This tool has a few revisions to keep up with changes at NCBI. Using the most current would be strongly recommended. With so many Galaxy servers and so many tools, all under constant revision and with custom settings, you might need to update tools that are included in workflows on specific servers to match what that server hosts.
Now, this tool might be failing anywhere, any container. I’ll double check and work with the GTN to update as needed.
What to do
If you are working at UseGalaxy.org (where I was testing) the most current version is Galaxy Version 0.5.5+galaxy1 for three of the tools included, and the adaptor tool didn’t change and is still at Galaxy Version 0.5.0+galaxy0.
I was able to simply update the tool version in the GTN workflow, save, and run without any complicated changes to the parameters. This works about the same as the tool form directly. Open the workflow in the editor, click on the tool, modify the version(s), double check parameters are OK (new params, defaults), save, and run.
Please give that a try and let us know if you need more help! 