#----------------------- PIMA 1.40 (BF 4/10/06) ----------------------------
#
# Add the contents of this file to your GDEHELP/.GDEmenus menu file
# somewhere in the protein menu part.  Also copy ../doc/pima.help to GDEHELP.
#

item:PIMA
itemmethod:(pima-gde SEQ $NAME $TYPE -i "$OPEN" -d "$EXTEND" $NODES $MATRIX $OPTIONS) &
itemhelp:local/doc/PIMA/pima.help
itemopen:gde_help_viewer.csh

arg:NAME
argtype:text
arglabel:Cluster Name?
argtext:PIMA

arg:OPEN
argtype:text
arglabel:Gap Open Penalty?
argtext:44.0

arg:EXTEND
argtype:text
arglabel:Gap Extension Penalty?
argtext:4.0

arg:TYPE
argtype:chooser
arglabel:Cluster type?
argvalue:0
argchoice:Maximal Linkage:0
argchoice:Sequential Branching:1
argchoice:Both:2

arg:NODES
argtype:chooser
arglabel:Use numerical extensions on each step?
argchoice:Yes:
argchoice:No:-n
argvalue:1

arg:MATRIX
arglabel:Pattern matrix
argtype:choice_menu
argchoice:Pattern alphabet (default):
argchoice:Amino Acid Class Covering: -m $DAT/pima/class1.mat
argchoice:Amino Acid Class Covering, pattern alphabet: -m $DAT/pima/class2.mat
argvalue:0

arg:OPTIONS
argtype:text
arglabel:Additional Options?
argtext:

in:SEQ
informat:genbank
insave: