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?
Ir. Jeroen Crappé, PhD Student
Lab of Bioinformatics and Computational Genomics (Biobix)
FBW - Ghent University
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