[galaxy-dev] Downsampling of SAM/BAM files

Hello,

I am running a local galaxy server and tried to add the downsampling script for SAM/BAM files from Brad Longhorst which I found on Github. It uses a modified picard_wrapper.py. I get everything running except that the end file shows up empty. I realised when looking at the log file that the Input directory differs from the output directory also instead of adding a .data file it produces a .metrics.txt file.

Does anyone know how to fix this, or does anyone have another script which can be used on Galaxy for downsampling SAM/BAM files?

Thanks a lot,

Alex