<tool id="WaveletTransform" name="Wavelet analysis" version="1.0.0">
  <description>across a genomic interval</description>
  <command interpreter="bash">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>