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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