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Adding a ballgown wrapper (test not working) #1366
@bgruening Can you add this wrapper to the Tool shed of Galaxy? If it needs any further enhancements, I'm open to it.
@CollardT at the moment we can not merge this as the test are failing. See here for more details: https://travis-ci.org/galaxyproject/tools-iuc/jobs/261304875
Using external python/r/... scripts is not a problem and you don't need to use the Galaxy API here. Have a look at this example for a simple r script: https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq
Essentially, just write a python script that you can call from your command section if this is really needed.