source: tags/arb-6.0.2/GDEHELP/MENUS/align.menu

Last change on this file was 11874, checked in by westram, 12 years ago
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 14.7 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 $REPS probcons_in > probcons_out;)); \
11            arb_sed 's/>HASH_/#/' <probcons_out | \
12            arb_sed 's/>PERCENT_/%/' | \
13            arb_sed 's/>QUOTE_/"/' | \
14            arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(probcons_in* probcons_out* TmpInputFile) )
15
16arg:REPS
17argtype:choice_menu
18arglabel:Passes of consistency transformation
19argtype:slider
20argmin:0
21argmax:5
22argvalue:2
23
24
25arg:PASSES
26arglabel:Passes of iterative refinement
27argtype:slider
28argmin:0
29argmax:1000
30argvalue:100
31
32arg:PRE_TRAINING_REPS
33arglabel:Rounds of pre-training before aligning the sequences
34argtype:slider
35argmin:0
36argmax:20
37argvalue:0
38
39in:TmpInputFile
40informat:flat
41intyped:detailed
42insave:
43
44out:TmpOutputFile
45outformat:flat
46
47//----------------------------------------------------
48
49item:Muscle
50itemmeta: M
51seqtype:*
52itemmethod:(GOTO_LOCAL_DIR; \
53            arb_sed 's/#/>HASH_/' <TmpInputFile | \
54            arb_sed 's/%/>PERCENT_/' | \
55            arb_sed 's/"/>QUOTE_/'| \
56            arb_sed 's/@/>AT_/' | \
57            arb_sed '/^[^>]/ y/./-/' > muscle_in; \
58            RUN_IN_WINDOW(($ARBHOME/bin/muscle $SCORE $DIAGS $ANCHORS $DIMER $BRENNER -in muscle_in -out muscle_out -maxiters $MAXITERS;)); \
59            arb_sed 's/>HASH_/#/' <muscle_out | \
60            arb_sed 's/>PERCENT_/%/' | \
61            arb_sed 's/>QUOTE_/"/' | \
62            arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(muscle_in* muscle_out* TmpInputFile))
63
64arg:MAXITERS
65argtype:text
66arglabel:Maximum number of iterations to run(Use 2 for large datasets)
67argtext:16
68
69//arg:ANCHORS
70//argtype:choice_menu
71//arglabel:Use anchor optimization in tree dependent refinement iterations
72//argchoice:Yes(default):-anchors
73//argchoice:No:-noanchors
74
75//arg:BRENNER
76//argtype:choice_menu
77//arglabel:Use Steven Brenner's method for computing the root alignment
78//argchoice:No(default):
79//argchoice:Yes:-brenner
80
81//arg:DIMER
82//argtype:choice_menu
83//arglabel:Use dimer approximation for the SP score\n(faster, slightly less accurate)
84//argchoice:No(default):
85//argchoice:Yes:-dimer
86
87//arg:DIAGS
88//argtype:choice_menu
89//arglabel:Use diagonal optimizations\n(faster, especially for closely related sequences,\nbut may be less accurate)
90//argchoice:No(default):
91//argchoice:Yes:-diags
92
93//arg:SCORE
94//argtype:choice_menu
95//arglabel:Scoring
96//argchoice:Log-expectation profile score (VTML240)(default):-le
97//argchoice:Sum-of-pairs protein profile score (PAM200):-sp
98//argchoice:Sum-of-pairs profile score (VTML240):-sv
99
100
101in:TmpInputFile
102informat:flat
103intyped:detailed
104insave:
105
106out:TmpOutputFile
107outformat:flat
108
109//-------------------------------------------------------------------
110
111item:Mafft
112itemmeta: f
113seqtype:*
114itemmethod:(GOTO_LOCAL_DIR; \
115            arb_sed 's/#/>HASH_/' <TmpInputFile | \
116            arb_sed 's/%/>PERCENT_/' | \
117            arb_sed 's/"/>QUOTE_/'| \
118            arb_sed 's/@/>AT_/' | \
119            arb_sed '/^[^>]/ y/./-/' > mafft_in; \
120            RUN_IN_WINDOW(($ARBHOME/bin/$COMMAND $METHOD --preservecase --ep $OFFSET $SCORING_MATRIX mafft_in > mafft_out;)); \
121            arb_sed 's/>HASH_/#/' <mafft_out | \
122            arb_sed 's/>PERCENT_/%/' | \
123            arb_sed 's/>QUOTE_/"/' | \
124            arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(mafft_in* TmpInputFile mafft_out*))
125
126itemhelp:mafft.help
127
128
129arg:COMMAND
130argtype:choice_menu
131arglabel:Method
132argchoice:Auto:mafft --auto
133argchoice:L-INS-i:mafft-linsi
134argchoice:G-INS-i:mafft-ginsi
135argchoice:E-INS-i:mafft-einsi
136argchoice:Q-INS-i:mafft-qinsi
137argchoice:X-INS-i:mafft-xinsi
138argchoice:FFT-NS-i:mafft-fftnsi
