It depends on what you mean by automatic. You could
create a Galaxy Workflow where a tool is run which
generates the bedgraph file, and then as the next
step it is converted to bigwig.

For this specific task, it might be possible to exploit
the Galaxy datatype definition for bedgraph to allow
automatic conversion to bigwig - is this working for you?

https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml

Peter

On Tue, Feb 28, 2017 at 4:47 PM, evan clark <eclar...@fau.edu> wrote:
> Is there a method to setup a command to run depending on the filetype of a
> job. Essentially I want to setup a task where everytime a bedgraph file is
> generated it will either automatically start a new job and convert it to
> bigwig or, within the same job file it will convert the bedgraph to bigwig.
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