How to remote desktop to Azure App?
You can run basic commands even for Azure app Services. Just navigate to "Tools" in the essentials blade of your App service and then click on "console" link to navigate to the Command Prompt.
Thanks,Prawin
If you just need to run something in the command line you can log in to the Kudu instance for your app (just go to http://your_appname.scm.azurewebsites.net in your browser) and open the Debug Console. You can choose between CMD and PowerShell.