since John patch is applied I created a pull request for that feature:
> thanks to the awesome work from John Chilton in pull request #160  I
> hacked up a first version of a tool customization that can be controlled
> by the user . Requested as trello card #727.
> The user will have a new preference panel (see the attached screenshot)
> and can toggle several customization options. The options can be
> specified by each administrator as filter modules under
> lib/galaxy/tools/filters/. More details in John's original pull request.
> For example, one use case would be to offer different module sets for
> different studies.
> You can specify system-customizations (John's work) with
> tool_filters = module:function, module:function2
> tool_label_filters = ...
> tool_section_filters = ...
> and offer user-customizations with:
> user_tool_filters = examples:restrict_upload_to_admins
> user_tool_section_filters = examples:restrict_text
> user_tool_label_filters = ...
> at the same time.
> Only user-customizations will be shown in the preference panel. The
> description of each filter is parsed from the docstring and shown to the
> The patch requires no modification to the database, all user preferences
> will be stored in user_preference with three special names.
> Is there any plan from the core development team how such a feature
> should be addressed. Is that approach flexible enough? It would be great
> to get some feedback in which direction such a feature should evolve and
> if its worth to put more time on it.
> Thanks John, hope you code will be merged!
> Thanks for your comments,
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