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comparison Codonlogo.xml @ 4:4d47ab2b7bcc

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author davidmurphy
date Fri, 13 Jan 2012 07:18:19 -0500
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3:09d2dac9ef73 4:4d47ab2b7bcc
1 <tool id="codonlogo" name="Codon Logo" version="3">
2 <description>generator for fasta (eg Clustal alignments)</description>
3 <command interpreter="python -W ignore::DeprecationWarning">
4 codonlogo -F $outformat -s $size -f $input -o $output -t "$logoname" -m $frame -n $stacks -X $showxaxis --show-yaxis $showyaxis --errorbars $errorbars
5
6 #if str($ylabel) != ''
7 -x $xlabel
8 #end if
9
10 #if str( $ylabel) != ''
11 -y $ylabel
12 #end if
13 #if $range.mode == 'part'
14 -l "$range.seqstart" -u "$range.seqend"
15 #end if
16 #if $comp.mode == 'equiprobable'
17 --composition 'equiprobable'
18 #end if
19 #if $comp.mode == 'none'
20 --composition 'none'
21 #end if
22 #if $comp.mode == 'file'
23 -R $compfile
24 #end if
25
26 #if $colours.colour == 'part'
27
28 #if str( $colours.colorAAA) != ''
29 -C $colours.colorAAA AAA ""
30 #end if
31
32 #if str( $colours.colorAAC) != ''
33 -C $colours.colorAAC AAC ""
34 #end if
35
36 #if str( $colours.colorAAG) != ''
37 -C $colours.colorAAG AAG ""
38 #end if
39
40 #if str( $colours.colorAAU) != ''
41 -C $colours.colorAAU AAU ""
42 -C $colours.colorAAU AAT ""
43 #end if
44
45 #if str( $colours.colorACA) != ''
46 -C $colours.colorACA ACA ""
47 #end if
48
49 #if str( $colours.colorACC) != ''
50 -C $colours.colorACC ACC ""
51 #end if
52
53 #if str( $colours.colorACG) != ''
54 -C $colours.colorACG ACG ""
55 #end if
56
57 #if str( $colours.colorACU) != ''
58 -C $colours.colorACU ACU ""
59 -C $colours.colorACU ACT ""
60 #end if
61
62 #if str( $colours.colorAGA) != ''
63 -C $colours.colorAGA AGA ""
64 #end if
65
66 #if str( $colours.colorAGC) != ''
67 -C $colours.colorAGC AGC ""
68 #end if
69
70 #if str( $colours.colorAGG) != ''
71 -C $colours.colorAGG AGG ""
72 #end if
73
74 #if str( $colours.colorAGU) != ''
75 -C $colours.colorAGU AGU ""
76 -C $colours.colorAGU AGT ""
77 #end if
78
79 #if str( $colours.colorAUA) != ''
80 -C $colours.colorAUA AUA ""
81 -C $colours.colorAUA ATA ""
82 #end if
83
84 #if str( $colours.colorAUC) != ''
85 -C $colours.colorAUC AUC ""
86 -C $colours.colorAUC ATC ""
87 #end if
88
89 #if str( $colours.colorAUG) != ''
90 -C $colours.colorAUG AUG ""
91 -C $colours.colorAUG ATG ""
92 #end if
93
94 #if str( $colours.colorAUU) != ''
95 -C $colours.colorAUU AUU ""
96 -C $colours.colorAUU ATT ""
97 #end if
98
99 #if str( $colours.colorCAA) != ''
100 -C $colours.colorCAA CAA ""
101 #end if
102
103 #if str( $colours.colorCAC) != ''
104 -C $colours.colorCAC CAC ""
105 #end if
106
107 #if str( $colours.colorCAG) != ''
108 -C $colours.colorCAG CAG ""
109 #end if
110
111 #if str( $colours.colorCAU) != ''
112 -C $colours.colorCAU CAU ""
113 -C $colours.colorCAU CAT ""
114 #end if
115
116 #if str( $colours.colorCCA) != ''
117 -C $colours.colorCCA CCA ""
118 #end if
119
120 #if str( $colours.colorCCC) != ''
121 -C $colours.colorCCC CCC ""
122 #end if
123
124 #if str( $colours.colorCCG) != ''
125 -C $colours.colorCCG CCG ""
126 #end if
127
128 #if str( $colours.colorCCU) != ''
129 -C $colours.colorCCU CCU ""
130 -C $colours.colorCCU CCT ""
131 #end if
132
133 #if str( $colours.colorCGA) != ''
134 -C $colours.colorCGA CGA ""
