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

Last change on this file was 12834, checked in by westram, 10 years ago
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 14.8 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 $MAXITERS;)); \
60            arb_sed 's/>HASH_/#/' <muscle_out | \
61            arb_sed 's/>PERCENT_/%/' | \
62            arb_sed 's/>QUOTE_/"/' | \
63            arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(muscle_in* muscle_out* TmpInputFile))
64
65arg:MAXITERS
66argtype:text
67arglabel:Maximum number of iterations to run(Use 2 for large datasets)
68argtext:16
69
70//arg:ANCHORS
71//argtype:choice_menu
72//arglabel:Use anchor optimization in tree dependent refinement iterations
73//argchoice:Yes(default):-anchors
74//argchoice:No:-noanchors
75
76//arg:BRENNER
77//argtype:choice_menu
78//arglabel:Use Steven Brenner's method for computing the root alignment
79//argchoice:No(default):
80//argchoice:Yes:-brenner
81
82//arg:DIMER
83//argtype:choice_menu
84//arglabel:Use dimer approximation for the SP score\n(faster, slightly less accurate)
85//argchoice:No(default):
86//argchoice:Yes:-dimer
87
88//arg:DIAGS
89//argtype:choice_menu
90//arglabel:Use diagonal optimizations\n(faster, especially for closely related sequences,\nbut may be less accurate)
91//argchoice:No(default):
92//argchoice:Yes:-diags
93
94//arg:SCORE
95//argtype:choice_menu
96//arglabel:Scoring
97//argchoice:Log-expectation profile score (VTML240)(default):-le
98//argchoice:Sum-of-pairs protein profile score (PAM200):-sp
99//argchoice:Sum-of-pairs profile score (VTML240):-sv
100
101
102in:TmpInputFile
103informat:flat
104intyped:detailed
105insave:
106
107out:TmpOutputFile
108outformat:flat
109outaligned:yes
110
111//-------------------------------------------------------------------
112
113item:Mafft
114itemmeta: f
115seqtype:*
116itemmethod:(GOTO_LOCAL_DIR; \
117            arb_sed 's/#/>HASH_/' <TmpInputFile | \
118            arb_sed 's/%/>PERCENT_/' | \
119            arb_sed 's/"/>QUOTE_/'| \
120            arb_sed 's/@/>AT_/' | \
121            arb_sed '/^[^>]/ y/./-/' > mafft_in; \
122            RUN_IN_WINDOW(($ARBHOME/bin/$COMMAND $METHOD --preservecase --ep $OFFSET $SCORING_MATRIX mafft_in > mafft_out;)); \
123            arb_sed 's/>HASH_/#/' <mafft_out | \
124            arb_sed 's/>PERCENT_/%/' | \
125            arb_sed 's/>QUOTE_/"/' | \
126            arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(mafft_in* TmpInputFile mafft_out*))
127
128itemhelp:mafft.help
129
130
131arg:COMMAND
132argtype:choice_menu
133arglabel:Method
134argchoice:Auto:mafft --auto
135argchoice:L-INS-i:mafft-linsi
136argchoice:G-INS-i:mafft-ginsi
137argchoice:E-INS-i:mafft-einsi
138argchoice:Q-INS-i:mafft-qinsi
139argchoice:X-INS-i:mafft-xinsi
140argchoice:FFT-NS-i:mafft-fftnsi
141argchoice:FFT-NS-2:mafft-fftns
142argchoice:NW-NS-i:mafft-nwnsi
143argchoice:NW-NS-2:mafft-nwns
144
145arg:SCORING_MATRIX
146argtype:choice_menu
147arglabel:Scoring matrix
148argchoice:BLOSUM62:--bl 62
149argchoice:BLOSUM30:--bl 30
150argchoice:BLOSUM45:--bl 45
151argchoice:BLOSUM80:--bl 80
152argchoice:JTT100:--jtt 100
153argchoice:JTT200:--jtt 200
154argchoice:JTT200:--jtt 200
155argchoice:1PAM / K=2:--kimura 1
156argchoice:20PAM / K=2:--kimura 20
157argchoice:200PAM / K=2:--kimura 200
158
159
160arg:OFFSET
161argtype:text
162arglabel:Offset value [0..1]\n(Use Values >0.1 for closely related sequences)
163argtext:0.5
164
165
166in:TmpInputFile
167informat:flat
168intyped:detailed
169insave:
170
171out:TmpOutputFile
172outformat:flat
173outaligned:yes
174
175//--------------------------------------------------------
176
177item:ClustalW automatic
178itemmeta: W
179seqtype:*
180itemmethod:(GOTO_LOCAL_DIR; \
181            tr '"%//' '>' <TmpInputFile >clus_in; \
