--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/WigCorrelate.xml	Wed Apr 25 16:53:48 2012 -0400
@@ -0,0 +1,48 @@
+<tool id="WigCorrelate" name="Correlate" version="1.0.0">
+  <description>multiple (Big)Wig files</description>
+  <command interpreter="sh">
+    galaxyToolRunner.sh wigmath.WigCorrelate -w $window -t $type -o $output
+      #for $input in $inputs
+        ${input.file}
+      #end for
+  </command>
+  <inputs>
+      <repeat name="inputs" title="(Big)Wig file">
+        <param name="file" type="data" format="bigwig,wig" />
+      </repeat>
+      <param name="window" type="integer" value="100" label="Window size (bp)" />
+      <param name="type" type="select" label="Correlation metric">
+      	<option value="pearson">Pearson</option>
+      	<option value="spearman">Spearman</option>
+      </param>
+  </inputs>
+  <outputs>
+      <data format="tabular" name="output" />
+  </outputs>
+  
+<help>
+  
+This tool will compute a correlation matrix between the supplied Wig or BigWig files. Each row/column in the matrix is added in the order that files are added above, starting from the top left. The Wig file is downsampled into non-overlapping windows with the specified size by computing the mean value in each window. These windows are then correlated using either  Pearson_'s Product-Moment correlation coefficient or Spearman_'s rank correlation coefficient. If the window size is set to 1, the correlation is calculated between all base pairs in the genome.
+  
+.. _Pearson: http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient
+
+.. _Spearman: http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient
+  
+-----
+
+.. class:: warningmark
+
+**WARN:** In order to calculate the correlation coefficient, the data is loaded into entirely into memory. For large genomes, this may require a lot of RAM unless comparably larger window sizes are used.
+
+-----
+
+**Citation**
+
+This tool was inspired by ACT_ from the Gerstein lab.
+
+.. _ACT: http://act.gersteinlab.org
+
+J Jee*, J Rozowsky*, KY Yip*, L Lochovsky, R Bjornson, G Zhong, Z Zhang, Y Fu, J Wang, Z Weng, M Gerstein. ACT: Aggregation and Correlation Toolbox for Analyses of Genome Tracks. (2011) Bioinformatics 27(8): 1152-4.
+  
+</help>
+</tool>