I'm guessing you're trying to use shell magic to read from filename and write to tmpWolfResult. In order to make that happen, you need:
progWolf = subprocess.Popen('runWolfPsortSummary fungi < %s > tmpWolfResult'%filename, shell=True)
I feel obligated to mention that since this input is coming from a commandline argument, it's technically not safe/trusted and a malicious user with access to run this script on your system could do some nasty things.
However, it's probably more likely that you're distributing this script (or just using it yourself) and you and your users probably aren't interested in messing up your own system...