <expand macro="strand2" />
+        <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue="" label="Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of -i covered by each file." />
+        <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue="" label="Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of the input file covered by each file." />
+    </inputs>
+
+    <outputs>
+        <data format="bed" name="output" label="" />
+    </outputs>
+    <help>
+    
+**What it does**
+
+bedtools annotate, well, annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command.
+
+@REFERENCES@
+
+    </help>
+    <expand macro="citations" />
+</tool>