Solved problem, I had not read this tutorial that explains how to edit the layout.
https://wiki.galaxyproject.org/GalaxyToolPanel#XML_configuration_files_used_to_populate_your_Galaxy_tool_panel


2014/1/12 Cristian Alejandro Rojas <alejandro.0317@gmail.com>
Hello All,

I'm trying to personalize my own galaxy instance, I'd like to know if editing the file shed_tool_conf.xml will make inestable my galaxy instance, I'd like to move tools from one to another section but I don't know if this will affect future updates of the tools.


Best,
--
Cristian Alejandro Rojas Quintero
Estudiante Ingeniería de Sistemas 
Universidad Distrital Francisco José de Caldas
Bogotá - Colombia




--
Cristian Alejandro Rojas Quintero
Estudiante Ingeniería de Sistemas 
Universidad Distrital Francisco José de Caldas
Bogotá - Colombia