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/dev... 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.Szakonyi.1@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
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