Hello Scott,

the tool named 'tophat' has been migrated out of distribution to the Tool
Shed over a year ago. Which means that if it is in your Galaxy and your
Galaxy is newer than a year it must have been installed from the Tool Shed.
Tool Shed acts like an app store for Galaxy Tools.
The tophat tool is hosted here:
https://toolshed.g2.bx.psu.edu/view/devteam/tophat
and developed here:
https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat

However the first thing I would check is whether the newer version of the
tool (named tophat2) that we recently updated would suit your needs. You
can try it on our Test instance here:
https://test.galaxyproject.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7

Please let me know if you have any questions and thank you for using Galaxy.

Martin, Galaxy Team

On Wed Feb 11 2015 at 4:36:08 PM Scott Szakonyi <scott.b.szakony...@nd.edu>
wrote:

> Hello all,
>
> I am a new Galaxy admin/developer, so if this is as stupid question please
> be kind.
>
> I am trying to add the ability for a user to choose additional parameters
> for Tophat for Illumina. After analyzing the Python and XML files
> in /galaxy-dist/tools/ngs_rna, I came to the conclusion that modifying
> these files would give me the desired results. However, no changes that I
> make to these files seem to have any effect whatsoever on the user
> experience inside the Galaxy server. I can not find any other likely
> candidates inside galaxy-dist.
>
> Am I looking in the wrong place? Is it even possible to add parameters to
> a tool interface?
>
> Thanks in advance for any help you can offer.
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>  ___________________________________________________________
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