def METHOD_NAME():
    mdata_query = mudata.read(par["input"].strip())
    adata_query = extract_proteins_to_anndata(mdata_query,
                                              rna_modality_key=par["query_modality"],
                                              protein_modality_key=par["query_proteins_modality"],
                                              input_layer=par["input_layer"],
                                              hvg_var_key=par["var_input"])
    if par["reference"].endswith(".h5mu"):
        logger.info("Reading reference")
        mdata_reference = mudata.read(par["reference"].strip())
        logger.info("Mapping query to the reference")
        vae_query, adata_query = map_query_to_reference(mdata_reference, mdata_query, adata_query)
    else:
        raise ValueError("Incorrect format of reference, please provide a .h5mu file")
    adata_query.uns["integration_method"] = "totalvi"
    logger.info("Getting the latent representation of query")
    mdata_query.mod[par["query_modality"]].obsm[par["obsm_output"]] = vae_query.get_latent_representation()
    norm_rna, norm_protein = vae_query.get_normalized_expression()
    mdata_query.mod[par["query_modality"]].obsm[par["obsm_normalized_rna_output"]] = norm_rna.to_numpy()
    if par["query_proteins_modality"] in mdata_query.mod:
        mdata_query.mod[par["query_proteins_modality"]].obsm[par["obsm_normalized_protein_output"]] = norm_protein.to_numpy()
    logger.info("Updating mdata")
    mdata_query.update()
    logger.info("Saving updated query data")
    mdata_query.write_h5mu(par["output"].strip())
    logger.info("Saving query model")
    vae_query.save(par["query_model_path"], overwrite=True)