Hello,
I would like to check if my Mikrotik router is well protected against ports attacks from outside, mainly all concerning smb protocol.
What is the best procedure to do that ? Has Mikrotik a tool for checking ?
I can define a firewall rule in the input chain but I want to also allow the smb protocol on my lan.
You can use some online port scanner (ask Google, there are several).
And you can block stuff selectively, depending on where it comes from (e.g. with in-interface). If you have default firewall, it blocks incoming connections from internet. If you have own firewall, you have it in your hands. 
SMB from the outside is firewalled by default (out-of-box config). There should be a default deny rule in your firewall.
With out-of-box config, your LAN ports would be in a bridge and there would be no firewall, so SMB within the LAN should be ok.
I like to firewall outbound SMB though, disallow SMB from going out on the internet.