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- Committer: Package Import Robot
- Author(s): Andreas Tille
- Date: 2012-12-11 09:59:08 UTC
- mfrom: (1.1.5)
- Revision ID: package-import@ubuntu.com-20121211095908-dfk71u2vzgbu9dr2
Tags: 5.5-1
* New upstream version (+adapted patches)
* Standards-Version: 3.9.4 (no changes needed)
* debian/po: Add Slovak po-debconf translation (Thanks to
Slavko <slavko@slavino.sk> for the translation)
Closes: #686275
* debian/rules: Add '-lm' as suggested in patch by Konstantinos Margaritis
<konstantinos.margaritis@freevec.org> to fix the build problem on armhf.
This together with new upstream closes: #692499
* Standards-Version: 3.9.4 (no changes needed)
* debian/po: Add Slovak po-debconf translation (Thanks to
Slavko <slavko@slavino.sk> for the translation)
Closes: #686275
* debian/rules: Add '-lm' as suggested in patch by Konstantinos Margaritis
<konstantinos.margaritis@freevec.org> to fix the build problem on armhf.
This together with new upstream closes: #692499
- files added:
- GDEHELP/cleanmenu.pl
- files removed:
- .pc/gcc-4.7.patch
- .pc/gcc-4.7.patch/AWTI
- files modified:
- !BRANCH_STATE
added
removed
GDEHELP/GDEmenus
1
menu:File
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item:New sequence <meta N>
4
itemmethod:echo "$Type$Name" > out1
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itemmeta:n
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itemhelp:new_sequence.help
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arg:Name
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argtype:text
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arglabel:New Sequence name?
11
argtext:New
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arg:Type
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argtype:choice_menu
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arglabel:Type?
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argchoice:DNA/RNA:#
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argchoice:Amino Acid:%
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argchoice:Text:\"
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argchoice:Mask:@
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out:out1
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outformat:flat
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item:Import Foreign Format
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itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
26
itemhelp:readseq.help
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arg:INPUTFILE
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argtype:text
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arglabel:Name of foreign file?
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out:OUTPUTFILE
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outformat:genbank
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item:Export Foreign Format
36
itemmethod:readseq in1 -pipe -all -form=$FORMAT > $OUTPUTFILE
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itemhelp:readseq.help
38
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arg:FORMAT
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argtype:choice_menu
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argchoice:GenBank:genbank
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argchoice:IG/Stanford:ig
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argchoice:NBRF:nbrf
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argchoice:EMBL:embl
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argchoice:GCG:gcg
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argchoice:DNA Strider:strider
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argchoice:Fitch:fitch
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argchoice:Pearson/Fasta:pearson
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argchoice:Zuker:zuker
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argchoice:Olsen:olsen
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argchoice:Phylip:phylip
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argchoice:Plain text:raw
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argchoice:ASN.1:asn
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argchoice:PIR:pir
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argchoice:MSF:msf
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argchoice:PAUP:paup
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argchoice:Pretty:pretty -nametop -nameleft=3 -numright -nameright -numtop
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arg:OUTPUTFILE
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argtype:text
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arglabel:Save as?
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in:in1
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informat:genbank
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item:Save Selection
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itemmethod: cat $SAVE_FUNC > $Name
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itemhelp:save_selection.help
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arg:SAVE_FUNC
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argtype:chooser
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arglabel:File format
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argchoice:Flat:in1
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argchoice:Genbank:in2
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argchoice:GDE/HGL:in3
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arg:Name
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argtype:text
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arglabel:File name?
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in:in1
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informat:flat
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in:in2
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informat:genbank
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in:in3
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informat:gde
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#
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#dgg addition for new readseq, 24 dec 92
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#
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item:Pretty Print
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itemmethod:readseq in1 -p -a -f=pretty $NAMELEFT $NAMERIGHT $NUMTOP $NUMBOT $NUMLEFT $NUMRIGHT -col=$COLS -width=$WIDTH $MATCH $GAPC > in1.pretty; (arb_textedit in1.pretty; /bin/rm -f in1 in1.pretty)&
97
itemhelp:readseq.help
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in:in1
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informat:genbank
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arg:NAMETOP
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argtype:chooser
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arglabel:Names at top ?
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argchoice:No:
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argchoice:Yes:-nametop
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arg:NAMELEFT
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argtype:chooser
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arglabel:Names at left ?
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argchoice:No:
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argchoice:Yes:-nameleft
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arg:NAMERIGHT
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argtype:chooser
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arglabel:Names at right?
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argchoice:Yes:-nameright
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argchoice:No:
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arg:NUMTOP
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argtype:chooser
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arglabel:Numbers at top ?
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argchoice:Yes:-numtop
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argchoice:No:
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arg:NUMBOT
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argtype:chooser
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arglabel:Numbers at tail ?
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argchoice:No:
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argchoice:Yes:-numbot
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arg:NUMLEFT
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argtype:chooser
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arglabel:Numbers at left ?
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argchoice:Yes:-numleft
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argchoice:No:
136
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arg:NUMRIGHT
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argtype:chooser
139
arglabel:Numbers at right?
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argchoice:Yes:-numright
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argchoice:No:
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arg:MATCH
144
argtype:chooser
145
arglabel:Show difference to current species?
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argchoice:No:
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argchoice:Yes:-match
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arg:GAPC
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argtype:chooser
151
arglabel:Count gap symbols?
152
argchoice:No:
153
argchoice:Yes:-gap
154
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arg:WIDTH
156
argtype:slider
157
arglabel:Sequence width?
158
argmin:10
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argmax:200
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argvalue:50
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arg:COLS
163
argtype:slider
164
arglabel:Column spacers?
