source: branches/help/GDEHELP/MENUS/align.menu

Last change on this file was 14622, checked in by westram, 9 years ago
  • reintegrates 'ui' into 'trunk'
    • implements #656
    • adds instant update for
      • next neighbour search
      • branch analysis (mark functions)
      • arb-phylo (filter setup)
  • adds: log:branches/ui@14588:14621
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 14.2 KB
Line 
1item:ProbCons
2itemmeta: P
3seqtype:*
4itemmethod:(GOTO_LOCAL_DIR; \
5            arb_sed 's/#/>HASH_/' <TmpInputFile | \
6            arb_sed 's/%/>PERCENT_/' | \
7            arb_sed 's/"/>QUOTE_/'| \
8            arb_sed 's/@/>AT_/' | \
9            arb_sed '/^[^>]/ y/./-/' > probcons_in; \
10            RUN_IN_WINDOW(($ARBHOME/bin/probcons -pre $PRE_TRAINING_REPS -ir $PASSES -c $REPS probcons_in > probcons_out;)); \
11            arb_sed 's/>HASH_/#/' <probcons_out | \
12            arb_sed 's/>PERCENT_/%/' | \
13            arb_sed 's/>QUOTE_/"/' | \
14            arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(probcons_in* probcons_out* TmpInputFile) )
15
16arg:REPS
17argtype:choice_menu
18arglabel:Passes of consistency transformation
19argtype:slider
20argmin:0
21argmax:5
22argvalue:2
23
24
25arg:PASSES
26arglabel:Passes of iterative refinement
27argtype:slider
28argmin:0
29argmax:1000
30argvalue:100
31
32arg:PRE_TRAINING_REPS
33arglabel:Rounds of pre-training before aligning the sequences
34argtype:slider
35argmin:0
36argmax:20
37argvalue:0
38
39in:TmpInputFile
40informat:flat
41intyped:detailed
42insave:
43
44out:TmpOutputFile
45outformat:flat
46outaligned:yes
47
48//----------------------------------------------------
49
50item:Muscle
51itemmeta: M
52seqtype:*
53itemmethod:(GOTO_LOCAL_DIR; \
54            arb_sed 's/#/>HASH_/' <TmpInputFile | \
55            arb_sed 's/%/>PERCENT_/' | \
56            arb_sed 's/"/>QUOTE_/'| \
57            arb_sed 's/@/>AT_/' | \
58            arb_sed '/^[^>]/ y/./-/' > muscle_in; \
59            RUN_IN_WINDOW(($ARBHOME/bin/muscle $SCORE $DIAGS $ANCHORS $DIMER $BRENNER -in muscle_in -out muscle_out -maxiters $MAXITERS;)); \
60            arb_sed 's/>HASH_/#/' <muscle_out | \
61            arb_sed 's/>PERCENT_/%/' | \
62            arb_sed 's/>QUOTE_/"/' | \
63            arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(muscle_in* muscle_out* TmpInputFile))
64
65arg:MAXITERS
66argtype:text
67arglabel:Maximum number of iterations to run\n(use 2 for large datasets)
68argtext:16
69
70//arg:ANCHORS
71//argtype:choice_menu
72//arglabel:Use anchor optimization in tree dependent refinement iterations
73//argchoice:Yes(default):-anchors
74//argchoice:No:-noanchors
75
76//arg:BRENNER
77//argtype:choice_menu
78//arglabel:Use Steven Brenner's method for computing the root alignment
79//argchoice:No(default):
80//argchoice:Yes:-brenner
81
82//arg:DIMER
83//argtype:choice_menu
84//arglabel:Use dimer approximation for the SP score\n(faster, slightly less accurate)
85//argchoice:No(default):
86//argchoice:Yes:-dimer
87
88//arg:DIAGS
89//argtype:choice_menu
90//arglabel:Use diagonal optimizations\n(faster, especially for closely related sequences,\nbut may be less accurate)
91//argchoice:No(default):
92//argchoice:Yes:-diags
93
94//arg:SCORE
95//argtype:choice_menu
96//arglabel:Scoring
