Wasserstein barycenters and variance-like criterion using Wasserstein distance are used in many problems to analyze the homo-geneity of collections of distributions and structural relationships between the observations. We propose the estimation of the quantiles of the empirical process of the Wasserstein's variation using a bootstrap procedure. Then we use these results for statistical inference on a distribution registration model for general deformation functions. The tests are based on the variance of the distributions with respect to their Wasserstein's barycenters for which we prove a central limit theorem.