Modify Bowtie2 DM so that it will not create duplicates when "Include Tophat2" is used

Reference: https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bowtie2_index_builder

If a Bowtie2 index already exists, and a Tophat2 index is needed, the only DM available is the one above.

**Issue** If Bowtie2 indexes already exists, a duplicate index is created.

**Suggested Solutions** Create a Tophat2 stand-alone DM - or better - modify the existing Bowtie DM to not create a duplicate Bowtie2 index if it already exists (whether it was created by a DM or by other means). Maybe add a small note to the DM to state that only Tophat2 indexes will be created (aka linked in) if Bowtie2 already exist. Would make usage less confusing by community.

Start with the referenced data_managers/data_manager_bowtie2_index_builder directory and trace how the Bowtie2 and Tophat2 indexes are handled when Bowtie2 already exists. Confirm the expected behavior for both DM-created and pre-existing Bowtie2 indexes, then verify that using “Include Tophat2” does not create a duplicate Bowtie2 index while still providing the Tophat2 index.

Written by the indexing model from the issue text.