source: tags/old_import_filter/GDEHELP/MENUS/align.menu

Last change on this file was 9750, checked in by westram, 11 years ago
  • applied (not merged!) [9668] from gtk_only.
    • merge did not work w/o conflicts since the patch mixes gtk-specific changes with general changes (better would have been applied to some non-gtk-branch and then merged into gtk-branch)
    • merging and resolving conflicts now would skip unmergeable parts. when gtk is merged someday, these parts would get lost.
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 9.8 KB
Line 
1
2item:ClustalW automatic
3itemmeta: W
4itemmethod:(GOTO_LOCAL_DIR; \
5            tr '"%//' '>' <in1 >clus_in; \
6            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align ; \
7                           cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; )); \
8            RM_LOCAL_FILES(clus_in* in1))
9
10itemhelp:clustalw.help
11
12
13in:in1
14informat:flat
15insave:
16
17out:out1
18outformat:flat
19
20// --------------------------------------------------------------------------------
21
22item:Create ClustalW Profile 2
23itemmeta: C
24itemmethod:(GOTO_LOCAL_DIR ; tr '"%//' '>' <in1 >../clus_prf ; RM_LOCAL_FILES(in1))
25
26itemhelp:clustalw.help
27
28in:in1
29informat:flat
30insave:
31
32// --------------------------------------------------------------------------------
33
34item:ClustalW Profile Alignment
35itemmeta: P
36itemmethod:(GOTO_LOCAL_DIR; \
37            tr '"%//' '>' <in1 >clus_in; \
38            RUN_IN_WINDOW((clustalw -output=PIR -profile1=clus_in -profile2=../clus_prf -align ; \
39                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >out1; )); \
40            RM_LOCAL_FILES(clus_in* in1))
41
42itemhelp:clustalw.help
43
44
45in:in1
46informat:flat
47insave:
48
49out:out1
50outformat:flat
51
52// --------------------------------------------------------------------------------
53
54item:ClustalW DNA Alignment (fast)
55seqtype: N
56itemmeta: N
57itemmethod:(GOTO_LOCAL_DIR; \
58            tr '"%//' '>' <in1 >clus_in ; \
59            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
60                                    -quicktree $INTERACTIVE \
61                                    -ktuple=$KTUPLE -topdiags=$TOPDIAGS \
62                                    -window=$WINDOW -pairgap=$PAIRGAP \
63                                    -score=$SCORE \
64                                    -type=DNA -transweight=$TRANSWEIGHT \
65                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
66                                    -dnamatrix=$DNAMATRIX; \
67                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >out1; )) ; \
68           RM_LOCAL_FILES(clus_in* in1))
69
70itemhelp:clustalw.help
71
72// parameters for fast pairwise alignment:
73
74arg:PAIRGAP
75arglabel:Gap penalty (pairwise ali)
76argtype:slider
77argmin:1
78argmax:500
79argvalue:5
80
81arg:KTUPLE
82arglabel:K-tuple size
83argtype:slider
84argmin:1
85argmax:4
86argvalue:2
87
88arg:TOPDIAGS
89arglabel:No. of top diagonals
90argtype:slider
91argmin:1
92argmax:50
93argvalue:4
94
95arg:WINDOW
96arglabel:Window size
97argtype:slider
98argmin:1
99argmax:50
100argvalue:4
101
102// parameters for multiple alignment:
103
104arg:DNAMATRIX
105argtype:choice_menu
106arglabel:Weighting matrix (multiple ali)
107argchoice:IUB:IUB
108argchoice:CLUSTALW:CLUSTALW
109
110arg:GOP
111argtype:slider
112arglabel:Gap Open Penalty
113argmin:0
114argmax:100
115argvalue:15
116
117arg:GEP
118arglabel:Gap Extend Penalty
119argtype:slider
120argmin:0
121argmax:10
122argvalue:6.66
123
124arg:MAXDIV
125arglabel:% identity for delay
126argtype:slider
127argmin:0
128argmax:100
129argvalue:30
130
131arg:TRANSWEIGHT
132arglabel:Transition weight
133argtype:slider
134argmin:0.0
135argmax:1.0
136argvalue:0.5
137
138arg:INTERACTIVE
139arglabel:Interactive
140argtype:choice_menu