135 #end if
136
137 #if str( $colours.colorCGC) != ''
138 -C $colours.colorCGC CGC ""
139 #end if
140
141 #if str( $colours.colorCGG) != ''
142 -C $colours.colorCGG CGG ""
143 #end if
144
145 #if str( $colours.colorCGU) != ''
146 -C $colours.colorCGU CGU ""
147 -C $colours.colorCGU CGT ""
148 #end if
149
150 #if str( $colours.colorCUA) != ''
151 -C $colours.colorCUA CUA ""
152 -C $colours.colorCUA CTA ""
153 #end if
154
155 #if str( $colours.colorCUC) != ''
156 -C $colours.colorCUC CUC ""
157 -C $colours.colorCUC CTC ""
158 #end if
159
160 #if str( $colours.colorCUG) != ''
161 -C $colours.colorCUG CUG ""
162 -C $colours.colorCUG CTG ""
163 #end if
164
165 #if str( $colours.colorCUU) != ''
166 -C $colours.colorCUU CUU ""
167 -C $colours.colorCUU CTT ""
168 #end if
169
170 #if str( $colours.colorGAA) != ''
171 -C $colours.colorGAA GAA ""
172 #end if
173
174 #if str( $colours.colorGAC) != ''
175 -C $colours.colorGAC GAC ""
176 #end if
177
178 #if str( $colours.colorGAG) != ''
179 -C $colours.colorGAG GAG ""
180 #end if
181
182 #if str( $colours.colorGAU) != ''
183 -C $colours.colorGAU GAU ""
184 -C $colours.colorGAU GAT ""
185 #end if
186
187 #if str( $colours.colorGCA) != ''
188 -C $colours.colorGCA GCA ""
189 #end if
190
191 #if str( $colours.colorGCC) != ''
192 -C $colours.colorGCC GCC ""
193 #end if
194
195 #if str( $colours.colorGCG) != ''
196 -C $colours.colorGCG GCG ""
197 #end if
198
199 #if str( $colours.colorGCU) != ''
200 -C $colours.colorGCU GCU ""
201 -C $colours.colorGCU GCT ""
202 #end if
203
204 #if str( $colours.colorGGA) != ''
205 -C $colours.colorGGA GGA ""
206 #end if
207
208 #if str( $colours.colorGGC) != ''
209 -C $colours.colorGGC GGC ""
210 #end if
211
212 #if str( $colours.colorGGG) != ''
213 -C $colours.colorGGG GGG ""
214 #end if
215
216 #if str( $colours.colorGGU) != ''
217 -C $colours.colorGGU GGU ""
218 -C $colours.colorGGU GGT ""
219 #end if
220
221 #if str( $colours.colorGUA) != ''
222 -C $colours.colorGUA GUA ""
223 -C $colours.colorGUA GTA ""
224 #end if
225
226 #if str( $colours.colorGUC) != ''
227 -C $colours.colorGUC GUC ""
228 -C $colours.colorGUC GTC ""
229 #end if
230
231 #if str( $colours.colorGUG) != ''
232 -C $colours.colorGUG GUG ""
233 -C $colours.colorGUG GTG ""
234 #end if
235
236 #if str( $colours.colorGUU) != ''
237 -C $colours.colorGUU GUU ""
238 -C $colours.colorGUU GTT ""
239 #end if
240
241 #if str( $colours.colorUAA) != ''
242 -C $colours.colorUAA UAA ""
243 -C $colours.colorUAA TAA ""
244 #end if
245
246 #if str( $colours.colorUAC) != ''
247 -C $colours.colorUAC UAC ""
248 -C $colours.colorUAC TAC ""
249 #end if
250
251 #if str( $colours.colorUAG) != ''
252 -C $colours.colorUAG UAG ""
253 -C $colours.colorUAG TAG ""
254 #end if
255
256 #if str( $colours.colorUAU) != ''
257 -C $colours.colorUAU UAU ""
258 -C $colours.colorUAU TAT ""
259 #end if
260
261 #if str( $colours.colorUCA) != ''
262 -C $colours.colorUCA UCA ""
263 -C $colours.colorUCA TCA ""
264 #end if
265
266 #if str( $colours.colorUCC) != ''
267 -C $colours.colorUCC UCC ""
268 -C $colours.colorUCC TCC ""
269 #end if
270
271 #if str( $colours.colorUCG) != ''
272 -C $colours.colorUCG UCG ""
273 -C $colours.colorUCG TCG ""
274 #end if
275
276 #if str( $colours.colorUCU) != ''
277 -C $colours.colorUCU UCU ""
278 -C $colours.colorUCU TCT ""
279 #end if
280
281 #if str( $colours.colorUGA) != ''
282 -C $colours.colorUGA UGA ""
