--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bed_to_bam.xml	Sat Mar 10 07:59:27 2012 -0500
@@ -0,0 +1,19 @@
+<tool id="bedToBam" name="bedToBam">
+  <description>convert BED or GFF or VCF to BAM</description>
+  <command>bedToBam -i $input -g $genome $bed12 $mapq $ubam > $outfile </command>
+  <inputs>
+    <param name="input" format="bed,gff,vcf" type="data" label="Input file (BED,GFF,VCF)" help="BED files must be at least BED4 to be amenable to BAM (needs name field)"/>
+    <param name="genome" type="select" label="Select genome">
+     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
+     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
+     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
+     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
+    </param>
+    <param name="mapq" size="10" type="integer" value="255" label="Set the mappinq quality for the BAM records"/>
+    <param name="bed12" label="The BED file is in BED12 format" help="The BAM CIGAR string will reflect BED blocks" type="boolean" truevalue="-bed12" falsevalue="" checked="False"/>
+    <param name="ubam" label="Write uncompressed BAM output" help="Default is to write compressed BAM" type="boolean" truevalue="-ubam" falsevalue="" checked="False"/>
+  </inputs>
+  <outputs>
+    <data format="bam" name="outfile" />
+  </outputs>
+</tool>