How do you plan to have vCO launch the workflow? If it is a manual launch, then you can set your input to MimeAttachment, then process the file upon workflow execution. For the SSH part, you can pre-define SSH hosts in the plug-in configuration, then vCO will connect using the logged in user's credentials so that user must be valid in each of the hosts you plan to SSH to... alternatively, you can use certificate based authentication for your SSH hosts... I've never done that one myself so you'll need to refer to the documentation.
Regarding the file for inputs; if the workflow is to be scheduled and you are NOT going to manually input the file during execution, then you could place the file on the vCO host, a share that the vCO host can read, a website, FTP site, etc... then have the workflow grab the file, parse, and execute as desired.
