2.8 years ago by
This is a GATK error - I would search their forum for the specific solution, then implement that on the Galaxy tool form.
Sometimes errors are specific (it could be that the wrapper does not cover this particular parameter). Other times the errors are secondary to the root problem (missing or malformed inputs or usage/tool form setting's conflicts). Format and usage are the most common reasons for GATK tool errors (and most other tool errors).
If you do find that this is a persistent bug and that the wrapper seems problematic - after reviewing the help at GATK - please submit the error dataset as a bug report.
Note that bug reports can only be sent in from the public Main Galaxy server. If you are not working there, see if the issue can be duplicated and submit if the problem is persistent.
This will also help to diagnose if the problem is with the tool wrapper itself or potentially another server's configuration for this installed tool. There are a few versions of GATK tools - if working on another server: you can compare what is on Main, those in the Tool Shed, and what is on the other server, which can also help to isolate where issues may be (if they are not due to usage/formatting).
Best, Jen, Galaxy team