Yes, there is:
http://oracc.museum.upenn.edu/doc/tools/cuneify/
Steve Tinney at UPENN has written a tool called “Cuneify” as part of the ATF* format for encoding cuneiform texts, itself in turn part of the ORACC project:
Oracc is a collaborative effort to develop a complete corpus of cuneiform whose rich annotation and open licensing support the next generation of scholarly research. Created by Steve Tinney, Oracc is steered by Jamie Novotny, Eleanor Robson, Tinney, and Niek Veldhuis.
Cuneify may be used via a web CGI interface, such as the one available here:
http://oracc.museum.upenn.edu/doc/help/visitingoracc/reusingoracc/index.html#h_cuneify
If one enters the transliteration in that search box (taking care to note the all-ASCII orthography used in ATF: j for ĝ, etc), then a link like this one will be generated:
http://oracc.museum.upenn.edu/cgi-bin/cuneify?input=ki.en.jir&button=Cuneify&project=doc2%2Fvisitor
Following that link will return this:
ki.en.jir
𒆠 𒂗 𒄫
Unfortunately it appears that the source code to Cuneify itself is not open source; it’s only accessible via this web interface.
* Despite the voluminous (and good) documentation for Tinney and company’s various and sundry projects, I have not found the expansion for the acronym “ATF”! Presumably “Assyriological Text Format” or something…