283 -C $colours.colorUGA TGA ""
284 #end if
285
286 #if str( $colours.colorUGC) != ''
287 -C $colours.colorUGC UGC ""
288 -C $colours.colorUGC TGC ""
289 #end if
290
291 #if str( $colours.colorUGG) != ''
292 -C $colours.colorUGG UGG ""
293 -C $colours.colorUGG TGG ""
294 #end if
295
296 #if str( $colours.colorUGU) != ''
297 -C $colours.colorUGU UGU ""
298 -C $colours.colorUGU TGT ""
299 #end if
300
301 #if str( $colours.colorUUA) != ''
302 -C $colours.colorUUA UUA ""
303 -C $colours.colorUUA TTA ""
304 #end if
305
306 #if str( $colours.colorUUC) != ''
307 -C $colours.colorUUC UUC ""
308 -C $colours.colorUUC TTC ""
309 #end if
310
311 #if str( $colours.colorUUG) != ''
312 -C $colours.colorUUG UUG ""
313 -C $colours.colorUUG TTG ""
314 #end if
315
316 #if str( $colours.colorUUU) != ''
317 -C $colours.colorUUU UUU ""
318 -C $colours.colorUUU TTT ""
319 #end if
320 #end if
321
322 </command>
323 <inputs>
324 <page>
325 <param format="fasta" name="input" type="data" label="txt" />
326
327 <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="" />
328
329 <param name="outformat" type="select" label="Output format for image (or text report)" >
330 <option value="png" selected="True">PNG screen quality</option>
331 <option value="png_print">High quality printable PNG</option>
332 <option value="pdf">PDF</option>
333 <option value="jpeg">JPG</option>
334 <option value="eps">EPS</option>
335 <option value="txt">Text (shows the detailed calculations for each position - no image)</option>
336 </param>
337 <param name="frame" type="select" label="Frame to view the alignment. If reverse complement is selected then codonlogo will read from the last symbol in the sequences backwards and replace each base with it's complement." >
338 <option value="0" selected="True">0</option>
339 <option value="1">+1</option>
340 <option value="2">-1</option>
341 <option value="3">reverse complement 0</option>
342 <option value="4">reverse complement +1</option>
343 <option value="5">reverse complement -1</option>
344 </param>
345 <param name="stacks" size="5" type="integer" value="20" label="Number of stacks per line, default 20" />
346 <param name="showxaxis" type="select" display="radio" label="Display sequence numbers along x-axis?" >
347 <option value="True" selected="True">Yes</option>
348 <option value="False">No</option>
349 </param>
350 <param name="xlabel" label="X-axis label" type="text" size="50" value="" />
351 <param name="ylabel" label="Y-axis label" type="text" size="50" value="" />
352
353 <param name="fineprint" label="The fine print." type="text" size="50" value="CodonLogo 1.0" />
354
355
356 <param name="showyaxis" type="select" display="radio" label="Display entropy scale along y-axis?" >
357 <option value="True" selected="True">Yes</option>
358 <option value="False">No</option>
359 </param>
360 <param name="errorbars" type="select" display="radio" label="Display error bars?" >
361 <option value="True" selected="True">Yes</option>
362 <option value="False">No</option>
363 </param>
364 <conditional name="range">
365 <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use">
366 <option value="complete" selected="true">complete sequence</option>
367 <option value="part">Only use a part of the sequence</option>
368 </param>
369 <when value="complete">
370 </when>
371 <when value="part">
372 <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!"
