How to deal with an author who worked on an analysis that never made it into the paper? I have come across the following situation a couple of times:

After an experiment has been designed and data collected, the first author of the paper wants to ascertain whether a special analysis would work. So he asks a colleague to help/do this special analysis, which requires significant thinking and effort. Alas, the results are either inconclusive or don't add anything useful to the conclusions of the paper, so they never make it into the manuscript. 

Should the colleague who worked hard on the specia analysis but produced no visible output be included as an author? I would think so, but I wonder how others would deal with this situation.
I had a situation like this come up once, where one person did an extensive analysis that turned out not to be particularly useful, so there was no point in including any details of it in the paper.  However, we did feel that having the analysis done did lead (indirectly) to a better understanding of what we were studying.  Moreover, we also felt that the person who did the analysis deserved some measure of credit in the final paper.  So we put a very short mention (one to three sentences) in the manuscript, just stating that we had done the analysis, but that it had not led to any useful conclusions, for such-and-such reasons.  Since the paper included this, it was unquestionably appropriate to include the person who had done the bulk of that analysis as an author.

I would suggest that you could do something similar, so your colleague could unambiguously be considered an author.