# HG changeset patch
# User luca_milaz
# Date 1724659937 0
# Node ID 3f1cfd63fb8124874e41cc00202af42ff397d020
# Parent  a00dba74f39bfa22a07e1b0769c147d2680c5284
Uploaded

diff -r a00dba74f39b -r 3f1cfd63fb81 marea_2/ras_to_bounds.xml
--- a/marea_2/ras_to_bounds.xml	Mon Aug 26 08:10:57 2024 +0000
+++ b/marea_2/ras_to_bounds.xml	Mon Aug 26 08:12:17 2024 +0000
@@ -75,18 +75,34 @@
 What it does
 -------------
 
-This tool generates two files containing reactions and rules respectively, starting from a custom model in JSON or XML format, that can be used as inputs for the RAS and RPS generator modules.
+This tool generates the reactions bounds for a given metabolic model (JSON or XML format) with and without the injection of the Reaction Activity Scores (RAS) within the metabolic model.
+Moreover, it enables to use custom/pre-defined growth mediums to constrain exchange reactions. For custom medium, It is suggested to use the template file returned by the Custom Data Generator tool.
+If the RAS matrix, generated by the RAS generator tool, is used, then a file of bounds is generated for each cell. Otherwise, a single bounds file is returned.
 
 Accepted files:
     - A model: JSON or XML file reporting reactions and rules contained in the model.   
+    - RAS matrix: tab-separated RAS file as returned by RAS generator.
+    - Medium: tab-separated file containing lower and upper-bounds of medium reactions.
+
+Example medium file
+-------------
+
+Custom medium:
+
++------------+----------------+----------------+
+| Reaction ID|   lower_bound   |   upper_bound |  
++============+================+================+
+| r1         |    0.123167    |    0.371355    | 
++------------+----------------+----------------+   
+| r2         |    0.268765    |    0.765567    |  
++------------+----------------+----------------+   
 
 
 Output:
 -------------
 
 The tool generates:
-    - rules: reporting the rules for each reaction in the custom model given. Format: csv or pickle.
-    - reactions: reporting the reactions in the custom model given. Format: csv or pickle.
+    - bounds: reporting the bounds of the model, or cells if RAS is used. Format: tab-separated.
     - a log file (.txt).
     ]]>
     </help>