source: trunk/GDEHELP/MENUS/align.menu

Last change on this file was 18865, checked in by westram, 4 years ago
  • add minimal documentation for
    • probcons and
    • muscle.
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 14.3 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 $REPS probcons_in > probcons_out;)); \
11            arb_sed 's/>HASH_/#/' <probcons_out | \
12            arb_sed 's/>PERCENT_/%/' | \
13            arb_sed 's/>QUOTE_/"/' | \
14            arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(probcons_in* probcons_out* TmpInputFile) )
15itemhelp:ProbCons.help
16
17arg:REPS
18argtype:choice_menu
19arglabel:Passes of consistency transformation
20argtype:slider
21argmin:0
22argmax:5
23argvalue:2
24
25
26arg:PASSES
27arglabel:Passes of iterative refinement
28argtype:slider
29argmin:0
30argmax:1000
31argvalue:100
32
33arg:PRE_TRAINING_REPS
34arglabel:Rounds of pre-training before aligning the sequences
35argtype:slider
36argmin:0
37argmax:20
38argvalue:0
39
40in:TmpInputFile
41informat:flat
42intyped:detailed
43insave:
44
45out:TmpOutputFile
46outformat:flat
47outaligned:yes
48
49//----------------------------------------------------
50
51item:Muscle
52itemmeta: M
53seqtype:*
54itemmethod:(GOTO_LOCAL_DIR; \
55            arb_sed 's/#/>HASH_/' <TmpInputFile | \
56            arb_sed 's/%/>PERCENT_/' | \
57            arb_sed 's/"/>QUOTE_/'| \
58            arb_sed 's/@/>AT_/' | \
59            arb_sed '/^[^>]/ y/./-/' > muscle_in; \
60            RUN_IN_WINDOW(($ARBHOME/bin/muscle $SCORE $DIAGS $ANCHORS $DIMER $BRENNER -in muscle_in -out muscle_out -maxiters $MAXITERS;)); \
61            arb_sed 's/>HASH_/#/' <muscle_out | \
62            arb_sed 's/>PERCENT_/%/' | \
63            arb_sed 's/>QUOTE_/"/' | \
64            arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(muscle_in* muscle_out* TmpInputFile))
65itemhelp:muscle.help
66
67arg:MAXITERS
68argtype:text
69arglabel:Maximum number of iterations to run\n(use 2 for large datasets)
70argtext:16
71
72//arg:ANCHORS
73//argtype:choice_menu
74//arglabel:Use anchor optimization in tree dependent refinement iterations
75//argchoice:Yes(default):-anchors
76//argchoice:No:-noanchors
77
78//arg:BRENNER
79//argtype:choice_menu
80//arglabel:Use Steven Brenner's method for computing the root alignment
81//argchoice:No(default):
82//argchoice:Yes:-brenner
83
84//arg:DIMER
85//argtype:choice_menu
86//arglabel:Use dimer approximation for the SP score\n(faster, slightly less accurate)
87//argchoice:No(default):
88//argchoice:Yes:-dimer
89
90//arg:DIAGS
91//argtype:choice_menu
92//arglabel:Use diagonal optimizations\n(faster, especially for closely related sequences,\nbut may be less accurate)
93//argchoice:No(default):
94//argchoice:Yes:-diags
95
96//arg:SCORE
97//argtype:choice_menu
98//arglabel:Scoring
99//argchoice:Log-expectation profile score (VTML240)(default):-le
100//argchoice:Sum-of-pairs protein profile score (PAM200):-sp
101//argchoice:Sum-of-pairs profile score (VTML240):-sv
102
103
104in:TmpInputFile
105informat:flat
106intyped:detailed
107insave:
108
109out:TmpOutputFile
110outformat:flat
111outaligned:yes
112
113//-------------------------------------------------------------------
114
115item:Mafft
116itemmeta: f
117seqtype:*
118itemmethod:(GOTO_LOCAL_DIR; \
119            arb_sed 's/#/>HASH_/' <TmpInputFile | \
120            arb_sed 's/%/>PERCENT_/' | \
121            arb_sed 's/"/>QUOTE_/'| \
122            arb_sed 's/@/>AT_/' | \
123            arb_sed '/^[^>]/ y/./-/' > mafft_in; \
124            RUN_IN_WINDOW(($ARBHOME/bin/$COMMAND $METHOD --preservecase --ep $OFFSET $SCORING_MATRIX mafft_in > mafft_out;)); \
125            arb_sed 's/>HASH_/#/' <mafft_out | \
126            arb_sed 's/>PERCENT_/%/' | \
127            arb_sed 's/>QUOTE_/"/' | \
128            arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(mafft_in* TmpInputFile mafft_out*))
129
130itemhelp:mafft.help
131
132
133arg:COMMAND
134argtype:choice_menu
135arglabel:Method
