--- a/galaxy-conf/WaveletTransform.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/WaveletTransform.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -9,7 +9,7 @@
       <param name="stop" type="integer" value="1000" label="Stop base pair" />
       <param name="min" type="integer" value="10" label="Minimum wavelet size (bp)" />
       <param name="max" type="integer" value="400" label="Maximum wavelet size (bp)" />
-      <param name="N" type="integer" value="1" label="Step size (bp)" />
+      <param name="N" type="integer" value="1" label="Scaling step size (bp)" />
   </inputs>
   <outputs>
       <data format="tabular" name="output" />
@@ -17,5 +17,24 @@
   
 <help>
   
+This tool will perform a Wavelet_ scaling_ analysis on an interval of genomic data. For each base pair in the interval, the similarity (correlation) is calculated between the data and the wavelet over a range of scales. This can be used to identify high-frequency and low-frequency features in the data. The output is a matrix in matrix2png format that can be used to generate a heatmap: along the x-axis (columns) are the base pairs in the interval, along the y-axis (rows) are the correlation coefficients for each Wavelet size, with the largest Wavelet scale at the top and the smallest scale at the bottom.
+
+.. _Wavelet: http://en.wikipedia.org/wiki/Wavelet
+
+.. _scaling: http://en.wikipedia.org/wiki/Scaleogram
+
+-----
+
+**Syntax**
+
+- **Input data** is the genomic data on which to compute the Wavelet scaling analysis.
+- **Wavelet** a single column of values representing a discrete Wavelet.
+- **Chromosome** a locus in the genome
+- **Start base pair** a locus in the genome
+- **Stop base pair** a locus in the genome
+- **Minimum wavelet size** the smallest Wavelet to analyze
+- **Minimum wavelet size** the largest Wavelet to analyze
+- **Scaling step size** the step size for the range of wavelet scales. The provided wavelet will be scaled to each size in the set min:step:max by interpolating the provided wavelet.
+  
 </help>
 </tool>