Hi all - I've got a bunch of fatsq files uploaded into a data library in Galaxy. The underlying files is gzipped however Galaxy strips the .gz from the filename and displays it as .fastq. When the python wrapper rgFastQC.py gets called, it correctly sees the fastq.gz file. The wrapper creates a symbolic link to the .gz file in a tmp directory. The link is .fastq. When FastQC tries to read this file, it fails because its compressed. So one of two things is going wrong here:
1) It looks like the wrapper is incorrectly renaming the file, but its using the name given to it in Galaxy.
2) When the file is uploaded into the data library, Galaxy is stripping off the .gz extension.
I think #2 is the more correct problem. How can I keep Galaxy from stripping the .gz extension?