139argchoice:FFT-NS-2:mafft-fftns
140argchoice:NW-NS-i:mafft-nwnsi
141argchoice:NW-NS-2:mafft-nwns
142
143arg:SCORING_MATRIX
144argtype:choice_menu
145arglabel:Scoring matrix
146argchoice:BLOSUM62:--bl 62
147argchoice:BLOSUM30:--bl 30
148argchoice:BLOSUM45:--bl 45
149argchoice:BLOSUM80:--bl 80
150argchoice:JTT100:--jtt 100
151argchoice:JTT200:--jtt 200
152argchoice:JTT200:--jtt 200
153argchoice:1PAM / K=2:--kimura 1
154argchoice:20PAM / K=2:--kimura 20
155argchoice:200PAM / K=2:--kimura 200
156
157
158arg:OFFSET
159argtype:text
160arglabel:Offset value [0..1]\n(Use Values >0.1 for closely related sequences)
161argtext:0.5
162
163
164in:TmpInputFile
165informat:flat
166intyped:detailed
167insave:
168
169out:TmpOutputFile
170outformat:flat
171
172//--------------------------------------------------------
173
174item:ClustalW automatic
175itemmeta: W
176seqtype:*
177itemmethod:(GOTO_LOCAL_DIR; \
178            tr '"%//' '>' <TmpInputFile >clus_in; \
179            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align ; \
180                           cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >TmpOutputFile; )); \
181            RM_LOCAL_FILES(clus_in* TmpInputFile))
182
183itemhelp:clustalw.help
184
185
186in:TmpInputFile
187informat:flat
188insave:
189
190out:TmpOutputFile
191outformat:flat
192
193// --------------------------------------------------------------------------------
194
195item:Create ClustalW Profile 2
196itemmeta: C
197seqtype:*
198itemmethod:(GOTO_LOCAL_DIR ; tr '"%//' '>' <TmpInputFile >../clus_prf ; RM_LOCAL_FILES(TmpInputFile))
199
200itemhelp:clustalw.help
201
202in:TmpInputFile
203informat:flat
204insave:
205
206// --------------------------------------------------------------------------------
207
208item:ClustalW Profile Alignment
209itemmeta: A
210seqtype:*
211itemmethod:(GOTO_LOCAL_DIR; \
212            tr '"%//' '>' <TmpInputFile >clus_in; \
213            RUN_IN_WINDOW((clustalw -output=PIR -profile1=clus_in -profile2=../clus_prf -align ; \
214                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )); \
215            RM_LOCAL_FILES(clus_in* TmpInputFile))
216
217itemhelp:clustalw.help
218
219
220in:TmpInputFile
221informat:flat
222insave:
223
224out:TmpOutputFile
225outformat:flat
226
227// --------------------------------------------------------------------------------
228
229item:ClustalW DNA Alignment (fast)
230seqtype: N
231itemmeta: N
232itemmethod:(GOTO_LOCAL_DIR; \
233            tr '"%//' '>' <TmpInputFile >clus_in ; \
234            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
235                                    -quicktree $INTERACTIVE \
236                                    -ktuple=$KTUPLE -topdiags=$TOPDIAGS \
237                                    -window=$WINDOW -pairgap=$PAIRGAP \
238                                    -score=$SCORE \
239                                    -type=DNA -transweight=$TRANSWEIGHT \
240                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
241                                    -dnamatrix=$DNAMATRIX; \
242                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | arb_sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
243           RM_LOCAL_FILES(clus_in* TmpInputFile))
244
245itemhelp:clustalw.help
246
247// parameters for fast pairwise alignment:
248
249arg:PAIRGAP
250arglabel:Gap penalty (pairwise ali)
251argtype:slider
252argmin:1
253argmax:500
254argvalue:5
255
256arg:KTUPLE
257arglabel:K-tuple size
258argtype:slider
259argmin:1
260argmax:4
261argvalue:2
262
263arg:TOPDIAGS
264arglabel:No. of top diagonals
265argtype:slider
266argmin:1
267argmax:50
268argvalue:4
269
270arg:WINDOW
271arglabel:Window size
272argtype:slider
273argmin:1
274argmax:50
275argvalue:4
276
277// parameters for multiple alignment:
278
279arg:DNAMATRIX
280argtype:choice_menu
281arglabel:Weighting matrix (multiple ali)
282argchoice:IUB:IUB
283argchoice:CLUSTALW:CLUSTALW
284
285arg:GOP
286argtype:slider
287arglabel:Gap Open Penalty
288argmin:0
289argmax:100
290argvalue:15
291
292arg:GEP
293arglabel:Gap Extend Penalty
294argtype:slider
