--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/DynaPro.xml	Wed Apr 25 16:53:48 2012 -0400
@@ -0,0 +1,48 @@
+<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.
+
+-----
+
+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/
+
+-----
+
+**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.
+
+-----
+
+**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>