--- a/galaxy-conf/PowerSpectrum.xml	Mon Apr 09 11:50:23 2012 -0400
+++ b/galaxy-conf/PowerSpectrum.xml	Wed Apr 25 16:53:48 2012 -0400
@@ -1,17 +1,59 @@
 <tool id="PowerSpectrum" name="Compute the power spectrum" version="1.0.0">
-  <description>on data in a Wiggle file</description>
-  <command interpreter="sh">galaxyToolRunner.sh ngs.PowerSpectrum -i $input -l $windows -o $output</command>
+  <description>of data in a Wiggle file</description>
+  <command interpreter="sh">galaxyToolRunner.sh ngs.PowerSpectrum -i $input -l $windows -m $max -o $output</command>
   <inputs>
       <param format="bigwig,wig" name="input" type="data" label="Input data" />
       <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" />
+      <param name="max" type="integer" value="40" label="Number of frequencies to output" />
   </inputs>
   <outputs>
       <data format="tabular" name="output" />
   </outputs>
   
 <help>
+  
+This tool computes the power spectrum of intervals of sequencing data. For each interval provided, the normalized power spectrum is calculated, representing the relative power in each frequency. Power spectra are normalized to have total power 1, with the DC component (0 frequency) removed. Power spectra are computed using the FFT_ implementation in JTransforms_.
+
+.. _FFT: http://en.wikipedia.org/wiki/Fast_Fourier_transform
+
+.. _JTransforms: http://sites.google.com/site/piotrwendykier/software/jtransforms
+
+-----
+
+**Syntax**
+
+- **Input data** is the genomic data on which to compute the power spectrum.
+- **List of intervals:** The power spectrum will be computed for each genomic interval specified in this list.
+- **Number of frequencies:** The power spectrum will be truncated at this frequency in the output
+
+-----
+
+**Output**
+
+The output has the following format ::
+
+  chr  start  stop  id  alignment  strand  freq1  freq2  ...
+  
+up to the maximum frequency specified. Frequencies are truncated to reduce the size of the output since signals are often band-limited.
+
+-----
+
 .. class:: warningmark
 
-This tool requires Wiggle/BigWig input data.
+**NOTE:** Even though frequencies may be truncated in the output, all frequencies in the power spectrum are computed and used for normalization.
+  
+.. class:: infomark
+
+**TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in Wig or BigWig format. Use "edit attributes" to set the correct format if it was not detected correctly. Intervals must be provided in Bed, BedGraph, or GFF format.
+
+-----
+
+This tool is equivalent to the following Matlab commands, where x is a vector with the interval of sequencing data ::
+
+    N = length(x);
+    f = fft(x);
+    p = abs(f(2:N/2)).^2;
+    p = p / sum(p);
+
 </help>
 </tool>