--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/WaveletTransform.xml	Tue Jun 19 22:15:09 2012 -0400
@@ -0,0 +1,40 @@
+<tool id="WaveletTransform" name="Wavelet analysis" version="1.0.0">
+  <description>across a genomic interval</description>
+  <command interpreter="sh">galaxyToolRunner.sh ngs.WaveletTransform -i $input -w $wavelet --chr $chr --start $start --stop $stop --min $min --max $max --step $N -o $output</command>
+  <inputs>
+      <param format="wig,bigwig" name="input" type="data" label="Sequencing data" />
+      <param format="tabular" name="wavelet" type="data" label="Wavelet" />
+      <param name="chr" type="text" label="Chromosome" />
+      <param name="start" type="integer" value="1" label="Start base pair" />
+      <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="Scaling step size (bp)" />
+  </inputs>
+  <outputs>
+      <data format="tabular" name="output" />
+  </outputs>
+  
+<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>