--- a/hicCorrelate.xml	Mon Nov 27 11:14:26 2017 -0500
+++ b/hicCorrelate.xml	Sat Dec 16 16:34:28 2017 -0500
@@ -100,11 +100,55 @@
     </tests>
     <help><![CDATA[
 
-**What it does**
+Matrix correlation
+==================
 
-Computes pairwise correlations between Hi-C matrices data.
+Computes pairwise correlations between Hi-C contact matrices.
 The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices.
 
+Input
+-----
+
+Parameters
+__________
+- Two contact matrices which are used for the correlation.
+- Choice if pearson or spearman correlation should be used.
+- log scale for the values
+- Correlate full matrix or only specific chromosomes
+- Correlate only within a given range.
+- colormap to use:  Colormap_ 
+
+Output
+------
+
+Pearson correlation
+___________________
+
+|pearson|  |pearson_scatter| 
+
+.. |pearson| image:: $PATH_TO_IMAGES/hicCorrelate_pearson.png
+   :width: 45%
+
+.. |pearson_scatter| image:: $PATH_TO_IMAGES/hicCorrelate_pearson_scatter.png
+ :width: 45%
+
+Scatter plot
+
+Spearman correlation
+_____________________
+
+|spearman| |spearman_scatter|
+
+.. |spearman| image:: $PATH_TO_IMAGES/hicCorrelate_spearman.png
+   :width: 45 %
+
+.. |spearman_scatter| image:: $PATH_TO_IMAGES/hicCorrelate_spearman_scatter.png
+   :width: 45 %
+
+For more information about HiCExplorer please consider our documentation on readthedocs.io_.
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+.. _Colormap: https://matplotlib.org/examples/color/colormaps_reference.html
 
 ]]></help>
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