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argmin:0
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argmax:50
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argvalue:10
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item:Print Selection
170
itemmethod:(PrintStrat -in in1 -width $WIDTH -scale $SCALE -style $STYLE > in1.tmp; $CMD in1.tmp; /bin/rm -f in1 in1.tmp)&
171
itemhelp:PrintStrat.help
172
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arg:STYLE
174
arglabel:Printing Style
175
argtype:chooser
176
argchoice:Poster:poster
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argchoice:Compressed:comp
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arg:WIDTH
180
argtype:slider
181
arglabel:Number of Bases Per Line?
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argmin:10
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argmax:150
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argvalue:50
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arg:SCALE
187
argtype:slider
188
arglabel:Reduce printout by?
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argmin:1
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argmax:20
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argvalue:1
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arg:CMD
194
argtype:chooser
195
argchoice:Lpr:lpr
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argchoice:Enscript Gaudy:enscript -G$LAND $FONT -P$PNTER
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argchoice:Enscript Two column:enscript -2rG -P$PNTER
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argchoice:View in a Texteditor:arb_textedit
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arg:LAND
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arglabel:Landscape for Enscript Gaudy?
202
argtype:chooser
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argchoice:No:
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argchoice:Yes:r
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arg:FONT
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arglabel:Font for Enscript Gaudy?
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argtype:chooser
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argchoice:Medium:-fCourier10
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argchoice:Small:-fCourier7
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argchoice:Large:-fCourier-Bold13
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arg:PNTER
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argtype:text
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arglabel:Which printer?
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argtext:pt
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in:in1
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informat:gde
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insave:
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menu:Edit
224
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item:Sort
226
itemmethod:(heapsortHGL in1 $PRIM_KEY $SEC_KEY > in1.tmp ; gde in1.tmp;/bin/rm -f in1*)&
227
itemhelp:heapsortHGL.help
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arg:PRIM_KEY
230
argtype:choice_menu
231
argchoice:Group:group-ID
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argchoice:type:type
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argchoice:name:name
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argchoice:Sequence ID:sequence-ID
235
argchoice:creator:creator
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argchoice:offset:offset
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arglabel:Primary sort field?
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arg:SEC_KEY
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argtype:choice_menu
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argchoice:None:
242
argchoice:Group:group-ID
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argchoice:type:type
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argchoice:name:name
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argchoice:Sequence ID:sequence-ID
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argchoice:creator:creator
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argchoice:offset:offset
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arglabel:Secondary sort field?
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in:in1
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informat:gde
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insave:
253
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item:extract
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itemmethod:(gde in1;/bin/rm -f in1)&
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in:in1
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informat:gde
259
insave:
260
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menu:DNA/RNA
262
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item:Translate...
264
itemmethod:Translate -tbl $TBL -frame $FRAME -min_frame $MNFRM $LTRCODE $NOSEP in1 > out1
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arg:FRAME
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argtype:chooser
268
arglabel:Which reading frame?
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argchoice:First:1
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argchoice:Second:2
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argchoice:Third:3
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argchoice:All six:6
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arg:MNFRM
275
arglabel:Minimum length of NT sequence to translate?
276
argtype:slider
277
argmin:0
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argmax:500
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argvalue:20
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arg:LTRCODE
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argtype:chooser
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arglabel:Translate to:
284
argchoice:Single letter codes:
285
argchoice:Triple letter codes:-3
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arg:NOSEP
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argtype:chooser
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arglabel: Seperate?
290
argchoice:No:
291
argchoice:Yes:-sep
292
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arg:TBL
294
arglabel:Codon table?
295
argtype:chooser
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argchoice:mycoplasma:2
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argchoice:universal:1
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argchoice:yeast:3
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argchoice:Vert. mito.:4
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in:in1
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informat:gde
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out:out1
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outformat:gde
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item:Dot plot
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itemmethod:(DotPlotTool in1 ; /bin/rm -f in1)&
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itemhelp:DotPlotTool.help
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in:in1
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informat:gde
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insave:
314
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item:Clustal alignment
316
itemmethod:(tr '"%#' '>'<in1>clus_in;clustalv /output=PIR /infile=clus_in /align /ktup=$KTUP /window=$WIN $Trans /fixedgap=$FIXED /floatgap=$FLOAT > in1.rpt;sed "s/>DL;/#/g" < clus_in.pir> in1;$REPORT gde in1; /bin/rm -f clus_in* in1* )&
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itemhelp:clustal_help
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arg:KTUP
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argtype:slider
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arglabel:K-tuple size for pairwise search
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argmin:1
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argmax:10
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argvalue:2
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arg:WIN
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argtype:slider
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arglabel:Window size
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argmin:1
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argmax:10
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argvalue:4
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arg:Trans
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argtype:chooser
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arglabel:Transitions weighted?
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argchoice:Yes:/TRANSIT
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argchoice:No:
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arg:FIXED
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argtype:slider
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arglabel:Fixed gap penalty
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argmin:1
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argmax:100
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argvalue:10
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arg:FLOAT
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arglabel:Floating gap penalty
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argtype:slider
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argmin:1
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argmax:100
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argvalue:10
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arg:REPORT
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argtype:chooser
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arglabel:View assembly report?
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argchoice:No:
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argchoice:Yes:arb_textedit in1.rpt&
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in:in1
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informat:flat
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insave:
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item:Variable Positions
366
itemmethod:varpos $REV < in1 > out1
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arg:REV
369
argtype:chooser
370
arglabel:Highlight (darken)
371
argchoice:Conserved positions:
372
argchoice:variable positions:-rev
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in:in1
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informat:flat
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out:out1
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outformat:colormask
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item:Find all <meta-f>
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itemmethod:findall $SEARCH $PRCNT $CASE $UT -match $MAT -mismatch $MIS < in1 > out1;
383
itemhelp:findall.help
384
itemmeta:f
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arg:SEARCH
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argtype:text
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arglabel:Search String
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arg:PRCNT
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argtype:slider
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arglabel:Percent mismatch
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argmin:0
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argmax:75
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argvalue:10
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arg:CASE
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argtype:chooser
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arglabel:Case
400
argchoice:Upper equals lower:
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argchoice:Upper not equal lower:-case
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arg:UT
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argtype:chooser
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arglabel:U equal T?
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argchoice:Yes:-u=t
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argchoice:No:
408
argvalue:0
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arg:MAT
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arglabel:Match color
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argtype:choice_menu
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argchoice:yellow:1
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argchoice:violet:2
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argchoice:red:3
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argchoice:aqua:4
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argchoice:green:5
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argchoice:blue:6
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argchoice:grey:11
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argchoice:black:8
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argvalue:2
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arg:MIS
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argtype:choice_menu
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arglabel:Mismatch color
426
argchoice:yellow:1
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argchoice:violet:2
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argchoice:red:3
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argchoice:aqua:4
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argchoice:green:5
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argchoice:blue:6
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argchoice:grey:11
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argchoice:black:8
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argvalue:7
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in:in1
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informat:flat
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out:out1
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outformat:colormask
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item:Sequence Consensus
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itemmethod:(MakeCons in1 $METHOD $MASK > out1)
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itemhelp:MakeCons.help
445
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arg:METHOD
447
arglabel:Method
448
argtype:chooser
449
argchoice:IUPAC:-iupac
450
argchoice:Majority:-majority $PERCENT
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arg:MASK
453
argtype:chooser
454
arglabel:Create a new:
455
argchoice:Sequence:
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argchoice:Selection Mask: | Consto01mask
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arg:PERCENT
459
arglabel:Minimum Percentage for Majority
460
argtype:slider
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argmin:50
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argmax:100
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argvalue:75
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in:in1
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informat:gde
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out:out1
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outformat:gde
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item:MFOLD
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itemmethod:(tr 'a-z' 'A-Z' < seqGB > .GDE.tmp.caps; ZUKERGDE.sh .GDE.tmp.caps $CT $GDE_HELP_DIR/ZUKER/ > out1 && $METHOD < out1; Zuk_to_gen < $CT >file.gen; gde file.gen&; arb_textedit RegionTable; /bin/rm -f RegionTable out1 seqGB* .GDE.tmp.caps)&
474
itemhelp:MFOLD.help
475
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in:seqGB
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informat:genbank
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insave:
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arg:METHOD
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argtype:chooser
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arglabel:RNA type
483
argchoice:Fold Linear RNA:lrna
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argchoice:Fold Circular RNA:crna
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arg:CT
487
argtype:text
488
arglabel:Pairing(ct) File Name
489
argtext:mfold_out
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item:Draw Secondary structure
493
itemmethod:(LoopTool $TEMPLATE in1 ; /bin/rm -f in1) &
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itemhelp:LoopTool.help
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arg:TEMPLATE
497
argtype:chooser
498
arglabel:Use template file ./loop.temp?
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argchoice:No:
500
argchoice:Yes:-t loop.temp
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in:in1
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informat:genbank
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insave:
505
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item:Highlight helix
507
itemmethod:readseq -a -f8 in1 | sed "s/>HELIX/\"HELIX/" > in1.flat; sho_helix < in1.flat > out1;rm in1.flat
508
itemhelp:sho_helix.help
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in:in1
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informat:genbank
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out:out1
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outformat:colormask
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#Menu for DNA/RNA
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item:blastn
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; blastn $BLASTDB in1.f W=$WORDLEN M=$MATCH N=$MMSCORE > in1.tmp; arb_textedit in1.tmp; rm in1*)&
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itemhelp:blast.help
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in:in1
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informat:flat
525
insave:
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arg:BLASTDB
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argtype:choice_menu
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arglabel:Which Database
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argchoice:genbank:$GDE_HELP_DIR/BLAST/genbank
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argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate
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arg:WORDLEN
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argtype:slider
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arglabel:Word Size
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argmin:4
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argmax:18
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argvalue:12
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arg:MATCH
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argtype:slider
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arglabel:Match Score
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argmin:1
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argmax:10
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argvalue:5
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arg:MMSCORE
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argtype:slider
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arglabel:Mismatch Score
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argmin:-10
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argmax:-1
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argvalue:-5
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item:blastx
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastx $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE> in1.tmp; arb_textedit in1.tmp; rm in1* PAM???)&
556
itemhelp:blast.help
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in:in1
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informat:flat
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insave:
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arg:BLASTDB
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argtype:choice_menu
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arglabel:Which Database
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argchoice:pir1:$GDE_HELP_DIR/BLAST/pir
566
argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept
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arg:WORDLEN
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argtype:slider
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arglabel:Word Size
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argmin:1
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argmax:5
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argvalue:3
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arg:Matrix
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arglabel:Substitution Matrix:
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argtype:choice_menu
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argchoice:PAM120:PAM120
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argchoice:PAM250:PAM250
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arg:CODE
582
argtype:choice_menu
583
arglabel:Genetic Code
584
argchoice:Standard or Universal:0
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argchoice:Vertebrate Mitochondrial:1
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argchoice:Yeast Mitochondrial:2
587
argchoice:Mold Mitochondrial and Mycoplasma:3
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argchoice:Invertebrate Mitochondrial:4
589
argchoice:Ciliate Macronuclear:5
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argchoice:Protozoan Mitochondrial:6
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argchoice:Plant Mitochondrial:7
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argchoice:Echinodermate Mitochondrial:8
593
594
595
item:FASTA (DNA/RNA)
596
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; arb_textedit in1.out;\rm in1*) &
597
itemhelp:FASTA.help
598
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in:in1
600
informat:flat
601
602
arg:DBASE
603
argtype:choice_menu
604
arglabel:Database
605
argchoice:GenBank Primate:$GDE_HELP_DIR/FASTA/GENBANK/gbpri.seq\ 1
606
argchoice:GenBank Rodent:$GDE_HELP_DIR/FASTA/GENBANK/gbrod.seq\ 1
607
argchoice:GenBank all Mammal:$GDE_HELP_DIR/FASTA/GENBANK/gbmam.seq\ 1
608
argchoice:GenBank verteBrates:$GDE_HELP_DIR/FASTA/GENBANK/gbvrt.seq\ 1
609
argchoice:GenBank Inverts:$GDE_HELP_DIR/FASTA/GENBANK/gbinv.seq\ 1
610
argchoice:GenBank pLants:$GDE_HELP_DIR/FASTA/GENBANK/gbpln.seq\ 1
611
argchoice:GenBank Struct RNA:$GDE_HELP_DIR/FASTA/GENBANK/gbrna.seq\ 1
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argchoice:GenBank euk. Organelles:$GDE_HELP_DIR/FASTA/GENBANK/gborg.seq\ 1
613
argchoice:GenBank phaGe:$GDE_HELP_DIR/FASTA/GENBANK/gbphg.seq\ 1
614
argchoice:GenBank bacTeria:$GDE_HELP_DIR/FASTA/GENBANK/gbbct.seq\ 1
615
argchoice:GenBank sYnthetic:$GDE_HELP_DIR/FASTA/GENBANK/gbsyn.seq\ 1
616
argchoice:GenBank Viral:$GDE_HELP_DIR/FASTA/GENBANK/gbvrl.seq\ 1
617
argchoice:GenBank Unannotated:$GDE_HELP_DIR/FASTA/GENBANK/gbuna.seq\ 1
618
619
arg:NUMOFALN
620
argtype:slider
621
arglabel:Number of Alignment to Report
622
argmin:1
623
argmax:100
624
argvalue:20
625
626
arg:MATRIX
627
arglabel:Which SMATRIX
