Geoprocessing Service Missing Layers

[BrianLeroux]

Hi All. I have a python toolbox that I have published on my old 10.1 server. It fetches a shape file from an external source and then hosts it a temprary dynamic map service layer. Now that I am moving up to 10.6 I need to republish this service. I have it working in ArcGIS Pro and I am able to publish the result as a GP service. When I look at the service details for the map service layer it says there are no layers which it did show in 10.1. 

When I use the GP Tool widget in WAB, it doesn't allow me to set things like pop ups as it doesn't recognize any layers in the service.

Any ideas?

[BrianLeroux]

I was able to get the tool to run from a web map analysis and the layer symbology is correct. My only remaining issue is the result Map Service Layer does not have pop ups on as default. I can't seem to get that to work. Might be a limitation of Portal but hopefully not.