Hi @Stephanieorch,
Thank you for updating your original question and adding your commands; now I have a better idea of what the confusion is.
Basically, to generate a tree you need to use the sequences, not the biom table, which your second command is doing. To get the sequences from your biom, you need to follow the command here: Importing deblur data from QIITA - #3 by antgonza, once you have your sequences you can import them as a new artifact type FeatureData[Sequence], which will be the input of your second command.
Hope this helps.