The PROTO format is an extension of the Webots WBT format.
So first I suggest you to import your model in Webots using the VRML format and the item option "Import VRML97" from the File menu. Once your model looks correct, then you can create the PROTO file.
At the moment, PROTO files has to be created manually.
Here are the required steps:
1. create <YourModel>.proto file with a default PROTO interface. For example for "MyProto.proto" (file and PROTO name have to match):
#VRML_SIM R2018a utf8
# You can add here the description of your model.
PROTO MyProto [
# this is the interface containing the open fields visible in the scene tree
# this is the body section: copy here your node definition
2. copy your node definition from the Webots WBT file and paste it to the PROTO body section marked in the example above
3. add the desired fields in the PROTO interface and link them to the nodes in the body section using the IS keywork or Lua statements
Please refer to the documentation of PROTO nodes
for further details, examples and instruction about how to use the IS keywork or Lua.
Don't hesitate to ask if you have issues.