373 label="Index (eg 1=first letter) of the start of the sequence range to include in the logo">
374 </param>
375 <param name="seqend" size="5" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" >
376 </param>
377 </when>
378 </conditional>
379 <conditional name="comp">
380 <param name="mode" type="select" label="Select expected composition: 'equiprobable', 'none' (no small sample correction), or supply a file">
381
382 <option value="equiprobable" >equiprobable</option>
383 <option value="none" >none</option>
384 <option value="file">from file</option>
385
386 </param>
387 <when value="auto">
388 </when>
389 <when value="equiprobable">
390 </when>
391 <when value="none">
392 </when>
393 <when value="file">
394 <param format="txt" name="compfile" type="data" label="File containing the expected composition of the sequence. expected: a file with 64 codons followed by their probability. it must have 64 lines and each line must have a codon followed by a space followed by a weigt." />
395 </when>
396
397 </conditional>
398 <conditional name="colours">
399 <param name="colour" type="select" label="Choose colours?(it is not required to set values for all of them. Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc. )">
400 <option value="no" selected="true">Default colours</option>
401 <option value="part">Set your own.</option>
402 </param>
403 <when value="no">
404 </when>
405 <when value="part">
406
407 <param name="colorAAA" size="10" type="text" value="" label="AAA" />
408 <param name="colorAAC" size="10" type="text" value="" label="AAC" />
409 <param name="colorAAG" size="10" type="text" value="" label="AAG" />
410 <param name="colorAAU" size="10" type="text" value="" label="AAU" />
411 <param name="colorACA" size="10" type="text" value="" label="ACA" />
412 <param name="colorACC" size="10" type="text" value="" label="ACC" />
413 <param name="colorACG" size="10" type="text" value="" label="ACG" />
414 <param name="colorACU" size="10" type="text" value="" label="ACU" />
415 <param name="colorAGA" size="10" type="text" value="" label="AGA" />
416 <param name="colorAGC" size="10" type="text" value="" label="AGC" />
417 <param name="colorAGG" size="10" type="text" value="" label="AGG" />
418 <param name="colorAGU" size="10" type="text" value="" label="AGU" />
419 <param name="colorAUA" size="10" type="text" value="" label="AUA" />
420 <param name="colorAUC" size="10" type="text" value="" label="AUC" />
421 <param name="colorAUG" size="10" type="text" value="" label="AUG" />
422 <param name="colorAUU" size="10" type="text" value="" label="AUU" />
423 <param name="colorCAA" size="10" type="text" value="" label="CAA" />
424 <param name="colorCAC" size="10" type="text" value="" label="CAC" />
425 <param name="colorCAG" size="10" type="text" value="" label="CAG" />
426 <param name="colorCAU" size="10" type="text" value="" label="CAU" />
427 <param name="colorCCA" size="10" type="text" value="" label="CCA" />
428 <param name="colorCCC" size="10" type="text" value="" label="CCC" />
429 <param name="colorCCG" size="10" type="text" value="" label="CCG" />
430 <param name="colorCCU" size="10" type="text" value="" label="CCU" />
431 <param name="colorCGA" size="10" type="text" value="" label="CGA" />
432 <param name="colorCGC" size="10" type="text" value="" label="CGC" />
433 <param name="colorCGG" size="10" type="text" value="" label="CGG" />
434 <param name="colorCGU" size="10" type="text" value="" label="CGU" />
435 <param name="colorCUA" size="10" type="text" value="" label="CUA" />
436 <param name="colorCUC" size="10" type="text" value="" label="CUC" />
437 <param name="colorCUG" size="10" type="text" value="" label="CUG" />
438 <param name="colorCUU" size="10" type="text" value="" label="CUU" />
439 <param name="colorGAA" size="10" type="text" value="" label="GAA" />
440 <param name="colorGAC" size="10" type="text" value="" label="GAC" />
441 <param name="colorGAG" size="10" type="text" value="" label="GAG" />
442 <param name="colorGAU" size="10" type="text" value="" label="GAU" />
443 <param name="colorGCA" size="10" type="text" value="" label="GCA" />
444 <param name="colorGCC" size="10" type="text" value="" label="GCC" />
445 <param name="colorGCG" size="10" type="text" value="" label="GCG" />