97//argchoice:Log-expectation profile score (VTML240)(default):-le
98//argchoice:Sum-of-pairs protein profile score (PAM200):-sp
99//argchoice:Sum-of-pairs profile score (VTML240):-sv
100
101
102in:TmpInputFile
103informat:flat
104intyped:detailed
105insave:
106
107out:TmpOutputFile
108outformat:flat
109outaligned:yes
110
111//-------------------------------------------------------------------
112
113item:Mafft
114itemmeta: f
115seqtype:*
116itemmethod:(GOTO_LOCAL_DIR; \
117            arb_sed 's/#/>HASH_/' <TmpInputFile | \
118            arb_sed 's/%/>PERCENT_/' | \
119            arb_sed 's/"/>QUOTE_/'| \
120            arb_sed 's/@/>AT_/' | \
121            arb_sed '/^[^>]/ y/./-/' > mafft_in; \
122            RUN_IN_WINDOW(($ARBHOME/bin/$COMMAND $METHOD --preservecase --ep $OFFSET $SCORING_MATRIX mafft_in > mafft_out;)); \
123            arb_sed 's/>HASH_/#/' <mafft_out | \
124            arb_sed 's/>PERCENT_/%/' | \
125            arb_sed 's/>QUOTE_/"/' | \
126            arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(mafft_in* TmpInputFile mafft_out*))
127
128itemhelp:mafft.help
129
130
131arg:COMMAND
132argtype:choice_menu
133arglabel:Method
134argchoice:Auto:mafft --auto
135argchoice:L-INS-i:mafft-linsi
136argchoice:G-INS-i:mafft-ginsi
137argchoice:E-INS-i:mafft-einsi
138argchoice:Q-INS-i:mafft-qinsi
139argchoice:X-INS-i:mafft-xinsi
140argchoice:FFT-NS-i:mafft-fftnsi
141argchoice:FFT-NS-2:mafft-fftns
142argchoice:NW-NS-i:mafft-nwnsi
143argchoice:NW-NS-2:mafft-nwns
144
145arg:SCORING_MATRIX
146argtype:choice_menu
147arglabel:Scoring matrix
148argchoice:BLOSUM62:--bl 62
149argchoice:BLOSUM30:--bl 30
150argchoice:BLOSUM45:--bl 45
151argchoice:BLOSUM80:--bl 80
152argchoice:JTT100:--jtt 100
153argchoice:JTT200:--jtt 200
154argchoice:JTT200:--jtt 200
155argchoice:1PAM / K=2:--kimura 1
156argchoice:20PAM / K=2:--kimura 20
157argchoice:200PAM / K=2:--kimura 200
158
159
160arg:OFFSET
161argtype:slider
162argmin:0.0
163argmax:1.0
164arglabel:Offset value [0..1]\n(use values >0.1 for closely related sequences)
165argtext:0.5
166
167
168in:TmpInputFile
169informat:flat
170intyped:detailed
171insave:
172
173out:TmpOutputFile
174outformat:flat
175outaligned:yes
176
177//--------------------------------------------------------
178
179item:ClustalW automatic
180itemmeta: W
181seqtype:*
182itemmethod:(GOTO_LOCAL_DIR; \
183            tr '"%//' '>' <TmpInputFile >clus_in; \
184            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align ; \
185                           cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >TmpOutputFile; )); \
186            RM_LOCAL_FILES(clus_in* TmpInputFile))
187
188itemhelp:clustalw.help
189
190
191in:TmpInputFile
192informat:flat
193insave:
194
195out:TmpOutputFile
196outformat:flat
197outaligned:yes
198
199// --------------------------------------------------------------------------------
200
201item:Create ClustalW Profile 2
202itemmeta: C
203seqtype:*
204itemmethod:(GOTO_LOCAL_DIR ; tr '"%//' '>' <TmpInputFile >../clus_prf ; RM_LOCAL_FILES(TmpInputFile))
205
206itemhelp:clustalw.help
207
208in:TmpInputFile
209informat:flat
210insave:
211
212// --------------------------------------------------------------------------------
213
214item:ClustalW Profile Alignment
215itemmeta: A
216seqtype:*