628
argtype:choice_menu
629
argchoice:Default:
630
argchoice:altdiag.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altdiag.mat
631
argchoice:altprot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altprot.mat
632
argchoice:dna.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/dna.mat
633
argchoice:prot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/prot.mat
634
635
menu:Protein
636
637
item:Clustal Protein Alignment
638
itemmethod:(tr '%#"' '>' <in1>clus_in;clustalv /output=PIR /infile=clus_in /align /ktup=$KTUP /window=$WIN $Matrx /fixedgap=$FIXED /floatgap=$FLOAT > in1.rpt;sed "s/>P1;/%/g" < clus_in.pir > in1;$REPORT gde in1;/bin/rm -f in1* clus_in* )&
639
itemhelp:clustal_help
640
641
arg:KTUP
642
argtype:slider
643
arglabel:K-tuple size for pairwise search
644
argmin:1
645
argmax:10
646
argvalue:2
647
648
arg:WIN
649
argtype:slider
650
arglabel:Window size
651
argmin:1
652
argmax:10
653
argvalue:4
654
655
arg:Matrx
656
argtype:chooser
657
arglabel:Weighting matrix
658
argchoice:PAM 250:PAM250
659
argchoice:PAM 100:PAM100
660
argchoice:Identity:ID
661
662
arg:FIXED
663
argtype:slider
664
arglabel:Fixed gap penalty
665
argmin:1
666
argmax:100
667
argvalue:10
668
669
arg:FLOAT
670
arglabel:Floating gap penalty
671
argtype:slider
672
argmin:1
673
argmax:100
674
argvalue:10
675
676
arg:REPORT
677
argtype:chooser
678
arglabel:View assembly report?
679
argchoice:No:
680
argchoice:Yes:arb_textedit in1.rpt&
681
682
in:in1
683
informat:flat
684
insave:
685
686
#Menu for Protein
687
688
item:blastp
689
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastp $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;arb_textedit in1.tmp; rm in1* PAM???)&
690
itemhelp:blast.help
691
692
in:in1
693
informat:flat
694
insave:
695
696
arg:BLASTDB
697
argtype:choice_menu
698
arglabel:Which Database
699
argchoice:pir:$GDE_HELP_DIR/BLAST/pir
700
argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept
701
argchoice:local:$GDE_HELP_DIR/BLAST/local_db
702
703
arg:Matrix
704
arglabel:Substitution Matrix:
705
argtype:choice_menu
706
argchoice:PAM120:PAM120
707
argchoice:PAM250:PAM250
708
709
arg:WORDLEN
710
argtype:slider
711
arglabel:Word Size
712
argmin:1
713
argmax:5
714
argvalue:3
715
716
item:tblastn
717
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; arb_textedit in1.tmp; rm in1* PAM???)&
718
itemhelp:blast.help
719
720
in:in1
721
informat:flat
722
insave:
723
724
arg:BLASTDB
725
argtype:choice_menu
726
arglabel:Which Database
727
argchoice:genbank:$GDE_HELP_DIR/BLAST/genbank
728
argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate
729
730
arg:Matrix
731
arglabel:Substitution Matrix:
732
argtype:choice_menu
733
argchoice:PAM120:PAM120
734
argchoice:PAM250:PAM250
735
736
arg:WORDLEN
737
argtype:slider
738
arglabel:Word Size
739
argmin:4
740
argmax:18
741
argvalue:12
742
743
arg:CODE
744
argtype:choice_menu
745
arglabel:Genetic Code
746
argchoice:Standard or Universal:0
747
argchoice:Vertebrate Mitochondrial:1
748
argchoice:Yeast Mitochondrial:2
749
argchoice:Mold Mitochondrial and Mycoplasma:3
750
argchoice:Invertebrate Mitochondrial:4
751
argchoice:Ciliate Macronuclear:5
752
argchoice:Protozoan Mitochondrial:6
753
argchoice:Plant Mitochondrial:7
754
argchoice:Echinodermate Mitochondrial:8
755
756
item:blast3
757
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blast3 $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;arb_textedit in1.tmp; rm in1* PAM???)&
758
itemhelp:blast3.help
759
760
in:in1
761
informat:flat
762
insave:
763
764
arg:BLASTDB
765
argtype:choice_menu
766
arglabel:Which Database
767
argchoice:pir1:$GDE_HELP_DIR/BLAST/pir
768
argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept
769
770
arg:Matrix
771
arglabel:Substitution Matrix:
772
argtype:choice_menu
773
argchoice:PAM120:PAM120
774
argchoice:PAM250:PAM250
775
776
arg:WORDLEN
777
argtype:slider
778
arglabel:Word Size
779
argmin:1
780
argmax:5
781
argvalue:3
782
783
item:FASTA (Protein)
784
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; arb_textedit in1.out;\rm in1*) &
785
itemhelp:FASTA.help
786
787
in:in1
788
informat:flat
789
790
arg:DBASE
791
argtype:choice_menu
792
arglabel:Database
793
argchoice:NBRF PIR1:$GDE_HELP_DIR/FASTA/PIR/pir1.dat\ 2
794
argchoice:NBRF PIR2:$GDE_HELP_DIR/FASTA/PIR/pir2.dat\ 2
795
argchoice:NBRF PIR3:$GDE_HELP_DIR/FASTA/PIR/pir3.dat\ 2
796
797
798
arg:NUMOFALN
799
argtype:slider
800
arglabel:Number of Alignment to Report
801
argmin:1
802
argmax:100
803
argvalue:20
804
805
arg:MATRIX
806
arglabel:Which SMATRIX
807
argtype:choice_menu
808
argchoice:Default:
809
argchoice:Minimum mutation matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/codaa.mat
810
argchoice:Identity matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/idnaa.mat
811
argchoice:Identity matrix for mismatches:-s $GDE_HELP_DIR/FASTA/MATRIX/idpaa.mat
812
argchoice:PAM250:-s $GDE_HELP_DIR/FASTA/MATRIX/pam250.mat
813
argchoice:PAM120:-s $GDE_HELP_DIR/FASTA/MATRIX/pam120.mat
814
815
menu:Seq management
816
817
item:Assemble Contigs
818
itemmethod:(sed "s/#/>/"<in1 >in1.tmp; CAP2 in1.tmp $OVERLAP $PMATCH > out1;/bin/rm -f in1.tmp)
819
itemhelp:CAP2.help
820
821
arg:OVERLAP
822
argtype:slider
823
arglabel:Minimum overlap?
824
argmin:5
825
argmax:100
826
argvalue:20
827
828
arg:PMATCH
829
argtype:slider
830
arglabel:Percent match required within overlap
831
argmin:25
832
argmax:100
833
argvalue:90
834
835
in:in1
836
informat:flat
837
838
out:out1
839
outformat:gde
840
outoverwrite:
841
842
item:Map View
843
itemmethod:(mapview in1 -pbl $PBL -npp $NPP; /bin/rm -f in1)&
844
itemhelp:mapview.help
845
846
in:in1
847
informat:gde
848
insave:
849
850
arg:PBL
851
arglabel:Pixel Between Lines
852
argtype:slider
853
argvalue:10
854
argmin:1
855
argmax:15
856
857
arg:NPP
858
arglabel:Nucleotides Per Pixel
859
argtype:slider
860
argvalue:1
861
argmin:1
862
argmax:20
863
864
arg:LWIDTH
865
arglabel:Line Thickness
866
argtype:slider
867
argvalue:2
868
argmin:1
869
argmax:5
870
871
872
item:Restriction sites
873
itemmethod:(cp $ENZ in1.tmp ; $PRE_EDIT Restriction in1.tmp in1 > out1 ; rm in1.tmp);
874
itemhelp:Restriction.help
875
876
arg:ENZ
877
argtype:text
878
arglabel:Enzyme file
879
argtext:$GDE_HELP_DIR/DATA_FILES/enzymes
880
881
arg:PRE_EDIT
882
argtype:chooser
883
arglabel:Edit enzyme file first?
884
argchoice:Yes:arb_textedit in1.tmp;
885
argchoice:No:
886
887
in:in1
888
informat:flat
889
890
out:out1
891
outformat:colormask
892
893
menu:Phylogeny
894
895
item:DeSoete Tree fit
896
itemmethod: (readseq -a -f8 in1>in1.flat;count -t $CORR in1.flat> in1.tmp ; lsadt<in1.tmp -seed $SEED -init $INIT -empty -99.9 > in1.out ; $DISPLAY_FUNC in1.out;/bin/rm -f in1* )&
897
itemhelp:lsadt.help
898
899
in:in1
900
informat:genbank
901
insave:
902
inmask:
903
904
arg:CORR
905
arglabel:Distance correction?
906
argtype:chooser
907
argchoice:Olsen:-c=olsen
908
argchoice:Jukes/Cantor:-c=jukes
909
argchoice:None:-c=none
910
911
arg:INIT
912
arglabel:Initial parameter estimate
913
argtype:choice_menu
914
argchoice:uniformly distributed random numbers:1
915
argchoice:error-perturbed data:2
916
argchoice:original distance data from input matrix:3
917
918
arg:SEED
919
argtype:slider
920
arglabel:Random number seed
921
argmin:0
922
argmax:65535
923
argvalue:12345
924
925
arg:DISPLAY_FUNC
926
argtype:chooser
927
arglabel:View tree using
928
argchoice:TextEdit:arb_textedit
929
argchoice:Treetool:treetool
930
931
item:Phylip help
932
itemmethod:(arb_textedit $GDE_HELP_DIR/PHYLIP/$FILE)&
933
934
arg:FILE
935
argtype:choice_menu
936
arglabel:Which program?
937
argchoice:clique:clique.doc
938
argchoice:coallike:coallike.doc
939
argchoice:consense:consense.doc
940
argchoice:contchar:contchar.doc
941
argchoice:contml:contml.doc
942
argchoice:contrast:contrast.doc
943
argchoice:discrete:discrete.doc
944
argchoice:distance:distance.doc
945
argchoice:dnacomp:dnacomp.doc
946
argchoice:dnadist:dnadist.doc
947
argchoice:dnainvar:dnainvar.doc
948
argchoice:dnaml:dnaml.doc
949
argchoice:dnamlk:dnamlk.doc
950
argchoice:dnamove:dnamove.doc
951
argchoice:dnapars:dnapars.doc
952
argchoice:dnapenny:dnapenny.doc
953
argchoice:dollop:dollop.doc
954
argchoice:dolmove:dolmove.doc
955
argchoice:dolpenny:dolpenny.doc
956
argchoice:draw:draw.doc
957
argchoice:drawgram:drawgram.doc
958
argchoice:drawtree:drawtree.doc
959
argchoice:factor:factor.doc
960
argchoice:fitch:fitch.doc
961
argchoice:gendist:gendist.doc
962
argchoice:kitsch:kitsch.doc
963
argchoice:main:main.doc
964
argchoice:makeinf:makeinf.doc
965
argchoice:mix:mix.doc
966
argchoice:move:move.doc
967
argchoice:neighbor:neighbor.doc
968
argchoice:penny:penny.doc
969
argchoice:protdist:protdist.doc
970
argchoice:protml:protml.doc
971
argchoice:protpars:protpars.doc
972
argchoice:restml:restml.doc
973
argchoice:retree:retree.doc
974
argchoice:seqboot:seqboot.doc
975
argchoice:sequence:sequence.doc
976
977
978
979
item:Phylip 3.5
980
981
itemmethod:(/bin/rm -f outfile infile treefile ; readseq -a -f12 in1 > infile;$PREEDIT $BOOTSTRP ${ARB_XCMD:-cmdtool} $PROGRAM; $CONS arb_textedit outfile $DISPLAY_FUNC; rm in1 )&
982
983
arg:PROGRAM
984
argtype:choice_menu
985
arglabel:Which program to run?
986
argchoice:DNAPARS:dnapars
987
argchoice:DNAML:dnaml
988
argchoice:DNAMLK:dnamlk
989
argchoice:DNACOMP:dnacomp
990
argchoice:DNAMOVE:dnamove
991
argchoice:DNAINVAR:dnainvar
992
argchoice:PROTPARS:protpars
993
#argchoice:PROTML:protml
994
995
arg:BOOTSTRP
996
arglabel:Bootstrap data?
997
argtype:chooser
998
argchoice:No:
999
argchoice:Yes: ${ARB_XCMD:-cmdtool} seqboot ; /bin/mv -f outfile infile;
1000
1001
arg:CONS
1002
arglabel:Consensus tree?
1003
argtype:chooser
1004
argchoice:No:
1005
argchoice:Yes: /bin/mv -f treefile infile; ${ARB_XCMD:-cmdtool} consense ;
1006
1007
arg:DISPLAY_FUNC
1008
argtype:chooser
1009
arglabel:View tree using treetool?
1010
argchoice:Yes:& treetool treefile
1011
argchoice:No:
1012
1013
1014
arg:PREEDIT
1015
argtype:chooser
1016
arglabel:Edit input before running?
1017
argchoice:No:
1018
argchoice:Yes:arb_textedit infile;
1019
1020
1021
1022
in:in1
1023
informat:genbank
1024
inmask:
1025
insave:
1026
1027
item:Phylip Distance methods
1028
itemmethod:(/bin/rm -f treefile infile outfile; readseq -a -f12 in1 > infile ; $PREEDIT ${ARB_XCMD:-cmdtool} $DPGM;mv -f outfile infile;$PROGRAM arb_textedit outfile & treetool treefile;/bin/rm -f in1 infile outfile)&
1029
1030
arg:PROGRAM
1031
arglabel:Which method?
1032
argtype:chooser
1033
argchoice:DNADIST:mv -f infile outfile;
1034
argchoice:Fitch:${ARB_XCMD:-cmdtool} fitch;
1035
argchoice:Kitsch:${ARB_XCMD:-cmdtool} kitsch;
1036
argchoice:Neighbor:${ARB_XCMD:-cmdtool} neighbor;
1037
1038
arg:DPGM
1039
arglabel:Treat data as..
1040
argtype:chooser
1041
argchoice:DNA:dnadist
1042
argchoice:RNA:dnadist
1043
argchoice:AA:protdist
1044
1045
arg:PREEDIT
1046
argtype:chooser
1047
arglabel:Edit input before running?
