How do I change the canvas size of a PNG with ImageMagick (GraphicsMagick)? (How to pad with transparency?)

This command will take any sized input file and fit it best to a 40x40 square and pad with transparency:

convert \
   original.png \
  -thumbnail '40x40>' \
  -background transparent \
  -gravity center \
  -extent 40x40 \
  -compose Copy_Opacity \
  -composite mask.png \
   original-resized.png

The gravity option ensures the image is centered in both directions, and transparent is used wherever there are no pixels. Then the compositing is done with the mask.png

One command to convert all PNGs from one folder:

mogrify \
 -resize 50x50 \
 -background transparent \
 -gravity center \
 -extent 50x50 \
 -format png \
 -path resized \
 *.png

mogrify is a command from ImageMagick package. You have to create output directory first.

Here's what I eventually went with. A two step process:

gm convert \
  -thumbnail '40x40>' \
  -background transparent \
  -gravity center \
  -extent 40x40 \
   original.png \
   intermediate.png

gm composite \
  -compose in \
   intermediate.png \
   mask.png \
   out.png

Where mask.png is white pixels for what I wanted to keep, and transparent pixels for what I wanted to mask out (discard).