<tool id="Autocovariance" name="Compute the autocovariance" version="2.0.0">
  <description>of data in a Wiggle file</description>
  <command interpreter="sh">galaxyToolRunner.sh ngs.Autocorrelation -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="200" label="Maximum shift" />
  </inputs>
  <outputs>
      <data format="tabular" name="output" />
  </outputs>
  
<help>
  
This tool computes the unnormalized autocovariance_ of intervals of data in a Wig file.

.. _autocovariance: http://en.wikipedia.org/wiki/Autocorrelation

-----

**Syntax**

- **Input data** is the genomic data on which to compute the autocorrelation.
- **List of intervals:** The autocorrelation will be computed for each genomic interval specified in this list.
- **Maximum shift:** In computing the autocorrelation, the data will be phase-shifted up to this limit.

-----

.. class:: infomark

**TIP:** For more information, see Wikipedia_ (right click to open this link in another window).

.. _Wikipedia: http://en.wikipedia.org/wiki/Autocorrelation

.. class:: infomark

**TIP:** If your input data 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. Similarly, the intervals must be in either Bed, BedGraph, or GFF format.

</help>
</tool>