# HG changeset patch
# User xuebing
# Date 1333244425 14400
# Node ID 7147b6e3ba069f1814c69db4c1ce84eb4406ccfe

Uploaded

diff -r 000000000000 -r 7147b6e3ba06 fimo_to_bed.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fimo_to_bed.xml	Sat Mar 31 21:40:25 2012 -0400
@@ -0,0 +1,19 @@
+<tool id="fimo_to_bed" name="FIMO-to-BED">
+  <description>convert FIMO output to BED</description>
+  <command interpreter="python">fimo_to_bed.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>