If you look at the usage statements this script prints:

Code:

echo "USAGE: cluster_on_lev3.csh -dir <full_path Lev3 gfeat cope directory> [options]"
echo "USAGE: cluster_on_lev3.csh -dir <full_path Lev3 gfeat cope directory> -t <value> -p <value> -c <value> -l <value> -h <value>"

you might notice that this script requires its options and option arguments to be presented as separate arguments. When a command line is presented as expected, flag will be set to an option introducer -dir, -t, -p, etc. The shift then removes the option introducer from the list of remaining arguments and $argv[1] refers to the option-argument corresponding to that option introducer. The switch statement then sets a variable corresponding to the given option introducer to the value of the option-argument (which is then also shifted off of the remaining list of unprocessed arguments).

Note that each case can do a shift in addition to the shift after picking up the option introducer because every option in this script requires an option-argument.

The command:

Code:

echo "Incorrect use of argument: $flag"

is only printed when an option introducer is found on the command line that does not match an expected option.