Welcome @tavovato
This behavior seems unexpected, but I confirmed that it reflects the tool’s current functionality rather than a technical issue with the integration on UseGalaxy.eu.
I opened a ticket requesting that more of the raw and intermediate data files be published as outputs. My request was intentionally broad, so please feel free to clarify which files would be most useful.
From what I can tell, the intermediate files are generated during the run but discarded when the job completes. To retain them in the Galaxy history, the tool wrapper would need to define those files in the output section of the tool XML.
This tool wrapper has not been updated in about ten years and is currently available only on UseGalaxy.eu, but let’s see what the developers think. There may be implementation details that make this more difficult than it initially appears.
Did I understand what you wanted correctly? Let me know! 
Related topic → MrBayes consensus tree file not shown in output - #2 by jennaj