You are working at the public Galaxy server in the quoted text below, correct?
They have custom versions of the Lefse tools, so contacting them is the best way to report potential bugs. Or, you can just try a different setting and see what happens. It seems your input choice on the C) Plot LEfSe Results (Galaxy Version 1.0) tool form should be valid as described within the form, but then down in the help section below it is described differently (?). I’m guessing that the second is the correct usage since that seems to match the type of output you are actually getting in the result.
Tool form advanced setting:
Number of label levels to be displayed (-1 means all)
Tool form help section:
Text and label options
- Number of label levels to be displayed: when dealing with hierarchical features this option sets the level to be displayed in the labels (-1 means the last level only, 1 means the highest level, 2 means the first two levels and so on).
Huttenhower Galaxy server info. You can do both – modify the usage yourself for a quicker result but also report the conflict in the instruction to them. Maybe the usage changed at some point and they missed changing the instructions in both places.