I think that
mogrify -resize \"1000>\" *.jpg
resizes a bunch of jpegs so that the shorter side is 1000px if that side was longer than 1000px
It should keep the aspect ratio / image proportions when using a geometry string with ">", so you can just do:
mogrify -resize "1000x1000>" *.jpg
So you're explicitly limiting the image to being, at most, 1000x1000 pixels, and keeping the current aspect ratio of the image.