295argmin:0
296argmax:10
297argvalue:6.66
298
299arg:MAXDIV
300arglabel:% identity for delay
301argtype:slider
302argmin:0
303argmax:100
304argvalue:30
305
306arg:TRANSWEIGHT
307arglabel:Transition weight
308argtype:slider
309argmin:0.0
310argmax:1.0
311argvalue:0.5
312
313arg:INTERACTIVE
314arglabel:Interactive
315argtype:choice_menu
316argchoice:No:
317argchoice:Yes:-interactive
318
319in:TmpInputFile
320informat:flat
321insave:
322
323out:TmpOutputFile
324outformat:flat
325
326// --------------------------------------------------------------------------------
327
328item:ClustalW DNA Alignment (slow & accurate)
329seqtype: N
330itemmeta: s
331itemmethod:(GOTO_LOCAL_DIR; \
332            tr '"%//' '>' <TmpInputFile >clus_in ; \
333            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
334                                     $INTERACTIVE \
335                                    -pwdnamatrix=$PWDNAMATRIX \
336                                    -pwgapopen=$PWGOP -pwgapext=$PWGEP \
337                                    -type=DNA -transweight=$TRANSWEIGHT \
338                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
339                                    -dnamatrix=$DNAMATRIX; \
340                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
341            RM_LOCAL_FILES(clus_in* TmpInputFile))
342
343itemhelp:clustalw.help
344
345// parameters for pairwise alignment:
346
347arg:PWDNAMATRIX
348argtype:choice_menu
349arglabel:Weighting matrix (pairwise ali)
350argchoice:IUB:IUB
351argchoice:CLUSTALW:CLUSTALW
352
353arg:PWGOP
354argtype:slider
355arglabel:Gap Open Penalty
356argmin:0
357argmax:100
358argvalue:15
359
360arg:PWGEP
361arglabel:Gap Extend Penalty
362argtype:slider
363argmin:0
364argmax:10
365argvalue:6.66
366
367// parameters for multiple alignment:
368
369arg:DNAMATRIX
370argtype:choice_menu
371arglabel:Weighting matrix (multiple ali)
372argchoice:IUB:IUB
373argchoice:CLUSTALW:CLUSTALW
374
375arg:GOP
376argtype:slider
377arglabel:Gap Open Penalty
378argmin:0
379argmax:100
380argvalue:15
381
382arg:GEP
383arglabel:Gap Extend Penalty
384argtype:slider
385argmin:0
386argmax:10
387argvalue:6.66
388
389arg:MAXDIV
390arglabel:% identity for delay
391argtype:slider
392argmin:0
393argmax:100
394argvalue:30
395
396arg:TRANSWEIGHT
397arglabel:Transition weight
398argtype:slider
399argmin:0.0
400argmax:1.0
401argvalue:0.5
402
403arg:INTERACTIVE
404arglabel:Interactive
405argtype:choice_menu
406argchoice:No:
407argchoice:Yes:-interactive
408
409in:TmpInputFile
410informat:flat
411insave:
412
413out:TmpOutputFile
414outformat:flat
415
416// --------------------------------------------------------------------------------
417
418item:ClustalW Protein Alignment (fast)
419seqtype: A
420itemmeta: o
421itemmethod:(GOTO_LOCAL_DIR; \
422            tr '"%//' '>' <TmpInputFile >clus_in ; \
423            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
424                                    -quicktree  $INTERACTIVE \
425                                    -ktuple=$KTUPLE -topdiags=$TOPDIAGS \
426                                    -window=$WINDOW -pairgap=$PAIRGAP \
427                                    -score=$SCORE \
428                                    -type=PROTEIN -transweight=$TRANSWEIGHT \
429                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
430                                    -matrix=$MATRIX $NEGMATRIX; \
431                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
432            RM_LOCAL_FILES(clus_in* TmpInputFile))
433
434itemhelp:clustalw.help
435
436// parameters for fast pairwise alignment:
437
438arg:PAIRGAP
439arglabel:Gap penalty (pairwise ali)
440argtype:slider
441argmin:1
442argmax:500
443argvalue:3
444
445arg:KTUPLE
446arglabel:K-tuple size
447argtype:slider
448argmin:1
449argmax:2
450argvalue:1
451
452arg:TOPDIAGS
453arglabel:No. of top diagonals
454argtype:slider
455argmin:1
456argmax:50
457argvalue:5
458
459arg:WINDOW
460arglabel:Window size
461argtype:slider
462argmin:1
463argmax:50
464argvalue:5
465
466// parameters for multiple alignment:
467
468arg:MATRIX
