--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BedToBam.xml	Wed Jun 18 15:07:04 2014 -0400
@@ -0,0 +1,35 @@
+<tool id="bedtools_bedtobam" name="Convert from BED to BAM" version="0.1.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        bedtools bedtobam
+        $ubam
+        $bed12
+        -mapq $mapq
+        -i '$input'
+        &gt; '$output'
+
+    </command>
+    <inputs>
+        <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/>
+        <param name="bed12" type="boolean" label="Indicate that the input BED file is in BED12 (a.k.a “blocked” BED) format" truevalue="-bed12" falsevalue="" checked="false" help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into “spliced” BAM alignments by creating an appropriate CIGAR string.."/>
+        <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" />
+        <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/>
+
+    </inputs>
+    <outputs>
+        <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
+    </outputs>
+    <help>
+
+**What it does**
+
+bedToBam converts features in a feature file to BAM format. This is useful as an efficient means of storing large genome annotations in a compact, indexed format for visualization purposes.
+
+@REFERENCES@
+    </help>
+</tool>