--- a/macros.xml	Wed Dec 20 18:03:04 2023 +0000
+++ b/macros.xml	Wed Jan 14 09:30:42 2026 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.20.0</token>
-    <token name="@SUFFIX_VERSION@">5</token>
+    <token name="@SUFFIX_VERSION@">6</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-isoformswitchanalyzer</requirement>
@@ -84,5 +84,23 @@
             </param>
             <param name="trans_counts" type="data" format="@FORMAT@" multiple="true" label="Transcript-level expression measurements"/> 
         </section>
+
+        <repeat name="cofactor" title="Confounding factor" min="0">
+            <param name="cofactor_name" type="text" value="CoFactorName" optional="false" label="Confounding factor name"
+                help="For example batch effect, age, sex etc. Only letters, numbers and underscores will be retained in this field">
+                <sanitizer>
+                    <valid initial="string.letters,string.digits"><add value="_" /></valid>
+                </sanitizer>
+            </param>
+            <repeat name="cofactor_level" title="Enter cofactor level" min="2">
+                <param name="cofactor_level_name" type="text" value="CoFactorLevel" optional="false" label="Confounding factor level name"
+                    help="For example, name of a batch or male/female in case of sex. Only letters, numbers and underscores will be retained in this field">
+                    <sanitizer>
+                        <valid initial="string.letters,string.digits"><add value="_" /></valid>
+                    </sanitizer>
+                </param>
+                <param name="cofactor_level_files" type="data" format="@FORMAT@" multiple="true" label="Select transcript-level measurement files associated with this cofactor level"/> 
+            </repeat>
+        </repeat>
     </xml>
 </macros>