469argtype:choice_menu
470arglabel:Weighting matrix (multiple ali)
471argchoice:Gonnet series:GONNET
472argchoice:Blosum series:BLOSUM
473argchoice:PAM series:PAM
474argchoice:ID matrix:ID
475
476arg:GOP
477argtype:slider
478arglabel:Gap Open Penalty
479argmin:0
480argmax:100
481argvalue:10
482
483arg:GEP
484arglabel:Gap Extend Penalty
485argtype:slider
486argmin:0
487argmax:10
488argvalue:0.2
489
490arg:MAXDIV
491arglabel:% identity for delay
492argtype:slider
493argmin:0
494argmax:100
495argvalue:30
496
497arg:TRANSWEIGHT
498arglabel:Transition weight
499argtype:slider
500argmin:0.0
501argmax:1.0
502argvalue:0.5
503
504arg:NEGMATRIX
505arglabel:Use negative matrix
506argtype:choice_menu
507argchoice:No:
508argchoice:Yes:-negative
509
510arg:INTERACTIVE
511arglabel:Interactive
512argtype:choice_menu
513argchoice:No:
514argchoice:Yes:-interactive
515
516in:TmpInputFile
517informat:flat
518insave:
519
520out:TmpOutputFile
521outformat:flat
522
523// --------------------------------------------------------------------------------
524
525item:ClustalW Protein Alignment (slow & accurate)
526seqtype: A
527itemmeta: l
528itemmethod:(GOTO_LOCAL_DIR; \
529            tr '"%//' '>' <TmpInputFile >clus_in ; \
530            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
531                                     $INTERACTIVE \
532                                    -pwmatrix=$PWMATRIX \
533                                    -pwgapopen=$PWGOP -pwgapext=$PWGEP \
534                                    -type=PROTEIN -transweight=$TRANSWEIGHT \
535                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
536                                    -matrix=$MATRIX $NEGMATRIX; \
537                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
538            RM_LOCAL_FILES(clus_in* TmpInputFile))
539
540itemhelp:clustalw.help
541
542// parameters for pairwise alignment:
543
544arg:PWMATRIX
545argtype:choice_menu
546arglabel:Weighting matrix (pairwise ali)
547argchoice:Gonnet series:GONNET
548argchoice:Blosum series:BLOSUM
549argchoice:PAM series:PAM
550argchoice:ID matrix:ID
551
552arg:PWGOP
553argtype:slider
554arglabel:Gap Open Penalty
555argmin:0
556argmax:100
557argvalue:10
558
559arg:PWGEP
560arglabel:Gap Extend Penalty
561argtype:slider
562argmin:0
563argmax:10
564argvalue:0.1
565
566// parameters for multiple alignment:
567
568arg:MATRIX
569argtype:choice_menu
570arglabel:Weighting matrix (multiple ali)
571argchoice:Gonnet series:GONNET
572argchoice:Blosum series:BLOSUM
573argchoice:PAM series:PAM
574argchoice:ID matrix:ID
575
576arg:GOP
577argtype:slider
578arglabel:Gap Open Penalty
579argmin:0
580argmax:100
581argvalue:10
582
583arg:GEP
584arglabel:Gap Extend Penalty
585argtype:slider
586argmin:0
587argmax:10
588argvalue:0.2
589
590arg:MAXDIV
591arglabel:% identity for delay
592argtype:slider
593argmin:0
594argmax:100
595argvalue:30
596
597arg:TRANSWEIGHT
598arglabel:Transition weight
599argtype:slider
600argmin:0.0
601argmax:1.0
602argvalue:0.5
603
604arg:NEGMATRIX
605arglabel:Use negative matrix
606argtype:choice_menu
607argchoice:No:
608argchoice:Yes:-negative
609
610arg:INTERACTIVE
611arglabel:Interactive
612argtype:choice_menu
613argchoice:No:
614argchoice:Yes:-interactive
615
616in:TmpInputFile
617informat:flat
618insave:
619
620out:TmpOutputFile
621outformat:flat
622
623// --------------------------------------------------------------------------------
624
625item:Assemble Contigs
626itemmeta: g
627seqtype:*
628itemmethod: ( GOTO_LOCAL_DIR; \
629              tr '"%//' '>' <TmpInputFile > tr.out; \
630              CAP2 tr.out $OVERLAP $PMATCH >  TmpOutputFile; \
631              RM_LOCAL_FILES(TmpInputFile tr.out) )
632itemhelp:CAP2.help
633
634arg:OVERLAP
635argtype:slider
636arglabel:Minimum overlap?
637argmin:5
638argmax:100
639argvalue:20
640
641arg:PMATCH
642argtype:slider
643arglabel:Percent match required within overlap
644argmin:25
645argmax:100
646argvalue:90
647
648in:TmpInputFile
649informat:flat
650insave:
651
652out:TmpOutputFile
653outformat:gde
654
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