Update 2-7-2018 5:34 EST
The Main Galaxy server at https://usegalaxy.org has been updated to correct the recent tool issues.
Please re-run any problematic jobs.
If your specific issue still persists, we can follow up on individual problems in your original post - just let us know the issue is still open. If you originally sent in a bug report, send a new one for the new error (rerun test). Please retain all error datasets, test rerun datasets, and all inputs as undeleted in your history.
Thanks, Jen, Galaxy team