Hmmm ... that looks like you figured out how to execute the php file via command line. Am I guessing right? Did you execute giving the dataroot parameter?
The 'missing required option' is for dataroot ... which one can find in the config.php file of the site.
Would think, also, that this script must have access rights to be able to write to moodledata/temp/somedirectory (where is might unzip the package) and to the moodle code directory and then the mod/block or whatever the update notification is about.
Maybe a little more info is necessary ... updating a plugin could be core or an add-on. Are we talking the inability to update an add-on? If so, which add-on? Those are third party 'contributions', I think, is that the term is as shown on the update plugins form. Does it say an update is available for a contribution and then provides a link to download? I've see some like that ... not updatable via Moodle GUI and was provided a link to download the upgrade for the mod/block.
Got any 'secure' logs which might complain about apache user attempting to write to a folder?
'spirit of sharing', Ken