[galaxy-user] fastq and index file upload problems

I'm trying to create a RNA-Seq Workflow with Bowtie/Tophat and Cufflinks using a newly assembled genome (not public). I created the genome index files via Bowtie locally but Galaxy will not accept the .ebwt index files (n=4)--"Inappropriate content" error. Second, for some reason, the Illumina fastq files will not load on the web version or my local version either. (FYI, I successfully ran these same files through our local command line version of Tophat and Cufflinks without problems) Please advise. Thanks, Shawn