Soft cut an atlas along a polygon:
#$ subatlas --polygon='POLYGON((-61 15,-61 16,-60 16,-60 15,-61 15))' file.atlas 
Hard cut a directory of atlases along a polygon, in parallel:
#$ subatlas dir/*.atlas --polygon='POLYGON((-61 15,-61 16,-60 16,-60 15,-61 15))' --parallel --cut-type=HARD_CUT
Cut an atlas containing only points within a given polygon:
#$ subatlas file.atlas --predicate 'e.getType() == ItemType.POINT' --polygon 'POLYGON((-61 15,-61 16,-60 16,-60 15,-61 15))'