s.update

#!/bin/tcsh
# This script will update s1-s5 afni processing scripts
# Usage: s.update [options] script1 script2 etc...
#		<script> options:
#			-all: all scripts
#			or you can type the name of one or more scripts to select which to update
#			-dir: directory for scripts to go, of no -dir specified, they will be written to your pwd
#			-h: show help file
#
# known issues to be solved later:


#<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
#<><><><><><><><><><><><><><><> Do Not Change  <><><><><><><><><><><><><><><><><>
#<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>


# set directory, if -dir specified this will be overwritten
set dir = `pwd`
# Variable initialization
set opts = ()
set count = 1
# Parse input
if ($#argv == 0) then
	echo " "
	echo "**** No options given ****"
	echo " "
	echo "Here, this may help you:"
	set argv = (-h)
endif
while ($count <= $#argv)
	switch("$argv[$count]")
		case "-h":
			echo " "
			echo "Usage: s.update [options] script1 script2 etc..."
			echo "  "
			echo "Scripts you can ask for:"
			echo "  s1.dataset"
			echo "  s2.make_spec"
			echo "  s3.rest_surf_preproc"
			echo " 	s3.rest_vol_preproc"
			echo "  s3.task_surf_preproc"
			echo "  s3.task_vol_preproc"
			echo "  s4.motion"
			echo "  s5.decon"
			echo " "
			echo "[options]:"
			echo "-all: 	will give you all of the above, you do not need to specify"
			echo "     	individual scripts if this option is used"
			echo "-dir: 	<dir> will copy the scripts to <dir>"
			echo "-h: 	display this help file "
			echo " "
		exit
		case "-all":
			set opts = ($opts 		\
				s1.dataset 		\
				s2.make_spec 		\
				s3.rest_surf_preproc 	\
				s3.rest_vol_preproc 	\
				s3.task_surf_preproc 	\
				s3.task_vol_preproc 	\
				s4.motion)
		breaksw
		case "s1.dataset":
			set opts = ($opts s1.dataset)
		breaksw
		case "s2.make_spec":
			set opts = ($opts s2.make_spec)
		breaksw
		case "s3.task_surf_preproc":
			set opts = ($opts s3.task_surf_preproc)
		breaksw
		case "s3.rest_surf_preproc":
			set opts = ($opts s3.rest_surf_preproc)
		breaksw
		case "s3.rest_vol_preproc":
			set opts = ($opts s3.rest_vol_preproc)
		breaksw
		case "s3.task_vol_preproc":
			set opts = ($opts s3.task_vol_preproc)
		breaksw
		case "s4.motion":
			set opts = ($opts s4.motion)
		breaksw
		case "s5.decon":
			set opts = ($opts s5.decon)
		breaksw
		case "-dir":
			@ count ++
			set dir = $argv[$count]
		breaksw
		default:
			echo " "
			echo "$1 not understood"
			echo "It's a trap! - Admiral Ackbar"
			echo " "
			exit
		breaksw
	endsw
	shift
end
# Directory check
if (! -d $dir) then
	echo " "
	echo "$dir is not a directory"
	echo "It's a trap! - Admiral Ackbar"
	echo " "
	exit
else
# Update scripts
	echo " "
	echo "Updating scripts to $dir"
	echo " "
	foreach s ($opts)
		cd $0:h
		cp -vi $s $dir
	end
endif
echo " "
echo "Scripts have been updated..."
echo " "
echo "================================================================"
echo "Now, witness the power of this fully operational battle station!"
echo "================================================================"
echo " "
exit