1048
argchoice:No:
1049
argchoice:Yes:arb_textedit infile;
1050
1051
in:in1
1052
informat:genbank
1053
inmask:
1054
insave:
1055
1056
menu:Email
1057
1058
item:Blastn (Nucleic Acid)
1059
itemmethod:(echo PROGRAM blastn > in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo HISTOGRAM $PLOT >> in1.tmp; echo ALIGNMENTS $SCORE >> in1.tmp; echo SPLIT 100000 >> in1.tmp; echo BEGIN >> in1.tmp; readseq -i1 -p -f8 in1 >> in1.tmp; cat in1.tmp | /bin/mail blast@ncbi.nlm.nih.gov; rm in1 in1.tmp) &
1060
1061
arg:DBASE
1062
argtype:choice_menu
1063
arglabel:Which Database?
1064
argchoice:Non-redundant database:nr
1065
argchoice:GenBank DNA sequence database:genbank
1066
argchoice:GenBank update (cumulative daily updates):gbupdate
1067
argchoice:EMBL DNA sequence database:embl
1068
argchoice:EMBL update (cumulative weekly updates):emblu
1069
argchoice:Vector subset of GenBank:vector
1070
argchoice:Database of Expressed Sequence Tags (ESTs):dbest
1071
argchoice:Eukaryotic promoterdatabase:epd
1072
argchoice:Kabat's database of immunological interest:kabatnuc
1073
1074
arg:PLOT
1075
argtype:chooser
1076
arglabel:Display Histogram?
1077
argvalue:1
1078
argchoice:Yes:yes
1079
argchoice:No:no
1080
1081
arg:SCORE
1082
argtype:slider
1083
arglabel:Number of High Scoring Pairs Displayed?
1084
argmin:1
1085
argmax:250
1086
argvalue:5
1087
1088
in:in1
1089
informat:genbank
1090
insave:
1091
1092
item:Blastp (Protein)
1093
itemmethod:(echo PROGRAM blastp >in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo HISTOGRAM $PLOT >> in1.tmp; echo ALIGNMENTS $SCORE >> in1.tmp; echo MATRIX $MATRX >> in1.tmp; echo SPLIT 100000 >> in1.tmp; echo BEGIN >> in1.tmp; readseq -i1 -p -f8 in1 >> in1.tmp; cat in1.tmp | /bin/mail blast@ncbi.nlm.nih.gov; rm in1 in1.tmp) &
1094
1095
arg:DBASE
1096
argtype:choice_menu
1097
arglabel:Which Database?
1098
argchoice:Non-redundant protein database:nr
1099
argchoice:Swiss-Prot protein database:swissprot
1100
argchoice:PIR protein database:pir
1101
argchoice:Cumulative update to Swiss-Prot major release:spupdate
1102
argchoice:GenPept (translated GenBank):genpept
1103
argchoice:GenPept update (cumulative daily updates):gpupdate
1104
argchoice:Brookhaven PDB:pdb
1105
argchoice:Kabat's database of immunological interest:kabatnuc
1106
argchoice:Transcription Factors Database:tfd
1107
argchoice:6-frame translations of human Alu repeats:palu
1108
1109
arg:PLOT
1110
argtype:chooser
1111
arglabel:Display Histogram?
1112
argvalue:1
1113
argchoice:Yes:yes
1114
argchoice:No:no
1115
1116
arg:SCORE
1117
argtype:slider
1118
arglabel:Number of High Scoring Pairs Displayed
1119
argmin:1
1120
argmax:250
1121
argvalue:5
1122
1123
arg:Matrx
1124
argtype:chooser
1125
arglabel:Weighting matrix
1126
argchoice:PAM 250:PAM250
1127
argchoice:PAM 120:PAM10
1128
argchoice:PAM 40:PAM40
1129
argchoice:BLOSUM62:BLOSUM62
1130
1131
1132
in:in1
1133
informat:genbank
1134
insave:
1135
1136
item:Fasta (Nucleic Acid)
1137
itemmethod:(echo LIB $DBASE > in1.tmp; echo WORD $KPL >> in1.tmp; echo LIST $TOP >> in1.tmp; echo ALIGN $ALNG >> in1.tmp; echo ONE >> in1.tmp; echo SEQ >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp;Mail FASTA@EMBL-Heidelberg.de < in1.tmp; rm in1 in1.tmp) &
1138
1139
arg:DBASE
1140
argtype:choice_menu
1141
arglabel:Which Database?
1142
argchoice:GenBank Qrtly & Updates:GBALL
1143
argchoice:GenBank Updates:GBNEW
1144
argchoice:Entries only in GenBank, not in EMBL:GBONLY
1145
argchoice:GenBank and EMBL entries (latest releases):GENEMBL
1146
argchoice:New EMBL entries (Since latest release):EMNEW
1147
argchoice:All EMBL entries (latest release + new ones):EMALL
1148
argchoice:EMBL fungi division only:EFUN
1149
argchoice:EMBL invertebrates division only:EINV
1150
argchoice:EMBL mammals division only:EMAM
1151
argchoice:EMBL organelles division only:EORG
1152
argchoice:EMBL phages division only:EPHG
1153
argchoice:EMBL plants division only:EPLN
1154
argchoice:EMBL primates division only:EPRI
1155
argchoice:EMBL prokaryotes division only:EPRO
1156
argchoice:EMBL rodents division only:EROD
1157
argchoice:EMBL synthetic sequences division only:ESYN
1158
argchoice:EMBL unannotated division only:EUNA
1159
argchoice:EMBL viruses division only:EVRL
1160
argchoice:EMBL vertebrates division only:EVRT
1161
1162
1163
1164
arg:KPL
1165
argtype:slider
1166
arglabel:K-tuple window
1167
argmin:3
1168
argmax:6
1169
argvalue:4
1170
1171
arg:TOP
1172
argtype:slider
1173
arglabel:Scores Displayed?
