--- a/COBRAxy/flux_to_map.xml	Wed Sep 18 12:45:28 2024 +0000
+++ b/COBRAxy/flux_to_map.xml	Wed Sep 18 12:49:47 2024 +0000
@@ -154,7 +154,7 @@
     - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
 
 The tool generates:
-    - 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
+    - 1) a tab-separated file: reporting fold-change and p-values of fluxes between a pair of conditions/classes;
     - 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
     - 3) a log file (.txt).
     
@@ -170,9 +170,9 @@
 Example input
 -------------
 
-"RAS of group 1 + RAS of group 2 + ... + RAS of group N" option:
+"Fluxes of group 1 + Fluxes of group 2 + ... + Fluxes of group N" option:
 
-RAS Dataset 1:
+Fluxes Dataset 1:
 
 +------------+----------------+----------------+----------------+ 
 | Reaction ID|   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |  
@@ -188,7 +188,7 @@
 | r1646      |    0.876543    |    0.786543    |    0.897654    |   
 +------------+----------------+----------------+----------------+
 
-RAS Dataset 2:
+Fluxes Dataset 2:
 
 +------------+----------------+----------------+----------------+ 
 | Reaction ID|   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |  
@@ -204,9 +204,9 @@
 | r1646      |    0.876543    |    0.786543    |    0.897654    |   
 +------------+----------------+----------------+----------------+
 
-"RAS of all samples + sample group specification" option:
+"Fluxes of all samples + sample group specification" option:
 
-RAS Dataset:
+Fluxes Dataset:
 
 +------------+----------------+----------------+----------------+ 
 | Reaction ID|   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |  
@@ -239,7 +239,6 @@
 
 .. class:: infomark
 
-**TIP**: This tool using the RAS scores computed by `Ras tool`_.
 
 ]]>
 	</help>