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I created a simple model that includes a near geoprocessing tool with a point feature layer as an input and a line feature layer as a near feature and it works perfectly in desktop. Now I would like to publish it to my server as a geoprocessing service to be able to consume it using javascript API and use feature layers as parameters. I know that the geoprocessing services in this case only accepts featuresets rather than feature layers as inputs but in my case I need to use the feature layers that are published in my server. How can I modify my model to successfully publish the service? and how should I set my inputs?

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Haven't tested this, but you can use the Copy Features tool to make a feature class from a feature layer.

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