Automated Generation of Galaxy tools

We will create a generalizable set of libraries and best practice guidelines for the programmatic creation of Galaxy tools.

We will leverage our experience in creating one-off scripts that automatically generate collections of Galaxy tools to create these libraries.

In our experience, Galaxy tool creation is most complete and production-ready when the tool generator is language aware.

For example, our prototype for creation of the anvi’o Galaxy tool suite (over 150 individual tools) makes use of Python specific introspection and language paradigms to create a set of polished interoperable tool wrappers.

A similar language-specific approach is leveraged within our R2G2 prototype to programmatically create R-based Galaxy tools from any available R package (including Bioconductor).

Using our previous experience, we will build language-specific tool generator libraries for the most popular programming languages for biomedical research.

We will also build more generalized non- language specific utilities for generating Galaxy tools from popular styles of help outputs, as is currently done in the case for prototypes of PLINK Galaxy tool wrappers.

We will finalize these prototype tool generators, and move these extensive and popular tool suites into production-ready states. These utilities will enable effective Galaxy tool interfaces that are easy to maintain across versions.