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Metadata API supports both file-based and CRUD-based development.
File-Based Development
The declarative or file-based asynchronous Metadata API deploy() and retrieve() operations deploy or retrieve a .zip file that holds components in a set of folders, and a manifest file named package.xml. For more information, see Deploying and Retrieving Metadata. The easiest way to access the file-based functionality is to use the Force.com IDE or Force.com Migration Tool.
CRUD-Based Development
The CRUD Metadata API calls act upon the metadata components in a manner similar to the way synchronous API calls in the enterprise WSDL act upon objects. For more information about the enterprise WSDL, see the SOAP API Developer's Guide.