changeset 352:9f5db0e377a6 draft

Uploaded
author luca_milaz
date Thu, 29 Aug 2024 20:24:59 +0000
parents 979337507901
children 978a883ab2f4
files marea_2/ras_to_bounds.xml
diffstat 1 files changed, 8 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/marea_2/ras_to_bounds.xml	Thu Aug 29 20:15:41 2024 +0000
+++ b/marea_2/ras_to_bounds.xml	Thu Aug 29 20:24:59 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="RAStoBounds" name="RAStoBounds" version="2.0.0">
+<tool id="RAStoBounds" name="RAS2Bounds" version="2.0.0">
     
     <macros>
         <import>marea_macros.xml</import>
@@ -74,21 +74,18 @@
 
 What it does
 -------------
-
-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.
+This tool generates reaction bounds for a given metabolic model (in JSON or XML format), both with and without the integration of Reaction Activity Scores (RAS) into the metabolic model. 
+Additionally, it allows the use of custom or pre-defined growth media to constrain exchange reactions (see format example here below).
+If a RAS matrix, generated by the **Expression2RAS** tool, is used, then a separate bounds file 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.
+**Accepted Files:**
+   - **Model:** A JSON or XML file containing the reactions and rules defined in the model.
+   - **RAS Matrix:** A tab-separated file with RAS data as generated by the **Expression2RAS** tool.
+   - **Medium:** A tab-separated file specifying the lower and upper bounds of medium reactions.
 
 Example medium file
 -------------
 
-Custom medium:
-
 +------------+----------------+----------------+
 | Reaction ID|   lower_bound   |   upper_bound |  
 +============+================+================+