MiRDeep2 identification of novel and known miRNAs

I’m not sure, but it certainly couldn’t hurt to remove the description line content from all fasta inputs. With any tool/workflow when working in Galaxy, and usually line command as well.

The error you are getting is from the underlying 3rd party tool, not some error trapping/format checks from the Galaxy wrapper around it. Meaning, you would hit these same format issues no matter where/how you use this tool.