On Wed, Jul 10, 2013 at 8:03 PM, Björn Grüning
<bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
> Hi VJ,
> 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.
> Cheers,
> Bjoern

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[1]
>> ...
>> 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[2]
>> ..
>> 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).


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