Hard to use this tool with godot 3.2.
Here's how i success. If i did other way, godot says errors message that i can't solve (dependance's errors but unsolvable !) :
Launch autotiler.AppImage
Useless to configure "Tile size" because the software determines it automaticaly.
Choose the file "Input File (Wang)" (murs.png for example) then "Export as Godot Tileset"
It creates 3 files : murs.png murs.import and murs.tres
Copy them at the ROOT of the godot's project using a file manager.
Launch godot and open the project. The 3 files are automaticaly imported.
In the dock "Filesystem" of godot, double-click on murs.tres
Godot tells that he can't load the scene because of lack of dependances.
Click on "Correct the dependances".
He tells that the ressource murs.png that as the path res://murs/murs.png isn't good.
Click on the icon to the right to choose manualy.
Select murs.png then validate.
The error window is still here but click on "Open anyway" (approximative traduction !).
In the tab "TileSet", everything displays : Region, Collision and Bitmask !
Create a "Tilemap" node and in the inspector, click on "Tile Set" -> load then select murs.tres
Configure Cell>Size as you want.
The Regions, Collisions and Bitmask are still present.
We can now move murs.png and murs.tres in a sub-folder via the godot's dock "Filesystem".
In the future, if we want to modify mur.png, we can do it with gimp for example by editing directly mur.png in the godot's project directory.