182            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align ; \
183                           cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >TmpOutputFile; )); \
184            RM_LOCAL_FILES(clus_in* TmpInputFile))
185
186itemhelp:clustalw.help
187
188
189in:TmpInputFile
190informat:flat
191insave:
192
193out:TmpOutputFile
194outformat:flat
195outaligned:yes
196
197// --------------------------------------------------------------------------------
198
199item:Create ClustalW Profile 2
200itemmeta: C
201seqtype:*
202itemmethod:(GOTO_LOCAL_DIR ; tr '"%//' '>' <TmpInputFile >../clus_prf ; RM_LOCAL_FILES(TmpInputFile))
203
204itemhelp:clustalw.help
205
206in:TmpInputFile
207informat:flat
208insave:
209
210// --------------------------------------------------------------------------------
211
212item:ClustalW Profile Alignment
213itemmeta: A
214seqtype:*
215itemmethod:(GOTO_LOCAL_DIR; \
216            tr '"%//' '>' <TmpInputFile >clus_in; \
217            RUN_IN_WINDOW((clustalw -output=PIR -profile1=clus_in -profile2=../clus_prf -align ; \
218                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )); \
219            RM_LOCAL_FILES(clus_in* TmpInputFile))
220
221itemhelp:clustalw.help
222
223
224in:TmpInputFile
225informat:flat
226insave:
227
228out:TmpOutputFile
229outformat:flat
230outaligned:yes
231
232// --------------------------------------------------------------------------------
233
234item:ClustalW DNA Alignment (fast)
235seqtype: N
236itemmeta: N
237itemmethod:(GOTO_LOCAL_DIR; \
238            tr '"%//' '>' <TmpInputFile >clus_in ; \
239            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
240                                    -quicktree $INTERACTIVE \
241                                    -ktuple=$KTUPLE -topdiags=$TOPDIAGS \
242                                    -window=$WINDOW -pairgap=$PAIRGAP \
243                                    -score=$SCORE \
244                                    -type=DNA -transweight=$TRANSWEIGHT \
245                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
246                                    -dnamatrix=$DNAMATRIX; \
247                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | arb_sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
248           RM_LOCAL_FILES(clus_in* TmpInputFile))
249
250itemhelp:clustalw.help
251
252// parameters for fast pairwise alignment:
253
254arg:PAIRGAP
255arglabel:Gap penalty (pairwise ali)
256argtype:slider
257argmin:1
258argmax:500
259argvalue:5
260
261arg:KTUPLE
262arglabel:K-tuple size
263argtype:slider
264argmin:1
265argmax:4
266argvalue:2
267
268arg:TOPDIAGS
269arglabel:No. of top diagonals
270argtype:slider
271argmin:1
272argmax:50
273argvalue:4
274
275arg:WINDOW
276arglabel:Window size
277argtype:slider
278argmin:1
279argmax:50
280argvalue:4
281
282// parameters for multiple alignment:
283
284arg:DNAMATRIX
285argtype:choice_menu
286arglabel:Weighting matrix (multiple ali)
287argchoice:IUB:IUB
288argchoice:CLUSTALW:CLUSTALW
289
290arg:GOP
291argtype:slider
292arglabel:Gap Open Penalty
293argmin:0
294argmax:100
295argvalue:15
296
297arg:GEP
298arglabel:Gap Extend Penalty
299argtype:slider
300argmin:0
301argmax:10
302argvalue:6.66
303
304arg:MAXDIV
305arglabel:% identity for delay
306argtype:slider
307argmin:0
308argmax:100
309argvalue:30
310
311arg:TRANSWEIGHT
312arglabel:Transition weight
313argtype:slider
314argmin:0.0
315argmax:1.0
316argvalue:0.5
317
318arg:INTERACTIVE
319arglabel:Interactive
320argtype:choice_menu
321argchoice:No:
322argchoice:Yes:-interactive
323
324in:TmpInputFile
325informat:flat
326insave:
327
328out:TmpOutputFile
329outformat:flat
330outaligned:yes
331
332// --------------------------------------------------------------------------------
333
334item:ClustalW DNA Alignment (slow & accurate)
