<tool id="PercusDecomposition" name="Derive Percus energy landscape" version="1.1.0">
  <description>from occupancy data</description>
  <command interpreter="bash">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).
  
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**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>