diff --git a/test/functional/tools/interactive_tool_askomics.xml b/test/functional/tools/interactive_tool_askomics.xml
index de9827b3eb5..71c3fe9a437 100644
--- a/test/functional/tools/interactive_tool_askomics.xml
+++ b/test/functional/tools/interactive_tool_askomics.xml
@@ -10,7 +10,7 @@
         </entry_point>
     </entry_points>
     <environment_variables>
-        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable>
+        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
         <environment_variable name="API_KEY" strip="True">
             #if $__user__:
                 #for $api_key in $__user__.api_keys:
diff --git a/test/functional/tools/interactive_tool_jupyter_notebook.xml b/test/functional/tools/interactive_tool_jupyter_notebook.xml
index 336a9a00b5a..27313f65527 100644
--- a/test/functional/tools/interactive_tool_jupyter_notebook.xml
+++ b/test/functional/tools/interactive_tool_jupyter_notebook.xml
@@ -9,10 +9,10 @@
         </entry_point>
     </entry_points>
     <environment_variables>
-        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($jupyter_notebook.history_id)}</environment_variable>
-        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable>
+        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($jupyter_notebook.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
         <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
-        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable>
+        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
         <environment_variable name="API_KEY" strip="True">
             #if $__user__:
                 #for $api_key in $__user__.api_keys: