The Cook 2013 paper asserts that 97% of relevant papers were in favor of the consensus opinion on anthropogenic global warmng backed by the IPCC. There are two problems with the paper.
The first is in the paper's misuse by propagandists. Right in the abstract it lays out that 2/3rds of papers don't actually express an opinion on global warming. The authors could go either way. This is almost never conveyed by propagandists supporting the consensus position.
The second problem is that some of the papers are mischaracterized with prominent skeptics being put into the pro-AGW camp. Cook has not retracted the paper at present. A rebuttal paper, Legates 2013 has been published showing that instead of 97.1% consensus supporting, only 0.3% of relevant papers support the standard definition of the consensus position.