141argchoice:No:
142argchoice:Yes:-interactive
143
144in:in1
145informat:flat
146insave:
147
148out:out1
149outformat:flat
150
151// --------------------------------------------------------------------------------
152
153item:ClustalW DNA Alignment (slow & accurate)
154seqtype: N
155itemmeta: s
156itemmethod:(GOTO_LOCAL_DIR; \
157            tr '"%//' '>' <in1 >clus_in ; \
158            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
159                                     $INTERACTIVE \
160                                    -pwdnamatrix=$PWDNAMATRIX \
161                                    -pwgapopen=$PWGOP -pwgapext=$PWGEP \
162                                    -type=DNA -transweight=$TRANSWEIGHT \
163                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
164                                    -dnamatrix=$DNAMATRIX; \
165                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >out1; )) ; \
166            RM_LOCAL_FILES(clus_in* in1))
167
168itemhelp:clustalw.help
169
170// parameters for pairwise alignment:
171
172arg:PWDNAMATRIX
173argtype:choice_menu
174arglabel:Weighting matrix (pairwise ali)
175argchoice:IUB:IUB
176argchoice:CLUSTALW:CLUSTALW
177
178arg:PWGOP
179argtype:slider
180arglabel:Gap Open Penalty
181argmin:0
182argmax:100
183argvalue:15
184
185arg:PWGEP
186arglabel:Gap Extend Penalty
187argtype:slider
188argmin:0
189argmax:10
190argvalue:6.66
191
192// parameters for multiple alignment:
193
194arg:DNAMATRIX
195argtype:choice_menu
196arglabel:Weighting matrix (multiple ali)
197argchoice:IUB:IUB
198argchoice:CLUSTALW:CLUSTALW
199
200arg:GOP
201argtype:slider
202arglabel:Gap Open Penalty
203argmin:0
204argmax:100
205argvalue:15
206
207arg:GEP
208arglabel:Gap Extend Penalty
209argtype:slider
210argmin:0
211argmax:10
212argvalue:6.66
213
214arg:MAXDIV
215arglabel:% identity for delay
216argtype:slider
217argmin:0
218argmax:100
219argvalue:30
220
221arg:TRANSWEIGHT
222arglabel:Transition weight
223argtype:slider
224argmin:0.0
225argmax:1.0
226argvalue:0.5
227
228arg:INTERACTIVE
229arglabel:Interactive
230argtype:choice_menu
231argchoice:No:
232argchoice:Yes:-interactive
233
234in:in1
235informat:flat
236insave:
237
238out:out1
239outformat:flat
240
241// --------------------------------------------------------------------------------
242
243item:ClustalW Protein Alignment (fast)
244seqtype: A
245itemmeta: o
246itemmethod:(GOTO_LOCAL_DIR; \
247            tr '"%//' '>' <in1 >clus_in ; \
248            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
249                                    -quicktree  $INTERACTIVE \
250                                    -ktuple=$KTUPLE -topdiags=$TOPDIAGS \
251                                    -window=$WINDOW -pairgap=$PAIRGAP \
252                                    -score=$SCORE \
253                                    -type=PROTEIN -transweight=$TRANSWEIGHT \
254                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
255                                    -matrix=$MATRIX $NEGMATRIX; \
256                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >out1; )) ; \
257            RM_LOCAL_FILES(clus_in* in1))
258
259itemhelp:clustalw.help
260
261// parameters for fast pairwise alignment:
262
263arg:PAIRGAP
264arglabel:Gap penalty (pairwise ali)
265argtype:slider
266argmin:1
267argmax:500
268argvalue:3
269
270arg:KTUPLE
271arglabel:K-tuple size
272argtype:slider
273argmin:1
274argmax:2
275argvalue:1
276
277arg:TOPDIAGS
278arglabel:No. of top diagonals
279argtype:slider
280argmin:1
281argmax:50
282argvalue:5
283
284arg:WINDOW
285arglabel:Window size
286argtype:slider
287argmin:1
288argmax:50
289argvalue:5
290
291// parameters for multiple alignment:
292
293arg:MATRIX
294argtype:choice_menu
295arglabel:Weighting matrix (multiple ali)
296argchoice:Gonnet series:GONNET
297argchoice:Blosum series:BLOSUM
