In botany terms the difference between flower and vaginula

is that flower is a reproductive structure in angiosperms (flowering plants), often conspicuously colourful and typically including sepals, petals, and either or both stamens and/or a pistil while vaginula is one of the tubular florets in composite flowers.

As nouns the difference between flower and vaginula

is that flower is a colorful, conspicuous structure associated with angiosperms, frequently scented and attracting various insects, and which may or may not be used for sexual reproduction while vaginula is a little sheath, such as that about the base of the pedicel of most mosses.

As a verb flower

is to put forth blooms.