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,

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