the --end-of-file option appears to pad all of the text in the string with an extra whitespace.

for example, when I do.

makeInput.py test.xyz -o test.com -p 16 -mem 16 -c title -m m062x -b "6-31G(d,p)" --route "opt=modredundant" --end-of-file "B 8 18 S 20 -0.05"

test.com ends with
B 8 1 8 S 2 0 - 0 . 0 5