<tool id="DynaPro" name="Compute equilibrium nucleosome positions" version="1.0.0">
  <description>using DynaPro</description>
  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.DynaPro -i $input -n $N 
    #if str( $mean ) != ''
      -m $mean 
    #end if
    
    #if str( $variance ) != ''
      -v $variance
    #end if
    -o $output
  </command>
  <inputs>
      <param format="bigwig,wig" name="input" type="data" label="Energy landscape" />
      <param name="N" type="integer" value="147" label="Nucleosome size (bp)" />
      <param name="mean" type="float" optional="true" label="Shift energy landscape to have mean" />
      <param name="variance" type="float" optional="true" label="Rescale energy landscape to have variance" />
  </inputs>
  <outputs>
      <data format="wig" name="output" metadata_source="input" />
  </outputs>
  <help>

.. class:: warningmark

At present, this tool is only suitable for small genomes (yeast) since entire chromosomes must be loaded into memory.

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Equilibrium nucleosome distribution is modeled as a one-dimensional fluid of hard rods adsorbing and moving within an external potential. This tool provides a simplified version of the DynaPro_ algorithm for a single factor interacting with hard-core repulsion.

.. _DynaPro: http://nucleosome.rutgers.edu/nucleosome/

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**Syntax**

- **Energy landscape** is the external potential function for each genomic base pair, and must be in Wig format.
- **Nucleosome size** is the hard-core interaction size.

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**Citation**

Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J and Siggia ED (2009) Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Nucleic Acids Res 37: 4707–4722.

  </help>
</tool>