Wasserstein barycenters and variance-like criterion using Wasserstein distance are used in many problems to analyze the homogeneity 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 central limit theorems, including bootstrap versions.