# HG changeset patch
# User bornea
# Date 1460990969 14400
# Node ID fbc857f87f5256ce30a1cc00c96aaea919a6dc7c
# Parent  609ecf4d57fe9cf76ab503b5a1e154e546fe3f65
Uploaded

diff -r 609ecf4d57fe -r fbc857f87f52 ProHits_DotPlot_Generator.xml
--- a/ProHits_DotPlot_Generator.xml	Thu Apr 14 16:37:38 2016 -0400
+++ b/ProHits_DotPlot_Generator.xml	Mon Apr 18 10:49:29 2016 -0400
@@ -42,21 +42,29 @@
     </test>
   </tests>
   <help>
-**Running ProHits DotPlot**
-
-This runs the biclustering version of the DotPlot tool found at http://prohitstools.mshri.on.ca/. A more interactive version can be found at http://prohits-viz.lunenfeld.ca/. This script will take a long time to run.
+Prohits Dotplot
+--------------
 
-INPUTS:
+This tool runs the biclustering version of the DotPlot tool found
+at http://prohitstools.mshri.on.ca/. A more interactive version
+can be found at http://prohits-viz.lunenfeld.ca/. Depending on
+your Galaxy distribution, this tool may take a few minutes to run.
 
-Saint Output: SAINTexpress generated "list.txt" file.
+**1) SAINT Output File**
+
+SAINTexpress generated *list.txt* file
 
-Primary False Discovery Rate
+**2) False Discovery Rate 1**
 
-Secondary False Discovery Rate
+Primary FDR cutoff in range 0-1 (default 0.01)
+
+**3) False Discovery Rate 2**
 
-Maximum Spectral Count
+Secondary FDR cutoff; must be higher than the primary (default 0.025)
 
-------
+**4) Maximum Spectral Count**
+
+Maximum spectral count to visualize (default 50)
 
 **Please cite**