Creating tool which requires specific input file extension

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I think you can do something with a symlink. See here for an example: Wrapping a script which implicitly expects a local file - #6 by astrov

If it is a python script you could do something like (no working code just an idea):

    if os.path.splitext(galaxyinputfile)[1] == ".dat":
        cwd = os.getcwd()
        jpginputFile=cwd+os.path.splitext(os.path.basename(galaxyinputfile))[0]+".jpg"
        shutil.copy(galaxyinputfile, jpginputFile)

There may be better ways but this could give some inspiration already

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