I do not believe that is possible (nor desirable in general,
not everyone will need or want the converted file and the
overhead that comes with creating and storing it).
What do you want to do with the bigwig file, and is the
automatic conversion working for you? i.e. If you have
tool X in Galaxy
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
auto
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 bigw
