Yes. Those types of clips. It works fine with the Tek and old HP clips that I have, except the flat hp logic analyzer clips which uses a crappy pin that are formed by folding.
If you haven't gone so far down the development, I would have suggested reprogramming/re-purposing those $4-$6 "USBasp" cables from China to use as USB to SPI dongles. USBasp is open source programmer for AVR chips, so the Chinese copies would have same design. It uses V-USB, a bit-banging software USB stack. The 10 pin connector has power, AtMega8 SPI port and 1 GPIO line which is pretty much what you need to program SPI Flash. »www.fischl.de/usbasp/