298argchoice:PAM series:PAM
299argchoice:ID matrix:ID
300
301arg:GOP
302argtype:slider
303arglabel:Gap Open Penalty
304argmin:0
305argmax:100
306argvalue:10
307
308arg:GEP
309arglabel:Gap Extend Penalty
310argtype:slider
311argmin:0
312argmax:10
313argvalue:0.2
314
315arg:MAXDIV
316arglabel:% identity for delay
317argtype:slider
318argmin:0
319argmax:100
320argvalue:30
321
322arg:TRANSWEIGHT
323arglabel:Transition weight
324argtype:slider
325argmin:0.0
326argmax:1.0
327argvalue:0.5
328
329arg:NEGMATRIX
330arglabel:Use negative matrix
331argtype:choice_menu
332argchoice:No:
333argchoice:Yes:-negative
334
335arg:INTERACTIVE
336arglabel:Interactive
337argtype:choice_menu
338argchoice:No:
339argchoice:Yes:-interactive
340
341in:in1
342informat:flat
343insave:
344
345out:out1
346outformat:flat
347
348// --------------------------------------------------------------------------------
349
350item:ClustalW Protein Alignment (slow & accurate)
351seqtype: A
352itemmeta: l
353itemmethod:(GOTO_LOCAL_DIR; \
354            tr '"%//' '>' <in1 >clus_in ; \
355            RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \
356                                     $INTERACTIVE \
357                                    -pwmatrix=$PWMATRIX \
358                                    -pwgapopen=$PWGOP -pwgapext=$PWGEP \
359                                    -type=PROTEIN -transweight=$TRANSWEIGHT \
360                                    -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \
361                                    -matrix=$MATRIX $NEGMATRIX; \
362                           cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >out1; )) ; \
363            RM_LOCAL_FILES(clus_in* in1))
364
365itemhelp:clustalw.help
366
367// parameters for pairwise alignment:
368
369arg:PWMATRIX
370argtype:choice_menu
371arglabel:Weighting matrix (pairwise ali)
372argchoice:Gonnet series:GONNET
373argchoice:Blosum series:BLOSUM
374argchoice:PAM series:PAM
375argchoice:ID matrix:ID
376
377arg:PWGOP
378argtype:slider
379arglabel:Gap Open Penalty
380argmin:0
381argmax:100
382argvalue:10
383
384arg:PWGEP
385arglabel:Gap Extend Penalty
386argtype:slider
387argmin:0
388argmax:10
389argvalue:0.1
390
391// parameters for multiple alignment:
392
393arg:MATRIX
394argtype:choice_menu
395arglabel:Weighting matrix (multiple ali)
396argchoice:Gonnet series:GONNET
397argchoice:Blosum series:BLOSUM
398argchoice:PAM series:PAM
399argchoice:ID matrix:ID
400
401arg:GOP
402argtype:slider
403arglabel:Gap Open Penalty
404argmin:0
405argmax:100
406argvalue:10
407
408arg:GEP
409arglabel:Gap Extend Penalty
410argtype:slider
411argmin:0
412argmax:10
413argvalue:0.2
414
415arg:MAXDIV
416arglabel:% identity for delay
417argtype:slider
418argmin:0
419argmax:100
420argvalue:30
421
422arg:TRANSWEIGHT
423arglabel:Transition weight
424argtype:slider
425argmin:0.0
426argmax:1.0
427argvalue:0.5
428
429arg:NEGMATRIX
430arglabel:Use negative matrix
431argtype:choice_menu
432argchoice:No:
433argchoice:Yes:-negative
434
435arg:INTERACTIVE
436arglabel:Interactive
437argtype:choice_menu
438argchoice:No:
439argchoice:Yes:-interactive
440
441in:in1
442informat:flat
443insave:
444
445out:out1
446outformat:flat
447
448// --------------------------------------------------------------------------------
449
450item:Assemble Contigs
451itemmeta: g
452itemmethod: ( GOTO_LOCAL_DIR; \
453              tr '"%//' '>' <in1 >in1.tmp; \
454              CAP2 in1.tmp $OVERLAP $PMATCH >  out1; \
455              RM_LOCAL_FILES(in1 in1.tmp) )
456itemhelp:CAP2.help
457
458arg:OVERLAP
459argtype:slider
460arglabel:Minimum overlap?
461argmin:5
462argmax:100
463argvalue:20
464
465arg:PMATCH
466argtype:slider
467arglabel:Percent match required within overlap
468argmin:25
469argmax:100
470argvalue:90
471
472in:in1
473informat:flat
474
475out:out1
476outformat:gde
477
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