335seqtype: N
336itemmeta: s
337itemmethod:(GOTO_LOCAL_DIR; \
338            tr '"%//' '>' <TmpInputFile >clus_in ; \
339            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
340                                     $INTERACTIVE \
341                                    -pwdnamatrix=$PWDNAMATRIX \
342                                    -pwgapopen=$PWGOP -pwgapext=$PWGEP \
343                                    -type=DNA -transweight=$TRANSWEIGHT \
344                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
345                                    -dnamatrix=$DNAMATRIX; \
346                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
347            RM_LOCAL_FILES(clus_in* TmpInputFile))
348
349itemhelp:clustalw.help
350
351// parameters for pairwise alignment:
352
353arg:PWDNAMATRIX
354argtype:choice_menu
355arglabel:Weighting matrix (pairwise ali)
356argchoice:IUB:IUB
357argchoice:CLUSTALW:CLUSTALW
358
359arg:PWGOP
360argtype:slider
361arglabel:Gap Open Penalty
362argmin:0
363argmax:100
364argvalue:15
365
366arg:PWGEP
367arglabel:Gap Extend Penalty
368argtype:slider
369argmin:0
370argmax:10
371argvalue:6.66
372
373// parameters for multiple alignment:
374
375arg:DNAMATRIX
376argtype:choice_menu
377arglabel:Weighting matrix (multiple ali)
378argchoice:IUB:IUB
379argchoice:CLUSTALW:CLUSTALW
380
381arg:GOP
382argtype:slider
383arglabel:Gap Open Penalty
384argmin:0
385argmax:100
386argvalue:15
387
388arg:GEP
389arglabel:Gap Extend Penalty
390argtype:slider
391argmin:0
392argmax:10
393argvalue:6.66
394
395arg:MAXDIV
396arglabel:% identity for delay
397argtype:slider
398argmin:0
399argmax:100
400argvalue:30
401
402arg:TRANSWEIGHT
403arglabel:Transition weight
404argtype:slider
405argmin:0.0
406argmax:1.0
407argvalue:0.5
408
409arg:INTERACTIVE
410arglabel:Interactive
411argtype:choice_menu
412argchoice:No:
413argchoice:Yes:-interactive
414
415in:TmpInputFile
416informat:flat
417insave:
418
419out:TmpOutputFile
420outformat:flat
421outaligned:yes
422
423// --------------------------------------------------------------------------------
424
425item:ClustalW Protein Alignment (fast)
426seqtype: A
427itemmeta: o
428itemmethod:(GOTO_LOCAL_DIR; \
429            tr '"%//' '>' <TmpInputFile >clus_in ; \
430            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
431                                    -quicktree  $INTERACTIVE \
432                                    -ktuple=$KTUPLE -topdiags=$TOPDIAGS \
433                                    -window=$WINDOW -pairgap=$PAIRGAP \
434                                    -score=$SCORE \
435                                    -type=PROTEIN -transweight=$TRANSWEIGHT \
436                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
437                                    -matrix=$MATRIX $NEGMATRIX; \
438                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
439            RM_LOCAL_FILES(clus_in* TmpInputFile))
440
441itemhelp:clustalw.help
442
443// parameters for fast pairwise alignment:
444
445arg:PAIRGAP
446arglabel:Gap penalty (pairwise ali)
447argtype:slider
448argmin:1
449argmax:500
450argvalue:3
451
452arg:KTUPLE
453arglabel:K-tuple size
454argtype:slider
455argmin:1
456argmax:2
457argvalue:1
458
459arg:TOPDIAGS
460arglabel:No. of top diagonals
461argtype:slider
462argmin:1
463argmax:50
464argvalue:5
465
466arg:WINDOW
467arglabel:Window size
468argtype:slider
469argmin:1
470argmax:50
471argvalue:5
472
473// parameters for multiple alignment:
474
475arg:MATRIX
476argtype:choice_menu
477arglabel:Weighting matrix (multiple ali)
478argchoice:Gonnet series:GONNET
479argchoice:Blosum series:BLOSUM
480argchoice:PAM series:PAM
481argchoice:ID matrix:ID
482
483arg:GOP
484argtype:slider
485arglabel:Gap Open Penalty
486argmin:0
487argmax:100
488argvalue:10
489
490arg:GEP
