When the tool form option "Is this library mate-paired?: Paired-end" is select, the form resets to permit the selection of two .fastqsanger datasets "RNA-Seq FASTQ file, forward reads:" and "RNA-Seq FASTQ file, reverse reads:"
These three options are the first listed on the tool form. Please double check the FASTQ input datasets and adjust the datatype/quality scaling as needed. Help is here:
Hopefully you have discovered this, but if not, this helps! Jen, Galaxy team