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

[jennaj]

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.