For example, if you wanted to access a secure wifi network you may use a particular tool but if you wanted to break a password you would use another.
Beyond tools there are also specific techniques used to penitrate SQL databases etc..
I purposely have been vague and not named the tools and techniques for doing this.
That being said, there is a certain live linux distribution that starts with K and ends with ALI which has alot of pentest tools pre installed and I see no reason why you couldn't write a Bash script to "automate" things.