Tophat is hidden as it is outdated. You can rerun old tophat jobs for the reproducibility purposes but for new jobs please use the superior version Tophat2. Given the naming issues in between first and second versions of the same software we decided to name the tool just Tophat in the Galaxy interface.
You can reach it directly on Main by visiting this link: https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9
You can also check Options/Requirements in the tool form menu to check the exact version of SW that is being used.