The bug manifests itself when running the tool with "use Defaults" selected results in the following error: cp: cannot stat `/data/galaxy-dev/galaxy-dev/database/job_working_directory/000/281/tophat_out/fusions.out': No such file or directory
It seems that somehow, the filter on the output dataset is not working properly when the value (params['fusion_search']['do_search']) is not explicitly set in the parameters.
Fixed in -central changeset 05a172868303
The second issue is more minor. It seems that the Tophat2 wrapper assumes that Tophat2 will use Bowtie2 (and not Bowtie). However, the actual Tophat2 program will only use Bowtie2 if it is found in the path. Otherwise it defaults to using bowtie which results in an error (Could not find Bowtie index files) since the wrapper points the tool to the bowtie2 index instead. To make things a bit more robust, I suggest adding bowtie2 as a requirement to the tophat2 wrapper. It also might be a good idea to add versions to those requirements. I've attached a small patch to do that (though it's fairly trivial).
I added the requirements tags for additional packages required by Tophat2; I've left out the version information for now because it's fairly brittle. FYI, due to limitations with Galaxy's location/index files, the Tophat2 wrapper will run with either Bowtie or Bowtie2 but not both.
Best, J.