Mercurial > repos > iuc > pygenometracks

comparison pyGenomeTracks.xml @ 0:5141268dba30 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
author iuc
date Sat, 23 Jun 2018 02:27:58 -0400
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children f4b8c2ccc5f7
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-1:000000000000 0:5141268dba30
1 <tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>plot genomic data tracks</description>
3 <macros>
4 <token name="@BINARY@">pyGenomeTracks</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code">
9 <![CDATA[
10
11 sed '/^$/d' '$tracks_config' &&
12 @BINARY@
13 --tracks '$tracks_config'
14 #if $region and $region is not None:
15 --region '$region'
16 #end if
17 --outFileName plot.$image_file_format
18 && mv plot.$image_file_format plot
19 ]]>
20 </command>
21 <configfiles>
22 <configfile name="tracks_config">
23 #if $x_axis.x_axis_select == "yes":
24 [x-axis]
25 #if $x_axis.fontsize:
26 fontsize = $x_axis.fontsize
27 #end if
28 #if $x_axis.where:
29 where = $x_axis.where
30 #end if
31 #end if
32 #for $counter, $track in enumerate($tracks):
33 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
34
35 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
36 [hic_section_$counter]
37 file = $data_matrix
38 file_type = hic_matrix
39 #if $track.track_file_style_conditional.title:
40 title = $track.track_file_style_conditional.title
41 #else:
42 title = $data_matrix.name
43 #end if
44 #if $track.track_file_style_conditional.depth:
45 depth = $track.track_file_style_conditional.depth
46 #end if
47 #if $track.track_file_style_conditional.colormap:
48 colormap = $track.track_file_style_conditional.colormap
49 #end if
50 #if $track.track_file_style_conditional.min_value:
51 min_value = $track.track_file_style_conditional.min_value
52 #end if
53 #if $track.track_file_style_conditional.max_value:
54 max_value = $track.track_file_style_conditional.max_value
55 #end if
56 transform = $track.track_file_style_conditional.transform
57 height = $track.track_file_style_conditional.height_matrix
58
59 #if $track.track_file_style_conditional.boundaries_file is not None:
60 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]
61 boundaries_file = $boundary_file
62 #end if
63
64 #if $track.track_file_style_conditional.x_labels:
65 x labels = $track.track_file_style_conditional.x_labels
66 #end if
67 #if $track.track_file_style_conditional.type:
68 type = $track.track_file_style_conditional.type
69 #end if
70 #if $track.track_file_style_conditional.show_masked_bins:
71 show_masked_bins = $track.track_file_style_conditional.show_masked_bins
72 #end if
73 #if $track.track_file_style_conditional.scale_factor:
74 scale factor = $track.track_file_style_conditional.scale_factor
75 #end if
76
77 [spacer]
78 #if $track.track_file_style_conditional.spacer_height:
79 height = $track.track_file_style_conditional.spacer_height
80 #end if
81 #end for
82
83 #end if
84
85
86
87 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":
88
89 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
90 [tad_score_$counter]
91 file = $data_bedgraph
92 #if $track.track_file_style_conditional.title:
93 title = $track.track_file_style_conditional.title
94 #else:
95 title = $data_bedgraph.name
96 #end if
97 #if $track.track_file_style_conditional.color:
98 color = $track.track_file_style_conditional.color
99 #end if
100 #if $track.track_file_style_conditional.height_tad:
101 height = $track.track_file_style_conditional.height_tad
102 #end if
103 #if $track.track_file_style_conditional.type_lines:
104 type = $track.track_file_style_conditional.type_lines
105 #end if
106 #if $track.track_file_style_conditional.show_data:
107 show data range = $track.track_file_style_conditional.show_data
108 #end if
109
110 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
111 #if $columns > 5:
112 file_type = bedgraph_matrix
113 #else:
114 file_type = bedgraph
115 #end if
116 type = lines
117 [spacer]
118 #if $track.track_file_style_conditional.spacer_height:
119 height = $track.track_file_style_conditional.spacer_height
120 #end if
121 #end for
122 #end if
123
124
125
126
127 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
128 #for $data_bed in $track.track_file_style_conditional.track_input_bed:
129
130 [chrom states_$counter]
131 file = $data_bed
132 #if $track.track_file_style_conditional.title:
133 title = $track.track_file_style_conditional.title
134 #else:
135 title = $data_bed.name
136 #end if
137 #if $track.track_file_style_conditional.color:
138 color = $track.track_file_style_conditional.color
139 #end if
140 display = collapsed
141 #if $track.track_file_style_conditional.height_chrom:
142 height = $track.track_file_style_conditional.height_chrom
143 #end if
144 #if $track.track_file_style_conditional.border_color:
145 border_color = $track.track_file_style_conditional.border_color
146 #end if
147 file_type = bed
148 [spacer]
149 #if $track.track_file_style_conditional.spacer_height:
150 height = $track.track_file_style_conditional.spacer_height
151 #end if
152 #end for
153
154 #end if
155
156
157
158
159 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
160 #for $data_bed in $track.track_file_style_conditional.track_input_bed:
161
162 [genes_$counter]
163 file = $data_bed
164 #if $track.track_file_style_conditional.title:
165 title = $track.track_file_style_conditional.title
166 #else:
167 title = $data_bed.name
168 #end if
169 #if $track.track_file_style_conditional.color:
170 color = $track.track_file_style_conditional.color
171 #end if
172
173 #if $track.track_file_style_conditional.height_bed:
174 height = $track.track_file_style_conditional.height_bed
175 #end if
176
177 #if $track.track_file_style_conditional.labels:
178 labels = $track.track_file_style_conditional.labels
179 #end if
180
181 #if $track.track_file_style_conditional.type:
182 type = $track.track_file_style_conditional.type
183 #end if
184
185 file_type = bed
186 #if $track.track_file_style_conditional.fontsize:
187 fontsize = $track.track_file_style_conditional.fontsize
188 #end if
189
190 #if $track.track_file_style_conditional.gene_rows:
191 gene rows = $track.track_file_style_conditional.gene_rows
192 #end if
193
194 #if $track.track_file_style_conditional.global_max_row:
195 global max row = $track.track_file_style_conditional.global_max_row
196 #end if
197 [spacer]
198 #if $track.track_file_style_conditional.spacer_height:
199 height = $track.track_file_style_conditional.spacer_height
200 #end if
201 #end for
202 #end if
203
204
205 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
206 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
207
208 [bedgraph_$counter]
209 file = $data_bedgraph
210 #if $track.track_file_style_conditional.title:
211 title = $track.track_file_style_conditional.title
212 #else:
213 title = $data_bedgraph.name
214 #end if
215 #if $track.track_file_style_conditional.color:
216 color = $track.track_file_style_conditional.color
217 #end if
218 #if $track.track_file_style_conditional.height_bedgraph:
219 height = $track.track_file_style_conditional.height_bedgraph
220 #end if
221 #if $track.track_file_style_conditional.show_data:
222 show data range = $track.track_file_style_conditional.show_data
223 #end if
224
225 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
226 #if $columns > 5:
227 file_type = bedgraph_matrix
228 #else:
229 file_type = bedgraph
230 #end if
231 type = lines
232 [spacer]
233 #if $track.track_file_style_conditional.spacer_height:
234 height = $track.track_file_style_conditional.spacer_height
235 #end if
236 #end for
237 #end if
238
239 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
240 #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig:
241 [bigwig_$counter]
242 file = $data_bigwig
243 #if $track.track_file_style_conditional.title:
244 title = $track.track_file_style_conditional.title
245 #else:
246 title = $data_bigwig.name
247 #end if
248 color = $track.track_file_style_conditional.color
249 #if $track.track_file_style_conditional.min_value:
250 min_value = $track.track_file_style_conditional.min_value
251 #else:
252 min_value = 0
253 #end if
254 #if $track.track_file_style_conditional.max_value:
255 max_value = $track.track_file_style_conditional.max_value
256 #else:
257 max_value = auto
258 #end if
259 height = $track.track_file_style_conditional.height_bigwig
260 #if $track.track_file_style_conditional.number_of_bins:
261 number of bins = $track.track_file_style_conditional.number_of_bins
262 #end if
263 nans to zeros = $track.track_file_style_conditional.nans_to_zeros
264 #if $track.track_file_style_conditional.type_conditional == 'fill_option':
265 type = fill
266 #elif $track.track_file_style_conditional.type_conditional == 'line_option':
267 type = line:$track.track_file_style_conditional.type_conditional.height_line
268 #elif $track.track_file_style_conditional.type_conditional == 'point_option':
269 type = points:$track.track_file_style_conditional.type_conditional.width_point
270 #end if
271 #if $track.track_file_style_conditional.data_range:
272 show data range = $track.track_file_style_conditional.data_range
273 #end if
274 file_type = bigwig
275 [spacer]
276 #if $track.track_file_style_conditional.spacer_height:
277 height = $track.track_file_style_conditional.spacer_height
278 #end if
279 #end for
280 #end if
281
