# .GDEmenus for OSX-Mac 
# This file was automatically generated by makemenus.py.
# Changes should be made to individual .item files,
# and the .GDEmenus file re-created using makemenus.py.
############################################################################
#                                                                          #
#                                                                          #
#         ####   #####   ######  #    #  ######  #    #  #    #   ####     #
#        #    #  #    #  #       ##  ##  #       ##   #  #    #  #         #
#        #       #    #  #####   # ## #  #####   # #  #  #    #   ####     #
#        #  ###  #    #  #       #    #  #       #  # #  #    #       #    #
#    ### #    #  #    #  #       #    #  #       #   ##  #    #  #    #    #
#    ###  ####   #####   ######  #    #  ######  #    #   ####    ####     #
#                                                                          #
#       .GDEmenus 1993 by Steven Smith                                     #
#       .GDEmenus Version   8/18/2004  by Brian Fristensky                 #
#                                                                          #
############################################################################


#
####################################################################
# This file creates menus for dgde, a pilot project aimed at 
# creating a database client program that facilitates the
# creation and manipulation of database subsets.



############################## File ##############################
menu:File

#-------------------------------- New dataset ----------------------------
item:New dataset   <meta N>
itemmethod:echo '"$Name' > out1
itemmeta:n
itemhelp:doc/GDE/new_sequence.help
itemopen:gde_help_viewer.csh
 
arg:Name 
argtype:text 
arglabel:New dataset name? 
argtext:New 

out:out1
outformat:flat


#------------------ Import Name List  (7/31/04) -------------------

item:Import namefile
itemmethod: python $BIRCH/script/list2flat.py $INPUTFILE out1
itemhelp:doc/fsap/funnel.asc
itemopen:gde_help_viewer.csh

arg:INPUTFILE
argtype:text
arglabel:Namefile

out:out1
outformat:flat
#------------------ Export Name List  (7/31/04) -------------------

item:Export namefile
itemmethod: python $BIRCH/script/flat2list.py in1 $INPUTFILE 
itemhelp:doc/fsap/funnel.asc
itemopen:gde_help_viewer.csh

arg:INPUTFILE
argtype:text
arglabel:Namefile

in:in1
informat:flat


#-------------------------------- Save selection --------------------------
item:Save Selection
itemmethod: cat $SAVE_FUNC > $Name
itemhelp:doc/GDE/save_selection.help
itemopen:gde_help_viewer.csh

arg:SAVE_FUNC
argtype:chooser
arglabel:File format
argchoice:Flat:in1
argchoice:Genbank:in2
argchoice:GDE/HGL:in3

arg:Name
argtype:text
arglabel:File name?

in:in1
informat:flat

in:in2
informat:genbank

in:in3
informat:gde
#------------------------------ Print selection ----------------------------
item:Print Selection
itemmethod:(PrintStrat -in in1 -scale $SCALE > in1.tmp; $CMD -P$PRINTER in1.tmp; $RM_CMD -f in1 in1.tmp)&
itemhelp:doc/GDE/print_alignment.help
itemopen:gde_help_viewer.csh
 
arg:SCALE
argtype:slider
arglabel:Reduce printout by?
argmin:1
argmax:20
argvalue:1

arg:CMD
argtype:chooser
argchoice:Lpr:lpr
#argchoice:Enscript Gaudy:enscript -G -q
#argchoice:Enscript Two column:enscript -2rG
argvalue:0 

arg:PRINTER
argtype:chooser
arglabel:Which printer?
argchoice:EPSON:$PRINTER
#argchoice:MACHRAY:machray
argchoice:copyctr:copyctr
argchoice:BLDGAGRIC.PLANT_HP3SI:bldgagric.plant_hp3si
 
in:in1
informat:gde
insave:


############################## Documentation ##############################
menu:Documentation

# ----------------------   DOCUMENTATION    ----------------------------


item:ViewDocumentation
itemmethod:($DOCUMENT)&

arg:DOCUMENT
arglabel:Documentation file
argtype:choice_menu
argchoice:GDE Documentation:$birch/script/browser.csh $tutorials/GDE/gde.html
argchoice:dGDE Interface Documentation:$birch/script/browser.csh $tutorials/GDE/overview/GDE.interfaces.html#dGDE
argchoice:GDE 2.2 Manual:$GDE_PDFVIEW $DOC/GDE/GDE2.2_manual.pdf
argchoice:SeqHound API:$BIRCH_NETSCAPE $DOC/dGDE/SeqHound.html
argvalue:0


############################## Edit ##############################
menu:Edit

# -------------------------------   sort    --------------------------------
item:Sort
itemmethod:(heapsortHGL in1 $PRIM_KEY $SEC_KEY > in1.tmp ; gde in1.tmp;$RM_CMD -f in1*)&
itemhelp:heapsortHGL.help
itemopen:gde_help_viewer.csh

arg:PRIM_KEY
argtype:choice_menu
argchoice:Group:group-ID
argchoice:type:type
argchoice:name:name
argchoice:Sequence ID:sequence-ID
argchoice:creator:creator
argchoice:offset:offset
arglabel:Primary sort field?

arg:SEC_KEY
argtype:choice_menu
argchoice:None:
argchoice:Group:group-ID
argchoice:type:type
argchoice:name:name
argchoice:Sequence ID:sequence-ID
argchoice:creator:creator
argchoice:offset:offset
arglabel:Secondary sort field?

in:in1
informat:gde
insave:

# ----------------------- Copy out ( 4/ 7/06)  ----------------------------
item:Copy out
itemmethod:sed -e "s/^LOCUS   /LOCUS/" -e "s/^ ACCESSION/ACCESSION /" -e "/^$/d"  in1 > $HOME/.dGDEclipboard

in:in1
informat:genbank

# ----------------------- Paste in  4/ 7/06) ----------------------------
item:Paste in
itemmethod:cp $HOME/.dGDEclipboard out1

out:out1
outformat:genbank

# -------------------------------- Extract --------------------------------
item:extract
itemmethod:(dgde in1;$RM_CMD -f in1)&

in:in1
informat:gde
insave:

############################## Convert ##############################
menu:Convert

#------------------- Convert to GI ( 4/10/06) --------------------------

item:Convert Name/Acc to GI

# For ACCESSION numbers in the form AB005432.1, the version number is deleted,
# because SeqHound can't handle it.
# This is a problem with SeqHound 2.5, and appears to be fixed in
# the most recent SeqHound.
itemmethod: python $BIRCH/script/flat2list.py in1 in1.tmp; cut -f1 -d"." <in1.tmp >in1.nam;  leash -mn $SHMETHOD -mpf in1.nam -of in1.gi; python $BIRCH/script/list2flat.py in1.gi in1.flat;rm in1.nam in1.tmp in1.gi; $GDEOUTPUT
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundFindAccList
itemopen:browser.csh

in:in1
informat:flat

arg:SHMETHOD
arglabel:Convert
argtype:chooser
argchoice:Name to GI:SHoundFindNameList
argchoice:Accession to GI:SHoundFindAccList
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.gi
argvalue:0

out:out1.gi
outformat:gde

#------------------- GI to Accession ( 4/10/06) --------------------------

item:Convert GI to Accession
itemmethod: python $BIRCH/script/flat2list.py in1 in1.nam; leash -mn SHoundAccFromGiList -mpf in1.nam -of in1.acc; python $BIRCH/script/list2flat.py in1.acc in1.flat;rm in1.nam in1.acc; $GDEOUTPUT
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundAccFromGiList
itemopen:browser.csh

in:in1
informat:flat

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.gi
argvalue:0


out:out1.gi
outformat:gde

#------------------- GI to TaxID ( 1/23/05) --------------------------

item:Convert GI to TaxID
itemmethod: python $BIRCH/script/flat2list.py in1 in1.nam; leash -mn SHoundTaxIDFromGiList -mpf in1.nam -of in1.taxid; python $BIRCH/script/list2flat.py in1.taxid in1.flat;rm in1.nam in1.taxid; $GDEOUTPUT
#itemmethod: (leashw -e .taxid -mn SHoundTaxIDFromGiList -mpf in1 -of in1.taxid; $GDEOUTPUT) &

itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundTaxIDFromGiList
itemopen:browser.csh

in:in1
informat:flat
insave:

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

out:out1.taxid
outformat:flat


############################## Retrieve ##############################
menu:Retrieve

#------------------- DNA - GenBank ( 4/10/06) --------------------------
# Note: This menu requires the script SHound.fixGenBank.py. 
# SHoundGetGenBankffList omits '//' characters from the end
# of GenBank entries. Since these characters are required to
# indicate the end of an entry, SHound.fixGenBank.py adds them
# to the SHound output. When SHound is fixed, this script
# can be deleted.
item:DNA (GenBank) from GI
itemmethod: (python $BIRCH/script/SHGet.py in1 -mn $METHOD in1.tmp; python $BIRCH/script/SHound.fixGenBank.py in1.tmp in1.gen; rm in1.tmp; $WHERE) &
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundGetGenBankffList
itemopen:browser.csh

arg:METHOD
arglabel:Retrieval method
argtype:choice_menu
argchoice:SHoundGetGenBankffList (default,fast):SHoundGetGenBankffList 
argchoice:SHoundGetGenBankff (slow,reliable):SHoundGetGenBankff
argvalue:0

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
# If GenBank file, read directly, otherwise, convert to GenBank.
argchoice:GDE:(gde in1.gen; rm in1.*)&
argchoice:Textedit window:($GDE_TEXTEDIT in1.gen;rm in1.*) &
argchoice:Output file:mv in1.gen $OUTFILE; echo ' SEQHOUND - GET completed'
argvalue:0

arg:OUTFILE
arglabel:Output file name
argtype:text

in:in1
informat:flat
insave:

#------------------- GenBank XML ( 4/10/06) --------------------------
item: GenBank XML file from GI
itemmethod: (python $BIRCH/script/SHGetSeq.py in1 -m SHoundGetXMLSeqEntry in1.xml; $WHERE) &
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundGetXMLSeqEntry
itemopen:browser.csh

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
# If GenBank file, read directly, otherwise, convert to GenBank.
# Need to fix Bluejay. Filename must be a fully qualified path.
#argchoice:Bluejay:(readseq -fXML -o=in1.xml in1.gen; bluejay file://in1.xml; rm in1.*)&
argchoice:Textedit window:($GDE_TEXTEDIT in1.xml;rm in1.*) &
argchoice:Output file:mv in1.xml $OUTFILE; echo ' SEQHOUND - GET completed'
argvalue:0

arg:OUTFILE
arglabel:Output file name
argtype:text

in:in1
informat:flat
insave:

#------------------- DNA - FASTA  ( 4/10/06) --------------------------
# Note: This menu requires that the shell script 'GBfilter' be
# in your bin directory.
item:DNA (FASTA) from GI
itemmethod: (python $BIRCH/script/SHGet.py in1 -mn $METHOD in1.tmp; $WHERE) &
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundGetFastaList
itemopen:browser.csh

arg:METHOD
arglabel:Retrieval method
argtype:choice_menu
argchoice:SHoundGetFastafList (default,fast):SHoundGetFastaList
argchoice:SHoundGetFasta (slow,reliable):SHoundGetFasta
argvalue:0

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
# If GenBank file, read directly, otherwise, convert to GenBank.
argchoice:GDE:(GBfilter in1.tmp in1.gen; gde in1.gen; rm in1.*)&
argchoice:Textedit window:($GDE_TEXTEDIT in1.tmp;rm in1.*) &
argchoice:Output file:mv in1.tmp $OUTFILE; echo ' SEQHOUND - GET completed'
argvalue:0

arg:OUTFILE
arglabel:Output file name
argtype:text

in:in1
informat:flat
insave:

#------------------- Protein  ( 2/22/06) --------------------------
# Note: This menu requires that the shell script 'GBfilter' be
# in your bin directory.
item:Protein from Protein GI
itemmethod: (python $BIRCH/script/SHGet.py in1 -mn $METHOD in1.tmp; $WHERE) &
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundGetFastaList
itemopen:browser.csh

arg:METHOD
arglabel:Retrieval method
argtype:choice_menu
argchoice:SHoundGetFastafList (default,fast):SHoundGetFastaList
argchoice:SHoundGetFasta (slow,reliable):SHoundGetFasta
argvalue:0

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
# If GenBank file, read directly, otherwise, convert to GenBank.
argchoice:GDE:(GBfilter in1.tmp in1.gen; gde in1.gen; rm in1.*)&
argchoice:Textedit window:($GDE_TEXTEDIT in1.tmp;rm in1.*) &
argchoice:Output file:mv in1.tmp $OUTFILE; echo ' SEQHOUND - GET completed'
argvalue:0

arg:OUTFILE
arglabel:Output file name
argtype:text

in:in1
informat:flat
insave:

#------------------- 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


############################## Taxonomy ##############################
menu:Taxonomy

#------------------- Genomes ( 4/10/06) --------------------------

item:TaxIDs for all complete genomes in SeqHound
itemmethod: $BIRCH/script/leash -mn SHoundAllGenomes -of allgenomes.taxid; python $BIRCH/script/list2flat.py allgenomes.taxid in1.flat; rm allgenomes.taxid; $GDEOUTPUT
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundAllGenomes
itemopen:browser.csh

in:in1
informat:flat

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

out:out1
outformat:gde

#------------------- Lineage ( 4/10/06) --------------------------

item:Get Lineage Descriptor
itemmethod: (python $BIRCH/script/flat2list.py in1 in1.nam; rm in1; leash_batch in1.nam in1.tmp -mn SHoundGetTaxLineageFromTaxID -mpi $LINFORMAT; rm in1.nam;$WHERE)&
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundGetTaxLineage_FULL
itemopen:browser.csh

in:in1
informat:flat
insave:

arg:LINFORMAT
arglabel:Lineage format
argtype:choice_menu
argchoice:FULL:SHoundGetTaxLineage_FULL 
argchoice:GenBank:SHoundGetTaxLineage_GENBANK
argchoice:TaxDB (short):SHoundGetTaxLineage_TAXDBSHORT
argvalue:0

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Textedit window:($GDE_TEXTEDIT in1.tmp;rm in1.tmp) &
argchoice:Output file:mv in1.tmp $OUTFILE
argvalue:0

arg:OUTFILE
arglabel:Output file name
argtype:text

------------------- Ancestors ( 4/10/06) --------------------------

item:Get All Taxonomy Ancestors
itemmethod: python $BIRCH/script/flat2list.py in1 in1.nam; leash.listarray in1.nam in1.flat taxid -mn SHoundGetAllTaxAncestors; rm in1.nam; $WHERE
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundGetAllTaxAncestors
itemopen:browser.csh

in:in1
informat:flat
insave:

arg:WHERE
arglabel:Send output to
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:New GDE window:echo '' > out1; (dgde in1.flat; $RM_CMD -f in1*)&
argchoice:Current GDE window:mv in1.flat out1; rm in1*
argchoice:Output file:echo '' > out1; mv in1.flat $OUTFILE; rm in1*; echo ' Get SHoundGetAllTaxAncestors completed'
argvalue:0

arg:OUTFILE
arglabel:Output file name
argtype:text

out:out1
outformat:flat


#------------------- Progeny ( 4/10/06) --------------------------

item:Get Taxonomy Progeny
itemmethod: (python $BIRCH/script/flat2list.py in1 in1.nam; leash.listarray in1.nam in1.flat taxid $WHATTOGET; rm in1.nam; $WHERE)&
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundGetTaxChildNodes
itemopen:browser.csh

in:in1
informat:flat
insave:

arg:WHATTOGET
arglabel:What to Get
argtype:chooser
argchoice:immediate child nodes:-mn SHoundGetTaxChildNodes 
argchoice:all taxonomy progeny:-mn SHoundGetAllTaxProgeny
argvalue:0

arg:WHERE
arglabel:Send output to
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:New GDE window:(dgde in1.flat; $RM_CMD -f in1*)&
argchoice:Output file:mv in1.flat $OUTFILE; rm in1*; echo ' Get TaxonomyProgeny completed'
argvalue:0

arg:OUTFILE
arglabel:Output file name
argtype:text

#------------------- Name ( 4/10/06) --------------------------

item:Get Name from TaxID
itemmethod: (python $BIRCH/script/flat2list.py in1 in1.nam; leash_batch in1.nam in1.tmp -mn SHoundGetTaxNameFromTaxIDByClass -mpi $NAMECLASS; rm in1.nam; $WHERE)&
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundGetTaxNameFromTaxIDByClass
itemopen:browser.csh

in:in1
informat:flat
insave:

arg:NAMECLASS
arglabel:Name Class
argtype:choice_menu
argchoice:none:SLRI_taxon_name_name_class_none 
argchoice:acronym:SLRI_taxon_name_name_class_acronym
argchoice:anamorph:SLRI_taxon_name_name_class_anamorph 
argchoice:blast_name:SLRI_taxon_name_name_class_blast_name
argchoice:common_name:SLRI_taxon_name_name_class_common_name
argchoice:equivalent_name:SLRI_taxon_name_name_class_equivalent_name
argchoice:includes:SLRI_taxon_name_name_class_includes
argchoice:in_part:SLRI_taxon_name_name_class_in_part
argchoice:misnomer:SLRI_taxon_name_name_class_misnomer 
argchoice:misspelling:SLRI_taxon_name_name_class_misspelling
argchoice:preferred_acronym:SLRI_taxon_name_name_class_preferred_acronym
argchoice:preferred_common_name:SLRI_taxon_name_name_class_preferred_common_name
argchoice:scientific_name:SLRI_taxon_name_name_class_scientific_name
argchoice:synonym:SLRI_taxon_name_name_class_synonym
argchoice:teleomorph:SLRI_taxon_name_name_class_teleomorph
argchoice:other:SLRI_taxon_name_name_class_other
argvalue:12

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Textedit window:($GDE_TEXTEDIT in1.tmp;rm in1.tmp) &
argchoice:Output file:mv in1.tmp $OUTFILE
argvalue:0

arg:OUTFILE
arglabel:Output file name
argtype:text

#------------------- DNA/Protein From Organism List ( 4/10/06) --------------------------

item:Get DNA/Protein from TaxID
#itemmethod: (python $BIRCH/script/flat2list.py in1 in1.nam; leash.listarray in1.nam in1.flat $WHATTOGET; rm  in1 in1.nam; $WHERE)&
itemmethod: (python $BIRCH/script/SHGet.py in1 -mn $SHMETHOD in1.flat; rm in1; $WHERE)&
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundDNAFromTaxID
itemopen:browser.csh

in:in1
informat:flat
insave:

arg:SHMETHOD
argtype:chooser
arglabel:What to get
# 8/23/04 - These two have stopped working, although they worked as recently
# as 8/17/04. 
#argchoice:DNA GI:dna.gi -mn SHoundDNAFromTaxIDIII
#argchoice:protein GI:pro.gi -mn SHoundProteinsFromTaxIDIII
# We'll use these two equivalent, though less efficient, methods
# until they're fixed.
argchoice:DNA GI:SHoundDNAFromTaxID -e dna.gi
argchoice:protein GI:SHoundProteinsFromTaxID -e pro.gi
argvalue:0

arg:WHERE
arglabel:Send output to
argtype:chooser
argchoice:GDE:(dgde in1.flat; $RM_CMD -f in1*)&
argchoice:Output file:mv in1.flat $OUTFILE; echo ' Get DNA/Protein from TaxID completed'
argvalue:0

arg:OUTFILE
arglabel:Output file name
argtype:text



############################## Statistics ##############################
menu:Statistics

#------------------- RawStats ( 1/23/05) --------------------------

item:Raw Statistics from Lists
itemmethod: (python $BIRCH/script/rawstats.py in1 in1.flat; $WHERE)&
itemhelp:$doc/dGDE/README.Leash
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:WHERE
arglabel:Send output to
argtype:chooser
argchoice:New GDE window:(dgde in1.flat; $RM_CMD -f in1*)&
argchoice:spreadsheet window:python $BIRCH/script/flatcnv.py in1.flat in1.csv -csv; ($GDE_SPREADSHEET in1.csv; rm in1*)&
argchoice:GDE Flat file: mv in1.flat $OUTFILE; rm in1*; echo ' RawStats completed'
argchoice:GDE CSV file:python $BIRCH/script/flatcnv.py in1.flat $OUTFILE -csv; rm in1*; echo ' RawStats completed'
argvalue:0

arg:OUTFILE
arglabel:Output file name
argtype:text


#------------------- SeqLength ( 4/10/06) --------------------------

item:gi to Sequence Length
# 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.
itemmethod:echo '' > out1; (python $BIRCH/script/SHGet.py in1 -mn SHoundSequenceLength -e len in1.flat; $WHERE)&
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundSequenceLength
itemopen:browser.csh

in:in1
informat:flat
insave:

arg:WHERE
arglabel:Send output to
argtype:chooser
argchoice:New GDE window:(dgde in1.flat; $RM_CMD -f in1 in1.flat)&
argchoice:Current GDE window:mv in1.flat out1; rm in1
argchoice:Output file:mv in1.flat $OUTFILE; rm in1*; echo ' Get gi to Sequence Length completed'
argvalue:0

arg:OUTFILE
arglabel:Output file name
argtype:text

out:out1
outformat:flat
outsave:

