7 months ago by
The problem is likely not that the wrapped tools are sourced from CWL, but rather that there is either something problematic with the tool wrapper(s) design for use in Galaxy or the configuration of your Galaxy instance. In one example from a prior case where this was reported, something as small as a difference in how dates were modeled between the tool/tool wrapper and Galaxy triggered a similar problem. In others, configuration and usage of the different available API methods were the root cause of the problem.
Are you running the most current Galaxy release 17_05? If not, please upgrade and see if that resolves the issue as first pass solution.
To test tool wrappers, try Planemo if you are not already using it. Or, if you are not the author, contact the tool author and explain the problem - the wrapper may need an update: https://galaxyproject.org/tools/
For more admin and development help, please see the most recent Admin training materials: https://github.com/galaxyproject/dagobah-training/
If you want to share more details, putting those into an email posted to email@example.com mailing list will reach the wider Galaxy development community for help and feedback when troubleshooting (many are involved with or have knowledge of both CWL and Galaxy). Include details about the Galaxy instance (version, admin modifications), what method was used to convert the CWL tools to Galaxy wrapped tools, plus the output from the database logs from when this error in the GUI comes up.
Thanks, Jen, Galaxy team