I am trying to create a submit filter to check for any -W arguments, but qsub
doesn't seem to be sending the entire command line arguments.

I just made this simple submit filter to test:

#!/bin/sh

echo "$@" >> /tmp/$USER.sh.args

while read i; do
    echo $i
done

I tried these submissions:
qsub -l nodes=1 -W group_list=Physics -I
qsub -l nodes=1 -W group_list=Physics hello.submit
qsub -W umask=002 hello.submit

I got this output from my submit filter file for the command line arguments:

-l nodes=1 -W group_list -I
-l nodes=1 -W group_list hello.submit
-W umask hello.submit

It seems anything after '=' is truncated for -W arguments.