Inconsistency in -u argument

[bernt-matthias]

When creating the Galaxy wrappers for kaiju I noticed that the parameter -u seems to be inconsistent between kaiju2table and kaiju2krona:

• -u Unclassified reads are not counted for the total reads when calculating percentages for classified reads.
• -u Include count for unclassified reads in output.

Is it just the docs or are they relly working opposite?

[pmenzel]

Yeah, it looks like they are a bit opposite to each other 😬 But the docs are correct.