AutoAnnotate provides several commands which allow basic features to be automated via scripts, the command line or REST.
To call commands via REST the CyREST App is required. CyREST is normally installed by default.
CyRest is updated often. There are two ways to install the latest version:
Open the App Manager dialog from the main menu at Apps > App Manager. Then go to the Check For Updates tab. If there is a newer version available it will be listed.
CyRest can also be installed or updated from the App Store Website
On-line documentation for AutoAnnotate commands can be accessed from the main menu at Help > Automation > CyREST Command API. This will open a web browser with documentation for all the commands that are available through CyREST. Navigate to the autoannotate entry and expand it for detailed documentation on each command.
Command Line Documentation¶
Open the Automation Panel from the main menu at View > Show Automation Panel.
help autoannotate to list the available commands provided by AutoAnnotate.
To get help on a particular command type, for example the
help autoannotate redraw.
For more details on the Automation Panel see the Cytoscape User Docs