There is a metaphlan2 plugin for QIIME 2 that @antonioggsousa could try out — that is not a core QIIME 2 plugin currently so I am not aware of the status of that plugin.
@antonioggsousa please let us know if this is shotgun data. It would still be possible to process using external software and then import a biom table into QIIME 2 for downstream analysis.