{
  "$schema": "http://schema.management.azure.com/schemas/2015-01-01/deploymentTemplate.json#",
  "contentVersion": "1.0.0.0",
  "parameters": {
    "appName": {
      "type": "string"
    },
    "location": {
      "type": "string"
    },
    "msdeployPackageUrl": {
      "type": "string"
    }
  },
  "resources": [
    {
      "apiVersion": "2016-03-01",
      "name": "[concat(parameters('appName'), '/MSDeploy')]",
      "location": "[parameters('location')]",
      "type": "Microsoft.Web/sites/Extensions",
      "properties": {
        "packageUri": "[parameters('msdeployPackageUrl')]"
      }
    }
  ]
}

Add sample template to do only msdeploy
Add sample template to do only msdeploy