1174
argmin:1
1175
argmax:200
1176
argvalue:100
1177
1178
arg:ALNG
1179
argtype:slider
1180
arglabel:# Alignments Displayed?
1181
argmin:1
1182
argmax:200
1183
argvalue:20
1184
1185
in:in1
1186
informat:flat
1187
insave:
1188
1189
item:Fasta (Protein)
1190
itemmethod:(echo LIB $DBASE > in1.tmp; echo WORD $TPL >> in1.tmp; echo LIST $SCRS >> in1.tmp; echo ALIGN $ALNMNTS >> in1.tmp; echo PROT >> in1.tmp; echo SEQ >> in1.tmp; sed "s/-//g" < in1 | tr '@%#$' '>' >> in1.tmp; Mail FASTA@EMBL-Heidelberg.de < in1.tmp; rm in1 in1.tmp) &
1191
1192
arg:DBASE
1193
argtype:choice_menu
1194
arglabel:Which Protein Database?
1195
argchoice:Swiss-Protein (latest release + new ones):SWALL
1196
argchoice:Swiss-Protein (since latest release):SWNEW
1197
argchoice:Swiss-Protein (latest release):SW
1198
argchoice:NBRF/PIR (latest release):NBRF
1199
argchoice:NBRF/PIR (not Swiss-Prot):PIRONLY
1200
argchoice:All Swiss-Prot and NBRF/PIR entries:SWISSPIRALL
1201
argchoice:PDB structure entries:BROOKHAVEN
1202
argchoice:PDB structure entries (NBRF version):NRL
1203
1204
arg:TPL
1205
argtype:slider
1206
arglabel:K-TUP window
1207
argmin:1
1208
argmax:2
1209
argvalue:1
1210
1211
arg:SCRS
1212
argtype:slider
1213
arglabel:# Scores Displayed?
1214
argmin:1
1215
argmax:200
1216
argvalue:100
1217
1218
arg:ALNMNTS
1219
argtype:slider
1220
arglabel:# Alignments Displayed?
1221
argmin:1
1222
argmax:200
1223
argvalue:20
1224
1225
in:in1
1226
informat:flat
1227
insave:
1228
1229
item:GeneID
1230
itemmethod:($REPRINT > in1.tmp; echo Genomic Sequence >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail geneid@darwin.bu.edu < in1.tmp; rm in1 in1.tmp) &
1231
1232
arg:REPRINT
1233
argtype:chooser
1234
arglabel:Do you want a GENEID reprint?
1235
argchoice:YES:echo "Preprint Request" >> in1.tmp
1236
argchoice:NO
1237
1238
in:in1
1239
informat:flat
1240
insave:
1241
1242
1243
1244
1245
1246
item:Sequence Retrieval
1247
itemmethod:(echo DATALIB $DBASE>> in1.tmp; echo MAXDOCS $NDOC >> in1.tmp;echo MAXLINES 100000 >> in1.tmp; echo BEGIN >> in1.tmp; echo $REGEXP >> in1.tmp; Mail retrieve@ncbi.nlm.nih.gov < in1.tmp; rm in1.tmp) &
1248
1249
arg:DBASE
1250
argtype:choice_menu
1251
arglabel:Which Database?
1252
argchoice:GenBank DNA sequence database:genbank
1253
argchoice:GenBank update (cumulative daily updates):gbupdate
1254
argchoice:EMBL DNA sequence database:embl
1255
argchoice:EMBL update (cumulative weekly updates):emblu
1256
argchoice:Vector subset of GenBank:vector
1257
argchoice:Database of Expressed Sequence Tags (ESTs):dbest
1258
argchoice:Swiss-Prot protein database:swissprot
1259
argchoice:PIR protein database:pir
1260
argchoice:GenPept (translated GenBank):genpept
1261
argchoice:GenPept update (cumulative daily updates):gpupdate
1262
argchoice:Transcription Factors Database:tfd
1263
1264
arg:NDOC
1265
argtype:slider
1266
arglabel:Number of Sequences Retrieved?
1267
argmin:1
1268
argmax:100
1269
argvalue:20
1270
1271
1272
arg:REGEXP
1273
argtype:text
1274
arglabel:key words, sequence IDs, boolean connectors
1275
1276
item:Grail
1277
itemmethod:(echo Sequences $TOTALSEQS $ID > in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail grail@ornl.gov <in1.tmp; rm in1 in1.tmp) &
1278
1279
arg:REGISTER
1280
argtype:chooser
1281
arglabel:Have you previously registered for Grail services?
1282
argchoice:YES
1283
argchoice:NO:echo "YOU MUST REGISTER"
1284
1285
arg:TOTALSEQS
1286
argtype:text
1287
arglabel:Number of Sequences Being Sent to Grail?
1288
1289
arg:ID
1290
argtype:text
1291
arglabel:User ID (MUST HAVE PREVIOUSLY REGISTERED)
1292
1293
in:in1
1294
informat:flat
1295
insave:
1296
1297
item:Grail Registration
1298
itemmethod:(echo Register > in1.tmp; echo $NAME >> in1.tmp; echo $ADDRESS >> in1.tmp; echo $PHONE >> in1.tmp; echo $EMAIL >> in1.tmp; Mail grail@ornl.gov < in1.tmp; rm in1.tmp)
1299
1300
arg:NAME
1301
argtype:text
1302
arglabel:Your Name
1303
1304
arg:ADDRESS
1305
argtype:text
1306
arglabel:Your Address
1307
1308
arg:PHONE
1309
argtype:text
1310
arglabel:Your Phone Number
1311
1312
arg:EMAIL
1313
argtype:text
1314
arglabel:Your E-Mail Address
1315
1316
Loggerhead is a web-based interface for Breezy
Version: 2.0.1