--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/PercusDecomposition.xml	Tue Jun 19 22:15:09 2012 -0400
@@ -0,0 +1,25 @@
+<tool id="PercusDecomposition" name="Derive Percus energy landscape" version="1.1.0">
+  <description>from occupancy data</description>
+  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.PercusDecomposition -d $dyads -n $N -o $output</command>
+  <inputs>
+      <param name="dyads" type="data" format="bigwig,wig" label="Dyad counts (smoothed)" />
+      <param name="N" type="integer" value="147" optional="true" label="Assumed nucleosome size" />
+  </inputs>
+  <outputs>
+      <data name="output" format="wig" />
+  </outputs>
+  
+<help>
+  
+This tool derives an external potential energy function from experimental nucleosome positioning data by assuming that nucleosomes interact with DNA like a fluid of hard rods. This energy function can then be used to derive sequence-specific nucleosome formation preferences, while accounting for hard-core steric restriction by adjacent nucleosomes. This tool is a reimplementation of the algorithm described in (Locke et al. 2010).
+  
+-----
+
+**Citations**
+
+Locke G, Tolkunov D, Moqtaderi Z, Struhl K and Morozov AV (2010) High-throughput sequencing reveals a simple model of nucleosome energetics. Proceedings of the National Academy of Sciences 107: 20998–21003
+
+Percus JK (1976) Equilibrium state of a classical fluid of hard rods in an external field. J Stat Phys 15: 505–511
+
+</help>
+</tool>