136argchoice:Auto:mafft --auto
137argchoice:L-INS-i:mafft-linsi
138argchoice:G-INS-i:mafft-ginsi
139argchoice:E-INS-i:mafft-einsi
140argchoice:Q-INS-i:mafft-qinsi
141argchoice:X-INS-i:mafft-xinsi
142argchoice:FFT-NS-i:mafft-fftnsi
143argchoice:FFT-NS-2:mafft-fftns
144argchoice:NW-NS-i:mafft-nwnsi
145argchoice:NW-NS-2:mafft-nwns
146
147arg:SCORING_MATRIX
148argtype:choice_menu
149arglabel:Scoring matrix
150argchoice:BLOSUM62:--bl 62
151argchoice:BLOSUM30:--bl 30
152argchoice:BLOSUM45:--bl 45
153argchoice:BLOSUM80:--bl 80
154argchoice:JTT100:--jtt 100
155argchoice:JTT200:--jtt 200
156argchoice:JTT200:--jtt 200
157argchoice:1PAM / K=2:--kimura 1
158argchoice:20PAM / K=2:--kimura 20
159argchoice:200PAM / K=2:--kimura 200
160
161
162arg:OFFSET
163argtype:slider
164argmin:0.0
165argmax:1.0
166arglabel:Offset value [0..1]\n(use values >0.1 for closely related sequences)
167argtext:0.5
168
169
170in:TmpInputFile
171informat:flat
172intyped:detailed
173insave:
174
175out:TmpOutputFile
176outformat:flat
177outaligned:yes
178
179//--------------------------------------------------------
180
181item:ClustalW automatic
182itemmeta: W
183seqtype:*
184itemmethod:(GOTO_LOCAL_DIR; \
185            tr '"%//' '>' <TmpInputFile >clus_in; \
186            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align ; \
187                           cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >TmpOutputFile; )); \
188            RM_LOCAL_FILES(clus_in* TmpInputFile))
189
190itemhelp:clustalw.help
191
192
193in:TmpInputFile
194informat:flat
195insave:
196
197out:TmpOutputFile
198outformat:flat
199outaligned:yes
200
201// --------------------------------------------------------------------------------
202
203item:Create ClustalW Profile 2
204itemmeta: C
205seqtype:*
206itemmethod:(GOTO_LOCAL_DIR ; tr '"%//' '>' <TmpInputFile >../clus_prf ; RM_LOCAL_FILES(TmpInputFile))
207
208itemhelp:clustalw.help
209
210in:TmpInputFile
211informat:flat
212insave:
213
214// --------------------------------------------------------------------------------
215
216item:ClustalW Profile Alignment
217itemmeta: A
218seqtype:*
219itemmethod:(GOTO_LOCAL_DIR; \
220            tr '"%//' '>' <TmpInputFile >clus_in; \
221            RUN_IN_WINDOW((clustalw -output=PIR -profile1=clus_in -profile2=../clus_prf -align ; \
222                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )); \
223            RM_LOCAL_FILES(clus_in* TmpInputFile))
224
225itemhelp:clustalw.help
226
227
228in:TmpInputFile
229informat:flat
230insave:
231
232out:TmpOutputFile
233outformat:flat
234outaligned:yes
235
236// --------------------------------------------------------------------------------
237
238item:ClustalW DNA Alignment (fast)
239seqtype: N
240itemmeta: N
241itemmethod:(GOTO_LOCAL_DIR; \
242            tr '"%//' '>' <TmpInputFile >clus_in ; \
243            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
244                                    -quicktree $INTERACTIVE \
245                                    -ktuple=$KTUPLE -topdiags=$TOPDIAGS \
246                                    -window=$WINDOW -pairgap=$PAIRGAP \
247                                    -score=$SCORE \
248                                    -type=DNA -transweight=$TRANSWEIGHT \
249                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
250                                    -dnamatrix=$DNAMATRIX; \
251                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | arb_sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
252           RM_LOCAL_FILES(clus_in* TmpInputFile))
253
254itemhelp:clustalw.help
255
256// parameters for fast pairwise alignment:
257
258arg:PAIRGAP
259arglabel:Gap penalty (pairwise ali)
260argtype:slider
261argmin:1
262argmax:500
263argvalue:5
264
265arg:KTUPLE
266arglabel:K-tuple size
267argtype:slider
268argmin:1
269argmax:4
270argvalue:2
271
272arg:TOPDIAGS
273arglabel:No. of top diagonals
274argtype:slider
275argmin:1
276argmax:50
277argvalue:4
278
279arg:WINDOW
