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I want to clip a vector-layer by another layer with ogr2ogr as explained here.

I always struggle to find out how to refer to a layer in ogr2ogr for input and output. Does anyone have a quick tip?

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Based on the ogr2ogr documentation, this should work:

ogr2ogr -clipsrc clip_polygons.gpkg -clipsrclayer clip_polygons_layer -nln output_layer output.gpkg input.gpkg input_layer

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