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.

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