There are three general ways to call mysqldump:
shell> mysqldump [options] db_name [tbl_name ...] shell> mysqldump [options] --databases db_name ... shell> mysqldump [options] --all-databases
Only the first one allows you to select the name of the database and table, but not allow multiple databases. If you use the second or third option, you will delete the selected databases (second) or all databases (third).
So you can do this, but you need to reset all the databases.
As Michael Paugaga said in the comments, you can also do this twice.
first time with > /tmp/file.sql
"
second time with " >> /tmp/file.sql to append
"
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