217itemmethod:(GOTO_LOCAL_DIR; \
218            tr '"%//' '>' <TmpInputFile >clus_in; \
219            RUN_IN_WINDOW((clustalw -output=PIR -profile1=clus_in -profile2=../clus_prf -align ; \
220                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )); \
221            RM_LOCAL_FILES(clus_in* TmpInputFile))
222
223itemhelp:clustalw.help
224
225
226in:TmpInputFile
227informat:flat
228insave:
229
230out:TmpOutputFile
231outformat:flat
232outaligned:yes
233
234// --------------------------------------------------------------------------------
235
236item:ClustalW DNA Alignment (fast)
237seqtype: N
238itemmeta: N
239itemmethod:(GOTO_LOCAL_DIR; \
240            tr '"%//' '>' <TmpInputFile >clus_in ; \
241            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
242                                    -quicktree $INTERACTIVE \
243                                    -ktuple=$KTUPLE -topdiags=$TOPDIAGS \
244                                    -window=$WINDOW -pairgap=$PAIRGAP \
245                                    -score=$SCORE \
246                                    -type=DNA -transweight=$TRANSWEIGHT \
247                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
248                                    -dnamatrix=$DNAMATRIX; \
249                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | arb_sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
250           RM_LOCAL_FILES(clus_in* TmpInputFile))
251
252itemhelp:clustalw.help
253
254// parameters for fast pairwise alignment:
255
256arg:PAIRGAP
257arglabel:Gap penalty (pairwise ali)
258argtype:slider
259argmin:1
260argmax:500
261argvalue:5
262
263arg:KTUPLE
264arglabel:K-tuple size
265argtype:slider
266argmin:1
267argmax:4
268argvalue:2
269
270arg:TOPDIAGS
271arglabel:No. of top diagonals
272argtype:slider
273argmin:1
274argmax:50
275argvalue:4
276
277arg:WINDOW
278arglabel:Window size
279argtype:slider
280argmin:1
281argmax:50
282argvalue:4
283
284// parameters for multiple alignment:
285
286arg:DNAMATRIX
287argtype:choice_menu
288arglabel:Weighting matrix (multiple ali)
289argchoice:IUB:IUB
290argchoice:CLUSTALW:CLUSTALW
291
292arg:GOP
293argtype:slider
294arglabel:Gap Open Penalty
295argmin:0
296argmax:100
297argvalue:15
298
299arg:GEP
300arglabel:Gap Extend Penalty
301argtype:slider
302argmin:0
303argmax:10
304argvalue:6.66
305
306arg:MAXDIV
307arglabel:% identity for delay
308argtype:slider
309argmin:0
310argmax:100
311argvalue:30
312
313arg:TRANSWEIGHT
314arglabel:Transition weight
315argtype:slider
316argmin:0.0
317argmax:1.0
318argvalue:0.5
319
320arg:INTERACTIVE
321arglabel:Interactive
322argtype:choice_menu
323argchoice:No:
324argchoice:Yes:-interactive
325
326in:TmpInputFile
327informat:flat
328insave:
329
330out:TmpOutputFile
331outformat:flat
332outaligned:yes
333
334// --------------------------------------------------------------------------------
335
336item:ClustalW DNA Alignment (slow & accurate)
337seqtype: N
338itemmeta: s
339itemmethod:(GOTO_LOCAL_DIR; \
340            tr '"%//' '>' <TmpInputFile >clus_in ; \
341            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
342                                     $INTERACTIVE \
343                                    -pwdnamatrix=$PWDNAMATRIX \
344                                    -pwgapopen=$PWGOP -pwgapext=$PWGEP \