282
283 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
284 #for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix:
285
286 [bedgraph_matrix_$counter]
287 file = $data_bedgraph_matrix
288 #if $track.track_file_style_conditional.title:
289 title = $track.track_file_style_conditional.title
290 #else:
291 title = $data_bedgraph_matrix.name
292 #end if
293 #if $track.track_file_style_conditional.height_bedgraph:
294 height = $track.track_file_style_conditional.height_bedgraph
295 #end if
296 orientation = inverted
297 #if $track.track_file_style_conditional.min_value:
298 min_value = $track.track_file_style_conditional.min_value
299 #end if
300 #if $track.track_file_style_conditional.max_value:
301 max_value = $track.track_file_style_conditional.max_value
302 #end if
303 #if $track.track_file_style_conditional.type_lines:
304 type = $track.track_file_style_conditional.type_lines
305 #end if
306 file_type = bedgraph_matrix
307 plot horizontal lines=False
308 [spacer]
309 #if $track.track_file_style_conditional.spacer_height:
310 height = $track.track_file_style_conditional.spacer_height
311 #end if
312 #end for
313 #end if
314
315 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
316
317 [vlines_$counter]
318 file = $track.track_file_style_conditional.track_input_bed_single
319 type = vlines
320 file_type = bed
321 #end if
322 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
323
324 [spacer]
325 #if $track.track_file_style_conditional.spacer_height:
326 height = $track.track_file_style_conditional.spacer_height
327 #end if
328 #end if
329 #end for</configfile>
330 </configfiles>
331 <inputs>
332 <expand macro="region" />
333
334 <repeat name="tracks" min="1" title="Include tracks in your plot"
335 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph">
336 <conditional name="track_file_style_conditional">
337 <param name="track_file_style_selector" type="select" label="Choose style of the track">
338 <option value="hic_matrix_option">TAD visualization</option>
339 <option value="chrom_states_option">Chromatine states</option>
340 <option value="tad_score_track_option">TAD score</option>
341 <option value="gene_track_option">Gene track / Bed track</option>
342 <option value="bigwig_track_option">Bigwig track</option>
343 <option value="bedgraph_track_option">Bedgraph track </option>
344 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
345 <option value="vlines_track_option">Vlines track</option>
346 <option value="spacer_option">Spacer</option>
347 </param>
348 <when value="hic_matrix_option">
349 <expand macro="plot_title" />
350 <expand macro="matrix_h5_cooler_multiple_macro" />
351
352 <expand macro="colormap" />
353 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
354 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
355 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
356 <param name="transform" type="select" label="Plot the transformed value">
357 <option value="log1p" selected="True" >log1p</option>
358 <option value="log">log</option>
359 <option value="-log">-log</option>
360
361 </param>
362 <param name="height_matrix" type="float" value="1.5" optional="True" label="height"/>
363
364 <param name="type" type="select" optional="True" label="Plotting type">
365 <option value="arcplot">arcplot</option>
366 <option value="interaction">interaction</option>
367 </param>
368 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false"
369 label="Show masked bins" />
370 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple='True'/> <!-- multiple='True'-->
371 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" />
372 <param name="x_labels" type="boolean" truevalue="yes" falsevalue="no" optional="True" label="Show x labels" />
373 <expand macro="spacer_macro" />
374
375 </when>
376 <when value="tad_score_track_option">
377 <expand macro="plot_title" />
378 <expand macro="track_input_bedgraph_macro" />
379 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
380 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
381 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
382 of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
383 <param name="height_tad" type="float" value="0.2" optional="True" label="height"/>
384 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
385 <expand macro="spacer_macro" />
386
387 </when>
388 <when value="chrom_states_option">
389 <expand macro="plot_title" />
390
391 <expand macro="track_input_bed_macro" />
392 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
393
394 <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
395 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/>
396 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
