--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bedpeToBam.xml	Wed Jun 18 12:40:28 2014 -0400
@@ -0,0 +1,39 @@
+<tool id="bedtools_bedpetobam" name="Convert from BEDPE to BAM" version="0.1.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        bedtools bedpetobam
+        $ubam
+        -mapq $mapq
+        -i '$input'
+        -g $genome
+        &gt; '$output'
+
+    </command>
+    <inputs>
+        <param format="bed,gff,vcf" name="input" type="data" label="BED/VCF/GFF file"/>
+        <expand macro="genome" />
+        <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" />
+        <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/>
+
+    </inputs>
+    <outputs>
+        <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
+    </outputs>
+    <help>
+
+**What it does**
+
+Converts feature records to BAM format.
+
+.. class:: warningmark
+
+BED files must be at least BED4 to create BAM (needs name field).
+
+@REFERENCES@
+    </help>
+</tool>