The excel template you get from Krona tools is about categories of granola. The instructions they give for using it for your own stuff were not clear to me. Therefore I have turned to Galaxy. All I want is a Krona graph of the taxonomy of my 16S microbial results. I already have all the Mothur analyses done. I do not want to redo them in Galaxy. I just want to give Galaxy my shared file and my taxonomy file that Mothur generates and get a Krona graph out of it. I imported those two files into Galaxy. The Krona tool asks if what I have is a taxonomy or MetaPhlAn (???) file. I chose taxonomy. There are two buttons after that. One is for dataset collections and one is for multiple datasets. Clicking on either one just gives a "no taxonomy dataset available" message. How do I get my Mothur output into Galaxy? How do I generate a Krona graph?????
The Galaxy wrapped version of Krona accepts a Galaxy Taxonomy (Mothur, Kraken) or a MetaPhlAn input. If you can reproduce the input format (either) and label it correctly, the tool should work.
In your case, if I understand it correctly, some Mothur steps may need to be re-run within Galaxy. Review the help on the tool form, link-outs to tool manual, and the tutorial linked below.
Galaxy Metagenomics tutorial: https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html
Thanks and hope this helps! Jen, Galaxy team