397 label="Plot labels" />
398 <expand macro="spacer_macro" />
399
400 </when>
401 <when value="gene_track_option">
402 <expand macro="plot_title" />
403
404 <expand macro="track_input_bed_macro" />
405 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
406 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/>
407 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
408 label="Plot labels" />
409 <param name="type" type="select" optional="True" label="Type">
410 <option value="genes">genes</option>
411 <option value="domains">domains</option>
412 </param>
413 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false"
414 label="Global max rows" />
415 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" />
416 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
417 <expand macro="spacer_macro" />
418
419 </when>
420 <when value="bedgraph_track_option">
421 <expand macro="plot_title" />
422 <expand macro="track_input_bedgraph_macro" />
423 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
424
425 <param name="height_bedgraph" type="float" value="0.2" optional="True" label="height"/>
426 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
427 <expand macro="spacer_macro" />
428
429 </when>
430 <when value="bigwig_track_option">
431 <expand macro="plot_title" />
432
433 <expand macro="track_input_bigwig_macro" />
434 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
435
436 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
437 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
438
439 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/>
440 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
441 <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false"
442 label="NAN's to zeros" />
443 <conditional name="type_conditional">
444 <param name="type_selector" type="select" label="Choose style of the plot.">
445 <option value="fill_option">fill</option>
446 <option value="line_option">line</option>
447 <option value="point_option">point</option>
448 </param>
449 <when value="line_option">
450 <param name="width_line" type="float" value="0.5" optional="True" label="Width"/>
451 </when>
452 <when value="point_option">
453 <param name="width_point" type="float" value="0.5" optional="True" label="Width"/>
454 </when>
455 <when value="fill_option" />
456 </conditional>
457 <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" />
458 <expand macro="spacer_macro" />
459
460 </when>
461
462
463 <when value="bedgraph_matrix_track_option">
464 <expand macro="plot_title" />
465
466 <expand macro="track_input_bedgraph_matrix_macro" />
467 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
468 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
469
470 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
471
472 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
473 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
474 of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
475 <expand macro="spacer_macro" />
476
477 </when>
478 <when value="vlines_track_option">
479 <expand macro="track_input_bed_single_macro" />
480 </when>
481 <when value="spacer_option">
482 <expand macro="spacer_macro" />
483 </when>
484 </conditional>
485
486 </repeat>
487
488
489 <conditional name="x_axis">
490 <param name="x_axis_select" type="select" label="Configure x-axis">
491 <option value="no" selected="True">No</option>
492 <option value="yes">Yes</option>
493 </param>
494 <when value="yes">
495 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
496 <param name="where" type="select" optional="True" label="Where to place the x-axis">
497 <option value="top">Top</option>
498 <option value="bottom">Bottom</option>
499 </param>
500 </when>
501 <when value="no" />
502 </conditional>
503 <param name="image_file_format" type="select" label="Image output format">
504 <option value="png">png</option>
505 <option value="svg">svg</option>
506 </param>
507 </inputs>
508 <outputs>
509 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on [${on_string}]: Plot">
510 <change_format>
511 <when input="image_file_format" value="png" format="png" />
512 <when input="image_file_format" value="svg" format="svg" />
513 </change_format>
514 </data>
515 </outputs>
516 <tests>
517 <test>
518 <param name="region" value="chrX:3000000-3500000"/>
519 <conditional name="x_axis">
520 <param name="x_axis_select" value="yes" />
521 </conditional>
522 <repeat name="tracks">
523 <conditional name="track_file_style_conditional">
524 <param name="track_file_style_selector" value="hic_matrix_option" />
525 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
526
527 <param name="title" value="Kc DpnII (Li et al. 2015)" />
528 <param name="colormap" value="RdYlBu_r" />
529 <param name="depth" value="200000" />
530 <param name="transform" value="log1p" />
531 <param name="boundaries_file" value="domains.bed" />
532 <param name="x_labels" value="True" />
533 </conditional>
534 </repeat>
535 <repeat name="tracks">
536 <conditional name="track_file_style_conditional">
537 <param name="track_file_style_selector" value="spacer_option" />
538 <param name="spacer_height" value="0.05" />
539 </conditional>
540 </repeat>
541 <repeat name="tracks">
542 <conditional name="track_file_style_conditional">
543 <param name="track_file_style_selector" value="chrom_states_option" />
544 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
545 <param name="title" value="TAD state" />
546 <param name="height_chrom" value="0.5" />
547 <param name="labels" value="off" />
548 </conditional>
549 </repeat>
550 <repeat name="tracks">
551 <conditional name="track_file_style_conditional">
552 <param name="track_file_style_selector" value="tad_score_track_option" />
553 <param name="track_input_bedgraph" value="tad_score.gz" ftype="bedgraph" />
554 <param name="title" value="TAD separation score (Ramirez et al.)" />
555 <param name="height_tad" value="10" />
556 </conditional>
557 </repeat>
558 <repeat name="tracks">
559 <conditional name="track_file_style_conditional">
560 <param name="track_file_style_selector" value="spacer_option" />
561 <param name="spacer_height" value="1" />
562 </conditional>
563 </repeat>
564 <repeat name="tracks">
565 <conditional name="track_file_style_conditional">
566 <param name="track_file_style_selector" value="bedgraph_track_option" />
567 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
568 <param name="title" value="bedgraph" />
569 <param name="height_bedgraph" value="4" />
570 <param name="color" value="blue" />
571 </conditional>
572 </repeat>
573 <repeat name="tracks">
574 <conditional name="track_file_style_conditional">
575 <param name="track_file_style_selector" value="bigwig_track_option" />
576 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
577 <param name="title" value="rep 1 test fill" />
578 <param name="height_bigwig" value="4" />
579 <param name="color" value="blue" />
580 <conditional name="type_conditional">
581 <param name="type_selector" value="fill_option" />
582 </conditional>
583 </conditional>
584 </repeat>
585
586 <repeat name="tracks">
587 <conditional name="track_file_style_conditional">
588 <param name="track_file_style_selector" value="bigwig_track_option" />
589 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
590 <param name="title" value="rep 1 test line" />
591 <param name="height_bigwig" value="4" />
592 <param name="color" value="red" />
593 <conditional name="type_conditional">
594 <param name="type_selector" value="line_option" />
595 <param name="width_line" value="1" />
596 </conditional>
597 </conditional>
598 </repeat>
599
600 <repeat name="tracks">
601 <conditional name="track_file_style_conditional">
602 <param name="track_file_style_selector" value="bigwig_track_option" />
603 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
604 <param name="title" value="rep 1 test lw=0.2" />
605 <param name="height_bigwig" value="4" />
606 <param name="color" value="red" />
607 <conditional name="type_conditional">
608 <param name="type_selector" value="line_option" />
609 <param name="width_line" value="0.1" />
610
611 </conditional>
612 </conditional>
613 </repeat>
614
615 <repeat name="tracks">
616 <conditional name="track_file_style_conditional">
617 <param name="track_file_style_selector" value="bigwig_track_option" />
618 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
619 <param name="title" value="rep 1 test point:0.5" />
620 <param name="height_bigwig" value="4" />
621 <param name="color" value="black" />
622 <conditional name="type_conditional">
623 <param name="type_selector" value="point_option" />
624 <param name="width_point" value="0.5" />
625
626 </conditional>
627 </conditional>
628 </repeat>
629
630 <repeat name="tracks">
631 <conditional name="track_file_style_conditional">
632 <param name="track_file_style_selector" value="spacer_option" />
633 <param name="spacer_height" value="0.5" />
634 </conditional>
635 </repeat>
636 <repeat name="tracks">
637 <conditional name="track_file_style_conditional">
638 <param name="track_file_style_selector" value="gene_track_option" />
639 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
640 <param name="title" value="genes" />
641 <param name="height_bed" value="5" />
642 <param name="fontsize" value="10" />
643 </conditional>
644 </repeat>
645 <repeat name="tracks">
646 <conditional name="track_file_style_conditional">
647 <param name="track_file_style_selector" value="spacer_option" />
648 <param name="spacer_height" value="1" />
649 </conditional>
650 </repeat>
651 <repeat name="tracks">
652 <conditional name="track_file_style_conditional">
653 <param name="track_file_style_selector" value="gene_track_option" />
654 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
655 <param name="title" value="max num rows 3" />
656 <param name="height_bed" value="3" />
657 <param name="fontsize" value="8" />
658 <param name="gene_rows" value="3" />
659 </conditional>
660 </repeat>
661 <repeat name="tracks">
662 <conditional name="track_file_style_conditional">
663 <param name="track_file_style_selector" value="spacer_option" />
664 <param name="spacer_height" value="1" />
665 </conditional>
666 </repeat>
667 <repeat name="tracks">
668 <conditional name="track_file_style_conditional">
669 <param name="track_file_style_selector" value="gene_track_option" />
670 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
671 <param name="title" value="bed6 global max row" />
672 <param name="height_bed" value="20" />
673 <param name="fontsize" value="10" />
674 <param name="global_max_row" value="True" />
675 </conditional>
676 </repeat>
677 <repeat name="tracks">
678 <conditional name="track_file_style_conditional">
679 <param name="track_file_style_selector" value="vlines_track_option" />
680 <param name="track_input_bed_single" value="domains.bed" ftype="bed" />
681 <param name="type" value="vlines" />
682 </conditional>
683 </repeat>
684 <param name="image_file_format" value="png" />
685 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
686 </test>
687 <test>
688 <param name="region" value="chrX:3000000-3500000"/>
689 <conditional name="x_axis">
690 <param name="x_axis_select" value="yes" />
691 </conditional>
692 <repeat name="tracks">
693 <conditional name="track_file_style_conditional">
694 <param name="track_file_style_selector" value="bigwig_track_option" />
695 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
696 <param name="title" value="rep 1 test line" />
697 <param name="height_bigwig" value="4" />
698 <param name="color" value="red" />
699 <conditional name="type_conditional">
700 <param name="type_selector" value="line_option" />
701 <param name="width_line" value="1" />
702 </conditional>
703 </conditional>
704 </repeat>
705 <param name="image_file_format" value="png" />
706 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" />
707 </test>
708 </tests>
709 <help><![CDATA[
710
711 pyGenomeTracks
712 ==============
713
714 **pyGenomeTracks** is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable.
715 Currently, it is possible to plot:
716
717 - bigwig
718 - bed (many options)
719 - bedgraph
720 - links (represented as arcs)
721 - Hi-C matrices
722
723 _________________
724
725 Usage
726 -----
727
728 This tool takes various types of tracks as input:
729
730 - **Chromatin states:** display blocks of different colors following a bed file.
731 - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off.
732 - **Bigwig track:** generic bigwig track plotting.
733 - **Bedgraph track:** generic bedgraph track plotting.
734 - **Bedgraph matrix track** is used to specifically plot bm files computed by HiCExplorer's ``hicFindTADs`` (TAD seperation scores).
735 - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer's ``hicFindTADs``.
736 - **Spacer:** Add some space between two tracks.
737 - **Hi-C tracks:**
738 - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap.
739 - **TAD score:** display TAD seperation score computed by HiCExplorer's ``hicFindTADs``.
740
741
742 For each track, parameters for the color, the width or the font size can be defined.
743
744 _________________
745
746 Output
747 ------
748
749 **pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files)
750 also contains Hi-C data. The plot is composed of tracks that need to be specified.
751 Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**.
752 TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to:
753 TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states,
754 principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track.
755 Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_.
756
757 .. image:: $PATH_TO_IMAGES/pyGenomeTracks.png
758 :width: 70 %
759
760 _________________
761
762 | For more information about pyGenomeTracks please consider our documentation on github_
763
764 .. _github: https://github.com/deeptools/pyGenomeTracks
765 .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9
766 ]]></help>
767 <expand macro="citations" />
768 </tool>