# HG changeset patch
# User luca_milaz
# Date 1728817382 0
# Node ID 226bee4715034f66926d382c22cfad5c172686c8
# Parent  a30013ece7103b026693f66d997c62e54f7b1624
Uploaded

diff -r a30013ece710 -r 226bee471503 COBRAxy/ras_to_bounds.xml
--- a/COBRAxy/ras_to_bounds.xml	Sun Oct 13 10:57:49 2024 +0000
+++ b/COBRAxy/ras_to_bounds.xml	Sun Oct 13 11:03:02 2024 +0000
@@ -29,6 +29,11 @@
         --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
         #end if
         --out_log $log
         ]]>
@@ -85,7 +90,7 @@
     - 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.
     - Medium: tab-separated file containing lower and upper-bounds of medium reactions.
 
-Example of custum growth medium fileeeee:
+Example of custum growth medium file:
 
 
 +------------+----------------+----------------+
@@ -98,7 +103,8 @@
 
 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).
++
+−    - 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: