On Wed, Jul 10, 2013 at 8:03 PM, Björn Grüning
you only can have one <command> tag in a tool, afaik. You can try to
write it with cheetah and concatenate several shell commands with && or
you can extend your python script to call your java tool at first step.
Also this part will break - Galaxy is telling you the filename,
if you add .txt to it then it no longer points to a file on disk:
> input_file = sys.argv
> txt_in = input_file + '.txt'
Likewise Galaxy has told you which output filename to use,
if you add .pdf to it Galaxy won't find it:
> output_file = sys.argv
> pdf_out = output_file + '.pdf'
The tool should just use the filenames Galaxy tells it
(and they will end in .dat regardless of the datatype).