# HG changeset patch
# User luca_milaz
# Date 1758551543 0
# Node ID 20dce065ed668c7b009f74b1a738c297c3b57f2b
# Parent  388b2bb55bf444679d61e0860bd3d870e25df4c5
Uploaded

diff -r 388b2bb55bf4 -r 20dce065ed66 COBRAxy/ras_to_bounds_beta.xml
--- a/COBRAxy/ras_to_bounds_beta.xml	Mon Sep 22 14:32:01 2025 +0000
+++ b/COBRAxy/ras_to_bounds_beta.xml	Mon Sep 22 14:32:23 2025 +0000
@@ -32,8 +32,8 @@
     </command>
     <inputs>
 
-        <param name="model_upload" argument="--model_upload" type="data" format="csv,tsv,tabular" 
-                label="Model rules file:" help="Upload a CSV/TSV file containing reaction rules generated by the Model Initialization tool." />
+        <param name="model_upload" argument="--model_upload" type="data" format="csv,tsv,tabular" multiple="false"
+                label="Model tabular file:" help="Upload a CSV/TSV file containing information generated by the Model Initialization tool." />
 
         <param name="input_ras" argument="--input_ras" multiple="true" type="data" format="tabular, csv, tsv" label="RAS matrix:" />
 
@@ -71,16 +71,7 @@
     - A tabular model: tab-separated file containing information about a metabolic model.
     - RAS matrix: tab-separated RAS file as returned by RAS generator. Multiple RAS files having different file name can be uploaded too (e.g. one RAS matrix for normal cells and one for cancer cells). Note that if multiple RAs matrices are uploaded, the bounds are normalzed across all cells.
 
-Example of tabular model:
-+-------------+----------+------+-------------+-------------+-------------------+-------------------+-----------+-----------+
-| Reaction ID | Formula  | GPR  | lower_bound | upper_bound | ObjectiveCoefficient | Pathways (one or more) | InMedium  |
-+=============+==========+======+=============+=============+===================+===================+===========+===========+
-| r1          |    a+b-->c   GeneA or GeneB   |      |   0.123167  |   0.371355  |    0               |     Glycolysis              |       True    |
-+-------------+----------+------+-------------+-------------+-------------------+-------------------+-----------+-----------+
-| r2          |    d+e-->f   GeneC   |      |   0.268765  |   0.765567  |            1       |        Glycolysis           |     False      |
-+-------------+----------+------+-------------+-------------+-------------------+-------------------+-----------+-----------+
- 
-		
+	
 Example for multiple RAS matrices:
     - cancer.csv and normal.csv generated by RAS generator tool (the two class names are 'cancer' and 'normal').
     - This tool returns one unique collection of bounds files for both cancer and normal cells (normalization is performed across all cells).
@@ -98,3 +89,5 @@
     <expand macro="citations" />
 
 </tool>
+
+