Minor 1. Currently to select a Bowtie index as input for TopHat a user should browse for the index directory and manually input the index name. It can be improved by allowing a user to select one of the index files and determining the directory path and the index basename from it.
2. The Bowtie version can also be determined from the input file.
3. It may occur that the parameters would still be configured incorrectly. Validation of the Bowtie version parameter should be added to the scheme validation step.
Make sure to implement/test the features in all Tuxedo wizards.
