In addition to general parameters docs, I think it would be useful for the documentation to describe what files are needed for each tool, and what each ile should look like.
e.g. the nucl2tax is NCBI genbank/refseq (etc) and the corersponding NCBI taxonomy id
The names.dmp is the various names of the possible species and then the taxid etc. etc.
Description of feature
In addition to general parameters docs, I think it would be useful for the documentation to describe what files are needed for each tool, and what each ile should look like.