--- a/COBRAxy/ras_to_bounds.xml	Sat Oct 12 19:57:09 2024 +0000
+++ b/COBRAxy/ras_to_bounds.xml	Sat Oct 12 19:57:19 2024 +0000
@@ -17,6 +17,8 @@
       	python $__tool_directory__/ras_to_bounds.py
         --tool_dir $__tool_directory__
         --model_selector $cond_model.model_selector
+        --cell_class $cell_class
+        --classes $classes
         #if $cond_model.model_selector == 'Custom'
             --model $model
             --model_name $model.element_identifier
@@ -46,7 +48,8 @@
                 	<option value="False">No</option>
         	</param>
             <when value="True">
-                <param name="input_ras" argument="--input_ras" multiple="false" type="data" format="tabular, csv, tsv" label="RAS matrix:" />
+                <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"  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, ignore this." />
             </when>
         </conditional>  
         
@@ -61,7 +64,7 @@
 
     <outputs>
         <data format="txt" name="log" label="RAStoBounds- Log" />
-        
+        <data format="tabular" name="cell_class" label="RAStoBounds - Cells class" />
         <collection name="ras_to_bounds" type="list" label="Ras to Bounds">
             <discover_datasets name = "collection" pattern="__name_and_ext__" directory="ras_to_bounds"/>
         </collection>
@@ -81,7 +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.
+    - 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:
@@ -101,6 +105,7 @@
 
 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). Format: tab-separated.
     - a log file (.txt).
     ]]>
     </help>