Glad to learn you have made some progress! I moved this over into a new topic so we can focus on the new tool error.
If you want to share your history with the work, we can try to help resolve the error. How to generate a history share link is explained here → FAQ: Sharing your History or you can capture screenshots and post those instead as explained in here → How to get faster help with your question. If you post screenshots – please try to capture all the details – the server URL, the full tool name/version, a peek at the input file, the parameters used, and the full log messages expanded. That’s a lot of information and why we suggest to share the history since it includes everything all together. 
If you want to troubleshoot it yourself first, we have some prior Q&A about one common issue: choosing the wrong Krona tool! See here for the details → Error with Visualize with Krona tool? Use Krona Pie Chart instead! with more at Search results for 'krona' - Galaxy Community Help
Let’s start there and please let us know if you resolve this! 