After a quick play, it sounds like this would be a starting point. Feeds all *.crypt files in the current directory through a command called "somedecrypter" specifying the output file name by stripping the .crypt extension off the source file and plugging .out on the end.
I am not a Python programmer, but I can Google and hack something up
Tested on Linux.
Code:
#!/usr/bin/python
import glob, os
for fileName in glob.glob( '*.crypt' ):
fileBase = os.path.splitext( fileName )[0]
os.system( "somedecrypter --in " + fileName + " --out " + fileBase + ".out" )