--- a/hicCorrectMatrix.xml	Mon Nov 27 11:13:14 2017 -0500
+++ b/hicCorrectMatrix.xml	Sat Dec 16 16:35:10 2017 -0500
@@ -144,19 +144,72 @@
     </tests>
     <help><![CDATA[
 
-**What it does**
+Matrix correction
+==================
 
-Runs Dekker's iterative correction over a Hi-C matrix.
+| ``hicCorrectMatrix`` runs Dekker's iterative correction over a Hi-C matrix (`Imakaev 2012`_.). For correcting the matrix, 
+| it is important to remove the unassembled scaffolds (e.g. `NT_`), mitochondrial DNA and Y chromosome and keep only 
+| chromosomes, as scaffolds create problems with matrix correction. Therefore 
+| we use the chromosome names (1-19, X, Y) here. 
+| 
+| **Important**: Use ‘chr1 chr2 chr3 etc.’ if your genome index uses chromosome names with the ‘chr’ prefix.
 
-correct:         Run the iterative correction.
+Matrix correction works in two steps: first a histogram containing the sum of contact  per bin (row sum) is produced. This plot needs to be inspected to decide the best threshold for removing bins with lower number of reads. The second steps removes the low scoring bins and does the correction.
 
-diagnostic_plot:  Plots a histogram of the coverage per bin together with the
+Input
+-----
+
+
+Diagnostic plot
+~~~~~~~~~~~~~~~~
+Plots a histogram of the coverage per bin together with the
 modified z-score based on the median absolute deviation
-method (see Boris Iglewicz and David Hoaglin 1993, Volume
-16: How to Detect and Handle Outliers The ASQC Basic
-References in Quality Control: Statistical Techniques,
+method.
+
+See Boris Iglewicz and David Hoaglin 1993, Volume 16: 
+How to Detect and Handle Outliers The ASQC Basic References in Quality Control: Statistical Techniques,
 Edward F. Mykytka, Ph.D., Editor.
 
+Parameters
+__________
+- the contact matrix
+- Max value for the x-axis in counts per bin
+- include chromosomes
+
+
+Correct
+~~~~~~~
+
+Run the iterative correction. 
+
+Parameters
+__________
+- number of iterations
+- inflation cutoff
+- trans region cutoff
+- sequenced count cutoff
+- skip diagonal counts
+- normalize each chromosome separately
+- remove bins of low coverage
+- remove bins of large coverage
+- include chromosomes
+
+Output
+------
+
+    Diagnostic plot:
+
+    .. image:: $PATH_TO_IMAGES/diagnostic_plot.png
+        :width: 70%
+    
+    Correct:
+    - the corrected contact matrix
+
+| For more information about HiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+
+.. _`Imakaev 2012`: http://doi.org/doi:10.1038/nmeth.2148
 ]]></help>
     <expand macro="citations" />
 </tool>