We are working on a galaxy tool suite for data analysis.

We use a sqlite db to keep result data centralised between the different tools. 

At one point the tool configuration options of a tool should be dependent on the rows within a table of the sqlite db that is the output of the previous step. In other words, we would like to be able to set selectable parameters based on an underlying sql statement. If sql is not possible, an alternative would be to output the table content into a txt file and subsequently parse the txt file instead of the sqlite_db within the xml configuration file. 

When looking through the galaxy wiki and mailing lists I came across the <code> tag which would be ideal, we could run a python script in the background to fetch date from the sqlite table, however that function is deprecated. 

Does anybody know of other ways to achieve this?  

Thanks!

Jeroen