--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/FindBoundaryNucleosomes.xml	Tue Jun 19 22:15:09 2012 -0400
@@ -0,0 +1,30 @@
+<tool id="FindNuke" name="Find boundary nucleosomes" version="2.0.0">
+  <description>in windows</description>
+  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.FindBoundaryNucleosomes -i $input -l $loci -o $output</command>
+  <inputs>
+    <param name="input" type="data" format="tabular" label="Nucleosome calls" />
+    <param name="loci" type="data" format="bed,bedgraph,gff" label="List of intervals" />
+  </inputs>
+  <outputs>
+    <data name="output" format="bed" metadata_source="loci" />
+  </outputs>
+  
+  <help>
+    
+.. class:: infomark
+    
+Use the Call Nucleosomes tool to create a file of called nucleosomes, then use this tool to identify the first nucleosome's dyad position (peak maximum) from the 5' and 3' end of the gene.
+
+.. class:: infomark
+
+**TIP:** Nucleosome calls must be in tabular format of the kind produced by the Nucleosomes -> Call nucleosomes tool. Intervals must be in either Bed, BedGraph, or GFF format.
+
+-----
+
+**Syntax**
+
+- **Nucleosome calls** is a list of stereotypic nucleosome position calls.
+- **List of intervals:** The 5' and 3' boundary nucleosomes will be found for each interval in this list
+
+  </help>
+</tool>