OK, rewrote it now in a more 'proper' way... I removed the zip file support mentioned in the previous post.
Trees should be uploaded directly as QZA files, and the uploader will automatically parse any tree.nwk file inside.
After the initial upload, the tree will have the original Qiime internal IDs, but I have now added support for direct drag-dropping of QZA files onto the tree. Other iTOL annotation files are processed client side, but QZAs will be uploaded to the server for processing (so that I can implement reading of biom files in the future).
At the moment, only taxonomy files will be processed (FeatureData[Taxonomy]). Leaf labels will be assigned from there, and a bar chart dataset with confidences created.
I'll create a new post in developer section for further discussion.