<tool id="WigCorrelate" name="Correlate" version="1.0.0">
  <description>multiple (Big)Wig files</description>
  <command interpreter="sh">
    galaxyToolRunner.sh wigmath.WigCorrelate -w $window -t $type -o $output
      #for $input in $inputs
        ${input.file}
      #end for
  </command>
  <inputs>
      <repeat name="inputs" title="(Big)Wig file">
        <param name="file" type="data" format="bigwig,wig" />
      </repeat>
      <param name="window" type="integer" value="100" label="Window size (bp)" />
      <param name="type" type="select" label="Correlation metric">
      	<option value="pearson">Pearson</option>
      	<option value="spearman">Spearman</option>
      </param>
  </inputs>
  <outputs>
      <data format="tabular" name="output" />
  </outputs>
  
<help>
  
This tool will compute a correlation matrix between the supplied Wig or BigWig files. Each row/column in the matrix is added in the order that files are added above, starting from the top left. The Wig file is downsampled into non-overlapping windows with the specified size by computing the mean value in each window. These windows are then correlated using either  Pearson_'s Product-Moment correlation coefficient or Spearman_'s rank correlation coefficient. If the window size is set to 1, the correlation is calculated between all base pairs in the genome.
  
.. _Pearson: http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient

.. _Spearman: http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient
  
-----

.. class:: warningmark

**WARN:** In order to calculate the correlation coefficient, the data is loaded into entirely into memory. For large genomes, this may require a lot of RAM unless comparably larger window sizes are used.

-----

**Citation**

This tool was inspired by ACT_ from the Gerstein lab.

.. _ACT: http://act.gersteinlab.org

J Jee*, J Rozowsky*, KY Yip*, L Lochovsky, R Bjornson, G Zhong, Z Zhang, Y Fu, J Wang, Z Weng, M Gerstein. ACT: Aggregation and Correlation Toolbox for Analyses of Genome Tracks. (2011) Bioinformatics 27(8): 1152-4.
  
</help>
</tool>