You can't use input file on Phonegap. It's not supported. You need make something like this:
function uploadDatabase(callback) {
// file.entry accessible from global scope; see other tutorial
var filepath = file.entry.fullPath,
uploadOptions = new FileUploadOptions(),
transfer = new FileTransfer(),
endpoint = "http://facepath.com/payload";
uploadOptions.fileKey = "db";
uploadOptions.fileName = "database.db";
uploadOptions.mimeType = "text/plain";
transfer.upload(filepath, endpoint, transferComplete,
transferError, uploadOptions);
}
in mime type put the type of file