280arglabel:Window size
281argtype:slider
282argmin:1
283argmax:50
284argvalue:4
285
286// parameters for multiple alignment:
287
288arg:DNAMATRIX
289argtype:choice_menu
290arglabel:Weighting matrix (multiple ali)
291argchoice:IUB:IUB
292argchoice:CLUSTALW:CLUSTALW
293
294arg:GOP
295argtype:slider
296arglabel:Gap Open Penalty
297argmin:0
298argmax:100
299argvalue:15
300
301arg:GEP
302arglabel:Gap Extend Penalty
303argtype:slider
304argmin:0
305argmax:10
306argvalue:6.66
307
308arg:MAXDIV
309arglabel:% identity for delay
310argtype:slider
311argmin:0
312argmax:100
313argvalue:30
314
315arg:TRANSWEIGHT
316arglabel:Transition weight
317argtype:slider
318argmin:0.0
319argmax:1.0
320argvalue:0.5
321
322arg:INTERACTIVE
323arglabel:Interactive
324argtype:choice_menu
325argchoice:No:
326argchoice:Yes:-interactive
327
328in:TmpInputFile
329informat:flat
330insave:
331
332out:TmpOutputFile
333outformat:flat
334outaligned:yes
335
336// --------------------------------------------------------------------------------
337
338item:ClustalW DNA Alignment (slow & accurate)
339seqtype: N
340itemmeta: s
341itemmethod:(GOTO_LOCAL_DIR; \
342            tr '"%//' '>' <TmpInputFile >clus_in ; \
343            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
344                                     $INTERACTIVE \
345                                    -pwdnamatrix=$PWDNAMATRIX \
346                                    -pwgapopen=$PWGOP -pwgapext=$PWGEP \
347                                    -type=DNA -transweight=$TRANSWEIGHT \
348                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
349                                    -dnamatrix=$DNAMATRIX; \
350                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
351            RM_LOCAL_FILES(clus_in* TmpInputFile))
352
353itemhelp:clustalw.help
354
355// parameters for pairwise alignment:
356
357arg:PWDNAMATRIX
358argtype:choice_menu
359arglabel:Weighting matrix (pairwise ali)
360argchoice:IUB:IUB
361argchoice:CLUSTALW:CLUSTALW
362
363arg:PWGOP
364argtype:slider
365arglabel:Gap Open Penalty
366argmin:0
367argmax:100
368argvalue:15
369
370arg:PWGEP
371arglabel:Gap Extend Penalty
372argtype:slider
373argmin:0
374argmax:10
375argvalue:6.66
376
377// parameters for multiple alignment:
378
379arg:DNAMATRIX
380argtype:choice_menu
381arglabel:Weighting matrix (multiple ali)
382argchoice:IUB:IUB
383argchoice:CLUSTALW:CLUSTALW
384
385arg:GOP
386argtype:slider
387arglabel:Gap Open Penalty
388argmin:0
389argmax:100
390argvalue:15
391
392arg:GEP
393arglabel:Gap Extend Penalty
394argtype:slider
395argmin:0
396argmax:10
397argvalue:6.66
398
399arg:MAXDIV
400arglabel:% identity for delay
401argtype:slider
402argmin:0
403argmax:100
404argvalue:30
405
406arg:TRANSWEIGHT
407arglabel:Transition weight
408argtype:slider
409argmin:0.0
410argmax:1.0
411argvalue:0.5
412
413arg:INTERACTIVE
414arglabel:Interactive
415argtype:choice_menu
416argchoice:No:
417argchoice:Yes:-interactive
418
419in:TmpInputFile
420informat:flat
421insave:
422
423out:TmpOutputFile
424outformat:flat
425outaligned:yes
426
427// --------------------------------------------------------------------------------
428
429item:ClustalW Protein Alignment (fast)
430seqtype: A
431itemmeta: o
432itemmethod:(GOTO_LOCAL_DIR; \
433            tr '"%//' '>' <TmpInputFile >clus_in ; \
434            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
435                                    -quicktree  $INTERACTIVE \
436                                    -ktuple=$KTUPLE -topdiags=$TOPDIAGS \
437                                    -window=$WINDOW -pairgap=$PAIRGAP \
438                                    -score=$SCORE \
439                                    -type=PROTEIN -transweight=$TRANSWEIGHT \
440                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
441                                    -matrix=$MATRIX $NEGMATRIX; \
442                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
443            RM_LOCAL_FILES(clus_in* TmpInputFile))
