--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tagBed.xml	Tue Apr 28 22:56:34 2015 -0400
@@ -0,0 +1,55 @@
+<tool id="bedtools_tagbed" name="TagBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        #set files = '" "'.join( [ str( $file ) for $file in $inputB ] )
+        bedtools tag
+        -i "${inputA}"
+        -files "${files}"
+        -f $overlap
+        $strand
+        -tag "${tag}"
+        $field
+        > "${output}"
+]]>
+    </command>
+    <inputs>
+        <param name="inputA" format="bam" type="data" label="BAM file"/>
+        <param name="inputB" format="bed,gff,vcf" multiple="True" type="data" label="BED/VCF/GFF file" />
+        <expand macro="strand2" />
+        <expand macro="overlap" />
+        <param name="tag" type="text" value="YB" label="Specify the tag to use" />
+        <param name="field" type="select" label="Field from the annotation files to populate tags?">
+            <option value="-labels" selected="True">Labels</option>
+            <option value="-scores">Scores</option>
+            <option value="-names">Names</option>
+            <option value="-labels -intervals">Intervals</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="bam" name="output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="srma_in3.bam" ftype="bam" />
+            <param name="inputB" value="tagBed1.bed" ftype="bed" />
+            <param name="field" value="-names" />
+            <output name="output" file="tagBed_result1.bam" ftype="bam" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in an input bam file
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>