--- a/COBRAxy/ras_to_bounds.xml	Sun Oct 13 11:03:02 2024 +0000
+++ b/COBRAxy/ras_to_bounds.xml	Sun Oct 13 11:05:23 2024 +0000
@@ -29,11 +29,7 @@
         --ras_selector $cond_ras.ras_choice
         #if $cond_ras.ras_choice == "True"
         	--input_ras $cond_ras.input_ras
-            #set $names = ""
-            #for $input_temp in $cond_ras.input_ras:
-                #set $names = $names + $input_temp.element_identifier + ","
-            #end for
-            --names $names
+            --classes $cond_ras.classes
         #end if
         --out_log $log
         ]]>
@@ -53,6 +49,7 @@
         	</param>
             <when value="True">
                 <param name="input_ras" argument="--input_ras" multiple="true" type="data" format="tabular, csv, tsv" label="RAS matrix:" />
+                <param name="classes" argument="--classes"  type="text"  value="None" label="Classes:" help="Write here the the classes to assign to each of the uploaded RAS matrices. Example for two RAS matrices:'cellNormal, cellCancer'. If you uploaded just one matrix, leave default value." />
             </when>
         </conditional>  
         
@@ -87,7 +84,8 @@
 
 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. Multiple RAS files 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.
+    - RAS matrix: tab-separated RAS file as returned by RAS generator. It can be a collection of RAS files 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.
+    - Classes: If multiple RAS matrices are uploaded, then the tool returns a simple file containing for each cell the class it belongs to (cells coming from the same RAS matrix are assigned to the same class). This file is useful in the Flux enrichment analysis tool.
     - Medium: tab-separated file containing lower and upper-bounds of medium reactions.
 
 Example of custum growth medium file:
@@ -101,18 +99,13 @@
 | r2         |    0.268765    |    0.765567    |  
 +------------+----------------+----------------+   
 
-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).
-    - The association cell-class is reported in the 'cell_class' file that is useful to perform flux enrichment analysis based on class partenrship.
 
 Output:
 -------------
 
 The tool generates:
     - bounds: reporting the bounds of the model, or cells if RAS is used. Format: tab-separated.
-    - Classes: a file containing the class of each cell (only if multiple RAS matrices were uploaded). The class name of a RAS matrix corresponds to its file name. Format: tab-separated.
+    - Classes: a file containing the class of each cell (only if multiple RAS matrices were uploaded). Format: tab-separated.
     - a log file (.txt).
     ]]>
     </help>