Ivan,

> #if $__user_email__ == ""
>        <display>You are not authorized to use this tool</display>
> #else
> 
> <command interpreter="python">
>        data_source.py $output $__app__.config.output_size_limit
> </command>

To make this approach work, the email check should go in the command tag.

More information:

If you're looking to require users to login before using any tools, you can use 
this flag in the universe config file:

# Force everyone to log in (disable anonymous access).
#require_login = False

If you're looking to implement tool-based access control, the best approach is 
probably to use the same role-based approach that libraries use:

https://bitbucket.org/galaxy/galaxy-central/issue/269/use-galaxy-security-to-restrict-tool

Thanks,
J.

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