345                                    -type=DNA -transweight=$TRANSWEIGHT \
346                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
347                                    -dnamatrix=$DNAMATRIX; \
348                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
349            RM_LOCAL_FILES(clus_in* TmpInputFile))
350
351itemhelp:clustalw.help
352
353// parameters for pairwise alignment:
354
355arg:PWDNAMATRIX
356argtype:choice_menu
357arglabel:Weighting matrix (pairwise ali)
358argchoice:IUB:IUB
359argchoice:CLUSTALW:CLUSTALW
360
361arg:PWGOP
362argtype:slider
363arglabel:Gap Open Penalty
364argmin:0
365argmax:100
366argvalue:15
367
368arg:PWGEP
369arglabel:Gap Extend Penalty
370argtype:slider
371argmin:0
372argmax:10
373argvalue:6.66
374
375// parameters for multiple alignment:
376
377arg:DNAMATRIX
378argtype:choice_menu
379arglabel:Weighting matrix (multiple ali)
380argchoice:IUB:IUB
381argchoice:CLUSTALW:CLUSTALW
382
383arg:GOP
384argtype:slider
385arglabel:Gap Open Penalty
386argmin:0
387argmax:100
388argvalue:15
389
390arg:GEP
391arglabel:Gap Extend Penalty
392argtype:slider
393argmin:0
394argmax:10
395argvalue:6.66
396
397arg:MAXDIV
398arglabel:% identity for delay
399argtype:slider
400argmin:0
401argmax:100
402argvalue:30
403
404arg:TRANSWEIGHT
405arglabel:Transition weight
406argtype:slider
407argmin:0.0
408argmax:1.0
409argvalue:0.5
410
411arg:INTERACTIVE
412arglabel:Interactive
413argtype:choice_menu
414argchoice:No:
415argchoice:Yes:-interactive
416
417in:TmpInputFile
418informat:flat
419insave:
420
421out:TmpOutputFile
422outformat:flat
423outaligned:yes
424
425// --------------------------------------------------------------------------------
426
427item:ClustalW Protein Alignment (fast)
428seqtype: A
429itemmeta: o
430itemmethod:(GOTO_LOCAL_DIR; \
431            tr '"%//' '>' <TmpInputFile >clus_in ; \
432            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
433                                    -quicktree  $INTERACTIVE \
434                                    -ktuple=$KTUPLE -topdiags=$TOPDIAGS \
435                                    -window=$WINDOW -pairgap=$PAIRGAP \
436                                    -score=$SCORE \
437                                    -type=PROTEIN -transweight=$TRANSWEIGHT \
438                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
439                                    -matrix=$MATRIX $NEGMATRIX; \
440                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
441            RM_LOCAL_FILES(clus_in* TmpInputFile))
442
443itemhelp:clustalw.help
444
445// parameters for fast pairwise alignment:
446
447arg:PAIRGAP
448arglabel:Gap penalty (pairwise ali)
449argtype:slider
450argmin:1
451argmax:500
452argvalue:3
453
454arg:KTUPLE
455arglabel:K-tuple size
456argtype:slider
457argmin:1
458argmax:2
459argvalue:1
460
461arg:TOPDIAGS
462arglabel:No. of top diagonals
463argtype:slider
464argmin:1
465argmax:50
466argvalue:5
467
468arg:WINDOW
469arglabel:Window size
470argtype:slider
471argmin:1
472argmax:50
473argvalue:5
474
475// parameters for multiple alignment:
476
477arg:MATRIX
478argtype:choice_menu
479arglabel:Weighting matrix (multiple ali)
480argchoice:Gonnet series:GONNET
481argchoice:Blosum series:BLOSUM