444
445itemhelp:clustalw.help
446
447// parameters for fast pairwise alignment:
448
449arg:PAIRGAP
450arglabel:Gap penalty (pairwise ali)
451argtype:slider
452argmin:1
453argmax:500
454argvalue:3
455
456arg:KTUPLE
457arglabel:K-tuple size
458argtype:slider
459argmin:1
460argmax:2
461argvalue:1
462
463arg:TOPDIAGS
464arglabel:No. of top diagonals
465argtype:slider
466argmin:1
467argmax:50
468argvalue:5
469
470arg:WINDOW
471arglabel:Window size
472argtype:slider
473argmin:1
474argmax:50
475argvalue:5
476
477// parameters for multiple alignment:
478
479arg:MATRIX
480argtype:choice_menu
481arglabel:Weighting matrix (multiple ali)
482argchoice:Gonnet series:GONNET
483argchoice:Blosum series:BLOSUM
484argchoice:PAM series:PAM
485argchoice:ID matrix:ID
486
487arg:GOP
488argtype:slider
489arglabel:Gap Open Penalty
490argmin:0
491argmax:100
492argvalue:10
493
494arg:GEP
495arglabel:Gap Extend Penalty
496argtype:slider
497argmin:0
498argmax:10
499argvalue:0.2
500
501arg:MAXDIV
502arglabel:% identity for delay
503argtype:slider
504argmin:0
505argmax:100
506argvalue:30
507
508arg:TRANSWEIGHT
509arglabel:Transition weight
510argtype:slider
511argmin:0.0
512argmax:1.0
513argvalue:0.5
514
515arg:NEGMATRIX
516arglabel:Use negative matrix
517argtype:choice_menu
518argchoice:No:
519argchoice:Yes:-negative
520
521arg:INTERACTIVE
522arglabel:Interactive
523argtype:choice_menu
524argchoice:No:
525argchoice:Yes:-interactive
526
527in:TmpInputFile
528informat:flat
529insave:
530
531out:TmpOutputFile
532outformat:flat
533outaligned:yes
534
535// --------------------------------------------------------------------------------
536
537item:ClustalW Protein Alignment (slow & accurate)
538seqtype: A
539itemmeta: l
540itemmethod:(GOTO_LOCAL_DIR; \
541            tr '"%//' '>' <TmpInputFile >clus_in ; \
542            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
543                                     $INTERACTIVE \
544                                    -pwmatrix=$PWMATRIX \
545                                    -pwgapopen=$PWGOP -pwgapext=$PWGEP \
546                                    -type=PROTEIN -transweight=$TRANSWEIGHT \
547                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
548                                    -matrix=$MATRIX $NEGMATRIX; \
549                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \
550            RM_LOCAL_FILES(clus_in* TmpInputFile))
551
552itemhelp:clustalw.help
553
554// parameters for pairwise alignment:
555
556arg:PWMATRIX
557argtype:choice_menu
558arglabel:Weighting matrix (pairwise ali)
559argchoice:Gonnet series:GONNET
560argchoice:Blosum series:BLOSUM
561argchoice:PAM series:PAM
562argchoice:ID matrix:ID
563
564arg:PWGOP
565argtype:slider
566arglabel:Gap Open Penalty
567argmin:0
568argmax:100
569argvalue:10
570
571arg:PWGEP
572arglabel:Gap Extend Penalty
573argtype:slider
574argmin:0
575argmax:10
576argvalue:0.1
577
578// parameters for multiple alignment:
579
580arg:MATRIX
581argtype:choice_menu
582arglabel:Weighting matrix (multiple ali)
583argchoice:Gonnet series:GONNET
584argchoice:Blosum series:BLOSUM
585argchoice:PAM series:PAM
586argchoice:ID matrix:ID
587
588arg:GOP
589argtype:slider
590arglabel:Gap Open Penalty
591argmin:0
592argmax:100
593argvalue:10
594
595arg:GEP
596arglabel:Gap Extend Penalty
597argtype:slider
598argmin:0
599argmax:10
600argvalue:0.2
601
602arg:MAXDIV
603arglabel:% identity for delay
604argtype:slider
605argmin:0
606argmax:100
607argvalue:30
608
609arg:TRANSWEIGHT
610arglabel:Transition weight
611argtype:slider
612argmin:0.0
613argmax:1.0
614argvalue:0.5
615
616arg:NEGMATRIX
617arglabel:Use negative matrix
618argtype:choice_menu
619argchoice:No:
620argchoice:Yes:-negative
621
622arg:INTERACTIVE
623arglabel:Interactive
624argtype:choice_menu
625argchoice:No:
626argchoice:Yes:-interactive
627
628in:TmpInputFile
629informat:flat
630insave:
631
632out:TmpOutputFile
633outformat:flat
634outaligned:yes
635
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