#------------------- Retrieve Protein GI ( 1/23/05) --------------------------

item:Retrieve protein GIs
itemmethod: python $BIRCH/script/flat2list.py in1 in1.nam; leash -mn $SHMETHOD -mpf in1.nam -of in1.pro.gi; python $BIRCH/script/list2flat.py in1.pro.gi in1.flat;rm in1.nam in1.pro.gi; $GDEOUTPUT
itemhelp:

in:in1
informat:flat

arg:SHMETHOD
arglabel:Retrieve
argtype:choice_menu
argchoice:Protein GIs from DNA GI List:SHoundProteinFromDNAList
argchoice:Protein GIs from Chromosome List:SHoundProteinFromChromosomeList
argchoice:Protein GIs from TaxId List:SHoundProteinFromTaxIDList

argvalue:0

arg:GDEOUTPUT
arglabel:Output to new GDE window?
argtype:chooser
# Problem with Linux-Intel version of GDE (doesn't affect Solaris):
# If we declare an 'out' file, then it must always exist,
# even if we don't use it. Otherwise, gde will look for the file
# after it is done, and crash.
argchoice:Yes:(echo '' > out1.gi; dgde in1.flat; $RM_CMD -f in1.*)&
argchoice:No:mv in1.flat out1.pro.gi
argvalue:0

out:out1.gi
outformat:gde