# HG changeset patch
# User ynewton
# Date 1350714534 14400
# Node ID 0c4dcd3980c1cd3d671c90cf4e7edb11bf00de32
# Parent  600872152be64467c7b45add1a087528372980e2
Uploaded

diff -r 600872152be6 -r 0c4dcd3980c1 normalize.xml
--- a/normalize.xml	Sat Oct 20 02:28:37 2012 -0400
+++ b/normalize.xml	Sat Oct 20 02:28:54 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="matrix_normalize" name="Matrix Normalize" version="1.0.0">
+<tool id="matrix_normalize" name="Matrix Normalize" version="2.0.0">
   <description>Matrix Normalize</description>
   <command interpreter="Rscript">normalize.r $genomicMatrix $normType $normBy 
 #if str($controlColumnLabelsList) != "None":
@@ -50,7 +50,7 @@
 6. Weibull normalizations: same as exponential normalization, but inverse quantile function of Weibull distribution is applied with appropriate scale and shape parameters.
 
 
-Normals parameter is an optional parameter which contains a list of column headers from the input matrix which should be considered as normals
+Normals/controls parameter is an optional parameter which contains either a list of column headers from the input matrix which should be considered as normals/controls, or a matrix of normal/control samples. The program is smart enough to distinguish between the two cases and will automatically process the normals/controls in a correct way. When specifying both the main expression matrix and the normals/controls matrix while performing column-wise normalization, the program will actually concatenate the two matrices and produce a combined matrix which contains both tumor and normal/control samples, in which samples are normalized.
 
   </help>   
 </tool>
\ No newline at end of file