Tophat has been deprecated and the replacement tool is HISAT2. For a current example RNA-seq tool usage/workflow, please start here:
Galaxy Tutorials: https://galaxyproject.org/learn/
- RNA-seq: Discovering and quantifying new transcripts - an in-depth transcriptome analysis example. https://galaxyproject.org/tutorials/nt_rnaseq
The tool is still on the Public Main server at https://usegalaxy.org in the tool panel for now. Use the search at the top of the tool panel to find it. Since the tool is deprecated, it may fail or produced odd results, so if you choose to use it, keep that in mind. Bug reports or questions do not need to be sent in as there will be no further changes or updates. Instead, switch to using HISAT2 going forward.
Thanks! Jen, Galaxy team