446 <param name="colorGCU" size="10" type="text" value="" label="GCU" />
447 <param name="colorGGA" size="10" type="text" value="" label="GGA" />
448 <param name="colorGGC" size="10" type="text" value="" label="GGC" />
449 <param name="colorGGG" size="10" type="text" value="" label="GGG" />
450 <param name="colorGGU" size="10" type="text" value="" label="GGU" />
451 <param name="colorGUA" size="10" type="text" value="" label="GUA" />
452 <param name="colorGUC" size="10" type="text" value="" label="GUC" />
453 <param name="colorGUG" size="10" type="text" value="" label="GUG" />
454 <param name="colorGUU" size="10" type="text" value="" label="GUU" />
455 <param name="colorUAA" size="10" type="text" value="" label="UAA" />
456 <param name="colorUAC" size="10" type="text" value="" label="UAC" />
457 <param name="colorUAG" size="10" type="text" value="" label="UAG" />
458 <param name="colorUAU" size="10" type="text" value="" label="UAU" />
459 <param name="colorUCA" size="10" type="text" value="" label="UCA" />
460 <param name="colorUCC" size="10" type="text" value="" label="UCC" />
461 <param name="colorUCG" size="10" type="text" value="" label="UCG" />
462 <param name="colorUCU" size="10" type="text" value="" label="UCU" />
463 <param name="colorUGA" size="10" type="text" value="" label="UGA" />
464 <param name="colorUGC" size="10" type="text" value="" label="UGC" />
465 <param name="colorUGG" size="10" type="text" value="" label="UGG" />
466 <param name="colorUGU" size="10" type="text" value="" label="UGU" />
467 <param name="colorUUA" size="10" type="text" value="" label="UUA" />
468 <param name="colorUUC" size="10" type="text" value="" label="UUC" />
469 <param name="colorUUG" size="10" type="text" value="" label="UUG" />
470 <param name="colorUUU" size="10" type="text" value="" label="UUU" />
471
472
473
474 </when>
475
476 </conditional>
477 <param name="size" type="select" label="Output CodonLogo size" >
478 <option value="large" selected="True">Large</option>
479 <option value="medium">Medium</option>
480 <option value="small">Small</option>
481 </param>
482
483 </page>
484 </inputs>
485 <outputs>
486 <data format="pdf" name="output" label="${logoname}_output.${outformat}">
487 <change_format>
488 <when input="outformat" value="png_print" format="png" />
489 <when input="outformat" value="png" format="png" />
490 <when input="outformat" value="jpeg" format="jpg" />
491 <when input="outformat" value="eps" format="eps" />
492 <when input="outformat" value="txt" format="txt" />
493 </change_format>
494 </data>
495 </outputs>
496 <help>
497
498 **Note**
499
500 This tool uses CodonLogo in Galaxy to generate a sequence logo from a provided alignment.
501 The input file must be an alignment in your current history.
502 The tool will attempt to read a provided file and if it is unable to it will generate an error.
503
504 A typical output looks like this
505
506 .. image:: ./static/images/CodonLogoExample.png
507
508 ----
509
510 **Warning about input files**
511
512 The program used by this tool will fail if your alignment files are not all the same length.
513
514 Fasta alignments from ClustalW Galaxy tool will work but many other fasta files may cause this tool to produce an error and fail - please do not file
515 a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta
516 sequences are the same length!
517
518 Files must first be converted to fasta format in order to be used with this tool.
519
520 ----
521
522 The default colour scheme is based on associated amino acid types:
523
524 Polar positive
525 H, K, R -Light Blue
526
527 Polar negative
528 D, E -Red
529
530 Polar neutral
531 S, T, N, Q -Green
532
533 Non-polar aliphatic
534 A, V, L, I, M -Blue
535
536 Non-polar aromatic
537 F, W, Y -Magenta
538 P, G -Brown
539 C -Yellow
540
541 Stop codons -Black
542
543
544 **Attribution**
545
546
547 This Galaxy wrapper was modified for CodonLogo by David Murphy and is based on the wrapper written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_
548
549 .. _Weblogo3: http://weblogo.berkeley.edu/
550 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
551 .. _CodonLogo: http://recode.ucc.ie/CodonLogo
552
553 </help>
554
555 </tool>
556
557