--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mytools/fimo2bed.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,19 @@
+<tool id="fimo2bed" name="fimo-to-bed">
+  <description>convert FIMO output to BED</description>
+  <command interpreter="python">fimo2bed.py $input $rc > $output</command>
+  <inputs>
+    <param name="input" format="txt" type="data" label="FIMO output file"/>
+    <param name="rc" label="Check if the sequences are reverse complement" type="boolean" truevalue="rc" falsevalue="none" checked="False"/>
+  </inputs>
+  <outputs>
+    <data format="bed" name="output" />
+  </outputs>
+  <help>
+
+  Only works if your original FIMO input fasta sequences have ids like:: 
+  
+    mm9_chr15_99358448_99360448_-
+  
+  
+  </help>
+</tool>