491arglabel:Gap Extend Penalty
492argtype:slider
493argmin:0
494argmax:10
495argvalue:0.2
496
497arg:MAXDIV
498arglabel:% identity for delay
499argtype:slider
500argmin:0
501argmax:100
502argvalue:30
503
504arg:TRANSWEIGHT
505arglabel:Transition weight
506argtype:slider
507argmin:0.0
508argmax:1.0
509argvalue:0.5
510
511arg:NEGMATRIX
512arglabel:Use negative matrix
513argtype:choice_menu
514argchoice:No:
515argchoice:Yes:-negative
516
517arg:INTERACTIVE
518arglabel:Interactive
519argtype:choice_menu
520argchoice:No:
521argchoice:Yes:-interactive
522
523in:TmpInputFile
524informat:flat
525insave:
526
527out:TmpOutputFile
528outformat:flat
529outaligned:yes
530
531// --------------------------------------------------------------------------------
532
533item:ClustalW Protein Alignment (slow & accurate)
534seqtype: A
535itemmeta: l
536itemmethod:(GOTO_LOCAL_DIR; \
537            tr '"%//' '>' <TmpInputFile >clus_in ; \
538            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
539                                     $INTERACTIVE \
540                                    -pwmatrix=$PWMATRIX \
541                                    -pwgapopen=$PWGOP -pwgapext=$PWGEP \
542                                    -type=PROTEIN -transweight=$TRANSWEIGHT \
543                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
544                                    -matrix=$MATRIX $NEGMATRIX; \
545                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
546            RM_LOCAL_FILES(clus_in* TmpInputFile))
547
548itemhelp:clustalw.help
549
550// parameters for pairwise alignment:
551
552arg:PWMATRIX
553argtype:choice_menu
554arglabel:Weighting matrix (pairwise ali)
555argchoice:Gonnet series:GONNET
556argchoice:Blosum series:BLOSUM
557argchoice:PAM series:PAM
558argchoice:ID matrix:ID
559
560arg:PWGOP
561argtype:slider
562arglabel:Gap Open Penalty
563argmin:0
564argmax:100
565argvalue:10
566
567arg:PWGEP
568arglabel:Gap Extend Penalty
569argtype:slider
570argmin:0
571argmax:10
572argvalue:0.1
573
574// parameters for multiple alignment:
575
576arg:MATRIX
577argtype:choice_menu
578arglabel:Weighting matrix (multiple ali)
579argchoice:Gonnet series:GONNET
580argchoice:Blosum series:BLOSUM
581argchoice:PAM series:PAM
582argchoice:ID matrix:ID
583
584arg:GOP
585argtype:slider
586arglabel:Gap Open Penalty
587argmin:0
588argmax:100
589argvalue:10
590
591arg:GEP
592arglabel:Gap Extend Penalty
593argtype:slider
594argmin:0
595argmax:10
596argvalue:0.2
597
598arg:MAXDIV
599arglabel:% identity for delay
600argtype:slider
601argmin:0
602argmax:100
603argvalue:30
604
605arg:TRANSWEIGHT
606arglabel:Transition weight
607argtype:slider
608argmin:0.0
609argmax:1.0
610argvalue:0.5
611
612arg:NEGMATRIX
613arglabel:Use negative matrix
614argtype:choice_menu
615argchoice:No:
616argchoice:Yes:-negative
617
618arg:INTERACTIVE
619arglabel:Interactive
620argtype:choice_menu
621argchoice:No:
622argchoice:Yes:-interactive
623
624in:TmpInputFile
625informat:flat
626insave:
627
628out:TmpOutputFile
629outformat:flat
630outaligned:yes
631
632// --------------------------------------------------------------------------------
633
634item:Assemble Contigs
635itemmeta: g
636seqtype:*
637itemmethod: ( GOTO_LOCAL_DIR; \
638              tr '"%//' '>' <TmpInputFile > tr.out; \
639              CAP2 tr.out $OVERLAP $PMATCH >  TmpOutputFile; \
640              RM_LOCAL_FILES(TmpInputFile tr.out) )
641itemhelp:CAP2.help
642
643arg:OVERLAP
644argtype:slider
645arglabel:Minimum overlap?
646argmin:5
647argmax:100
648argvalue:20
649
650arg:PMATCH
651argtype:slider
652arglabel:Percent match required within overlap
653argmin:25
654argmax:100
655argvalue:90
656
657in:TmpInputFile
658informat:flat
659insave:
660
661out:TmpOutputFile
662outformat:gde
663
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