I found your history. The input Tophat BAM datasets require that the metadata be reset before downstream tools can execute. Do this by clicking on the "reset metadata" link in the yellow alert box inside the expanded dataset or by clicking on the dataset's pencil icon to "detect metadata" using the Edit Attributes forms.
We realize this is inconvenient when running workflows and are now recommending that HISAT be used going forward instead of Tophat. Tophat is outdated software and will be soon deprecated at http://usegalaxy.org. That will very likely occur this week or early next.
Thanks and our apologies for the current problems with this tool.
Jen, Galaxy team