482argchoice:PAM series:PAM
483argchoice:ID matrix:ID
484
485arg:GOP
486argtype:slider
487arglabel:Gap Open Penalty
488argmin:0
489argmax:100
490argvalue:10
491
492arg:GEP
493arglabel:Gap Extend Penalty
494argtype:slider
495argmin:0
496argmax:10
497argvalue:0.2
498
499arg:MAXDIV
500arglabel:% identity for delay
501argtype:slider
502argmin:0
503argmax:100
504argvalue:30
505
506arg:TRANSWEIGHT
507arglabel:Transition weight
508argtype:slider
509argmin:0.0
510argmax:1.0
511argvalue:0.5
512
513arg:NEGMATRIX
514arglabel:Use negative matrix
515argtype:choice_menu
516argchoice:No:
517argchoice:Yes:-negative
518
519arg:INTERACTIVE
520arglabel:Interactive
521argtype:choice_menu
522argchoice:No:
523argchoice:Yes:-interactive
524
525in:TmpInputFile
526informat:flat
527insave:
528
529out:TmpOutputFile
530outformat:flat
531outaligned:yes
532
533// --------------------------------------------------------------------------------
534
535item:ClustalW Protein Alignment (slow & accurate)
536seqtype: A
537itemmeta: l
538itemmethod:(GOTO_LOCAL_DIR; \
539            tr '"%//' '>' <TmpInputFile >clus_in ; \
540            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
541                                     $INTERACTIVE \
542                                    -pwmatrix=$PWMATRIX \
543                                    -pwgapopen=$PWGOP -pwgapext=$PWGEP \
544                                    -type=PROTEIN -transweight=$TRANSWEIGHT \
545                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
546                                    -matrix=$MATRIX $NEGMATRIX; \
547                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
548            RM_LOCAL_FILES(clus_in* TmpInputFile))
549
550itemhelp:clustalw.help
551
552// parameters for pairwise alignment:
553
554arg:PWMATRIX
555argtype:choice_menu
556arglabel:Weighting matrix (pairwise ali)
557argchoice:Gonnet series:GONNET
558argchoice:Blosum series:BLOSUM
559argchoice:PAM series:PAM
560argchoice:ID matrix:ID
561
562arg:PWGOP
563argtype:slider
564arglabel:Gap Open Penalty
565argmin:0
566argmax:100
567argvalue:10
568
569arg:PWGEP
570arglabel:Gap Extend Penalty
571argtype:slider
572argmin:0
573argmax:10
574argvalue:0.1
575
576// parameters for multiple alignment:
577
578arg:MATRIX
579argtype:choice_menu
580arglabel:Weighting matrix (multiple ali)
581argchoice:Gonnet series:GONNET
582argchoice:Blosum series:BLOSUM
583argchoice:PAM series:PAM
584argchoice:ID matrix:ID
585
586arg:GOP
587argtype:slider
588arglabel:Gap Open Penalty
589argmin:0
590argmax:100
591argvalue:10
592
593arg:GEP
594arglabel:Gap Extend Penalty
595argtype:slider
596argmin:0
597argmax:10
598argvalue:0.2
599
600arg:MAXDIV
601arglabel:% identity for delay
602argtype:slider
603argmin:0
604argmax:100
605argvalue:30
606
607arg:TRANSWEIGHT
608arglabel:Transition weight
609argtype:slider
610argmin:0.0
611argmax:1.0
612argvalue:0.5
613
614arg:NEGMATRIX
615arglabel:Use negative matrix
616argtype:choice_menu
617argchoice:No:
618argchoice:Yes:-negative
619
620arg:INTERACTIVE
621arglabel:Interactive
622argtype:choice_menu
623argchoice:No:
624argchoice:Yes:-interactive
625
626in:TmpInputFile
627informat:flat
628insave:
629
630out:TmpOutputFile
631outformat:flat
632outaligned:yes
633
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