#------------------- Retrieve Protein GI ( 4/ 7/06) --------------------------

item:Retrieve protein GIs
#itemmethod: python $BIRCH/script/flat2list.py in1 in1.nam; leash -mn $SHMETHOD -mpf in1.nam -of in1.pro.gi; rm in1.nam in1.pro.gi; $GDEOUTPUT
itemmethod: python $BIRCH/script/SHGet.py in1 -mn $METHOD  -e pro.gi in1.pro; $GDEOUTPUT
itemhelp:doc/dGDE/SeqHound_API_Functions.html
itemopen:browser.csh

in:in1
informat:flat
insave:

arg:METHOD
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.pro.flat; dgde in1.pro; $RM_CMD -f in1*)&
argchoice:No:mv in1.pro out1.pro.flat
argvalue:0

out:out1.pro.flat
outformat:gde