Mercurial > repos > bgruening > hicexplorer_hicplottads

comparison hicPlotTADs.xml @ 8:7e535e3b71f3 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
author iuc
date Fri, 27 Apr 2018 03:38:47 -0400
parents 94fff1a6a899
children
comparison
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7:94fff1a6a899 8:7e535e3b71f3
1 <tool id="hicexplorer_hicplottads" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicplottads" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>Plots the diagonal, and some values close to the diagonal of a HiC matrix</description> 2 <description>plot Hi-C contact matrices heatmaps alongside other data tracks</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicPlotTADs</token> 4 <token name="@BINARY@">hicPlotTADs</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
28 #if $x_axis.where: 28 #if $x_axis.where:
29 where = $x_axis.where 29 where = $x_axis.where
30 #end if 30 #end if
31 #end if 31 #end if
32 #for $counter, $track in enumerate($tracks): 32 #for $counter, $track in enumerate($tracks):
33 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": 33 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
34 [hic_section_$counter] 34 [hic_section_$counter]
35 file = $track.track_file_style_conditional.matrix_h5_cooler 35 file = $track.track_file_style_conditional.matrix_h5_cooler
36 file_type = hic_matrix 36 file_type = hic_matrix
37 title = $track.track_file_style_conditional.title 37 title = $track.track_file_style_conditional.title
38 #if $track.track_file_style_conditional.depth: 38 #if $track.track_file_style_conditional.depth:
42 colormap = $track.track_file_style_conditional.colormap 42 colormap = $track.track_file_style_conditional.colormap
43 #end if 43 #end if
44 #if $track.track_file_style_conditional.min_value: 44 #if $track.track_file_style_conditional.min_value:
45 min_value = $track.track_file_style_conditional.min_value 45 min_value = $track.track_file_style_conditional.min_value
46 #end if 46 #end if
47 #if $track.track_file_style_conditional.max_value: 47 #if $track.track_file_style_conditional.max_value:
48 max_value = $track.track_file_style_conditional.max_value 48 max_value = $track.track_file_style_conditional.max_value
49 #end if 49 #end if
50 transform = $track.track_file_style_conditional.transform 50 transform = $track.track_file_style_conditional.transform
51 width = $track.track_file_style_conditional.width_matrix 51 width = $track.track_file_style_conditional.width_matrix
52 #if $track.track_file_style_conditional.boundaries_file: 52 #if $track.track_file_style_conditional.boundaries_file:
63 #end if 63 #end if
64 #if $track.track_file_style_conditional.scale_factor: 64 #if $track.track_file_style_conditional.scale_factor:
65 scale factor = $track.track_file_style_conditional.scale_factor 65 scale factor = $track.track_file_style_conditional.scale_factor
66 #end if 66 #end if
67 67
68 #end if 68 #end if
69 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option": 69 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":
70 70
71 [tad_score_$counter] 71 [tad_score_$counter]
72 file = $track.track_file_style_conditional.track_input_bedgraph 72 file = $track.track_file_style_conditional.track_input_bedgraph
73 title = $track.track_file_style_conditional.title 73 title = $track.track_file_style_conditional.title
89 file_type = bedgraph_matrix 89 file_type = bedgraph_matrix
90 #else: 90 #else:
91 file_type = bedgraph 91 file_type = bedgraph
92 #end if 92 #end if
93 type = lines 93 type = lines
94 #end if 94 #end if
95 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option": 95 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
96 96
97 [chrom states_$counter] 97 [chrom states_$counter]
98 file = $track.track_file_style_conditional.track_input_bed 98 file = $track.track_file_style_conditional.track_input_bed
99 title = $track.track_file_style_conditional.title 99 title = $track.track_file_style_conditional.title
114 [genes_$counter] 114 [genes_$counter]
115 file = $track.track_file_style_conditional.track_input_bed 115 file = $track.track_file_style_conditional.track_input_bed
116 title = $track.track_file_style_conditional.title 116 title = $track.track_file_style_conditional.title
117 #if $track.track_file_style_conditional.color: 117 #if $track.track_file_style_conditional.color:
118 color = $track.track_file_style_conditional.color 118 color = $track.track_file_style_conditional.color
119 #end if 119 #end if
120 120
121 #if $track.track_file_style_conditional.width_bed: 121 #if $track.track_file_style_conditional.width_bed:
122 width = $track.track_file_style_conditional.width_bed 122 width = $track.track_file_style_conditional.width_bed
123 #end if 123 #end if
124 124
125 #if $track.track_file_style_conditional.labels: 125 #if $track.track_file_style_conditional.labels:
126 labels = $track.track_file_style_conditional.labels 126 labels = $track.track_file_style_conditional.labels
127 #end if 127 #end if
128 128
129 #if $track.track_file_style_conditional.type: 129 #if $track.track_file_style_conditional.type:
130 type = $track.track_file_style_conditional.type 130 type = $track.track_file_style_conditional.type
131 #end if 131 #end if
132 132
133 file_type = bed 133 file_type = bed
134 #if $track.track_file_style_conditional.fontsize: 134 #if $track.track_file_style_conditional.fontsize:
135 fontsize = $track.track_file_style_conditional.fontsize 135 fontsize = $track.track_file_style_conditional.fontsize
136 #end if 136 #end if
137 137
138 #if $track.track_file_style_conditional.gene_rows: 138 #if $track.track_file_style_conditional.gene_rows:
139 gene rows = $track.track_file_style_conditional.gene_rows 139 gene rows = $track.track_file_style_conditional.gene_rows
140 #end if 140 #end if
141 141
142 #if $track.track_file_style_conditional.global_max_row: 142 #if $track.track_file_style_conditional.global_max_row:
143 global max row = $track.track_file_style_conditional.global_max_row 143 global max row = $track.track_file_style_conditional.global_max_row
144 #end if 144 #end if
145 145
146 #end if 146 #end if
147 147
148 148
149 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option": 149 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
150 150
151 [bedgraph_$counter] 151 [bedgraph_$counter]
166 file_type = bedgraph_matrix 166 file_type = bedgraph_matrix
167 #else: 167 #else:
168 file_type = bedgraph 168 file_type = bedgraph
169 #end if 169 #end if
170 type = lines 170 type = lines
171 #end if 171 #end if
172 172
173 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option": 173 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
174 174
175 [bigwig_$counter] 175 [bigwig_$counter]
176 file = $track.track_file_style_conditional.track_input_bigwig 176 file = $track.track_file_style_conditional.track_input_bigwig
193 nans to zeros = $track.track_file_style_conditional.nans_to_zeros 193 nans to zeros = $track.track_file_style_conditional.nans_to_zeros
194 #if $track.track_file_style_conditional.type_conditional == 'fill_option': 194 #if $track.track_file_style_conditional.type_conditional == 'fill_option':
195 type = fill 195 type = fill
196 #elif $track.track_file_style_conditional.type_conditional == 'line_option': 196 #elif $track.track_file_style_conditional.type_conditional == 'line_option':
197 type = line:$track.track_file_style_conditional.type_conditional.width_line 197 type = line:$track.track_file_style_conditional.type_conditional.width_line
198 #elif $track.track_file_style_conditional.type_conditional == 'point_option': 198 #elif $track.track_file_style_conditional.type_conditional == 'point_option':
199 type = points:$track.track_file_style_conditional.type_conditional.width_point 199 type = points:$track.track_file_style_conditional.type_conditional.width_point
200 #end if 200 #end if
201 #if $track.track_file_style_conditional.data_range: 201 #if $track.track_file_style_conditional.data_range:
202 show data range = $track.track_file_style_conditional.data_range 202 show data range = $track.track_file_style_conditional.data_range
203 #end if 203 #end if
204 file_type = bigwig 204 file_type = bigwig
205 #end if 205 #end if
206 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option": 206 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
207 207
208 [bedgraph_matrix_$counter] 208 [bedgraph_matrix_$counter]
209 file = $track.track_file_style_conditional.track_input_bedgraph_matrix 209 file = $track.track_file_style_conditional.track_input_bedgraph_matrix
210 title = $track.track_file_style_conditional.title 210 title = $track.track_file_style_conditional.title
221 #if $track.track_file_style_conditional.type_lines: 221 #if $track.track_file_style_conditional.type_lines:
222 type = $track.track_file_style_conditional.type_lines 222 type = $track.track_file_style_conditional.type_lines
223 #end if 223 #end if
224 file_type = bedgraph_matrix 224 file_type = bedgraph_matrix
225 plot horizontal lines=False 225 plot horizontal lines=False
226 #end if 226 #end if
227 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option": 227 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
228 228
229 [vlines_$counter] 229 [vlines_$counter]
230 file = $track.track_file_style_conditional.track_input_bed 230 file = $track.track_file_style_conditional.track_input_bed
231 type = vlines 231 type = vlines
232 file_type = bed 232 file_type = bed
233 #end if 233 #end if
234 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": 234 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
235 235
236 [spacer] 236 [spacer]
237 #if $track.track_file_style_conditional.spacer_width: 237 #if $track.track_file_style_conditional.spacer_width:
238 width = $track.track_file_style_conditional.spacer_width 238 width = $track.track_file_style_conditional.spacer_width
239 #end if 239 #end if
240 #end if 240 #end if
241 #end for</configfile> 241 #end for</configfile>
242 </configfiles> 242 </configfiles>
243 <inputs> 243 <inputs>
244 <expand macro="region" /> 244 <expand macro="region" />
245 245
247 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph"> 247 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph">
248 <conditional name="track_file_style_conditional"> 248 <conditional name="track_file_style_conditional">
249 <param name="track_file_style_selector" type="select" label="Choose style of the track"> 249 <param name="track_file_style_selector" type="select" label="Choose style of the track">
250 <option value="hic_matrix_option">TAD visualization</option> 250 <option value="hic_matrix_option">TAD visualization</option>
251 <option value="chrom_states_option">Chromatine states</option> 251 <option value="chrom_states_option">Chromatine states</option>
252 <option value="tad_score_track_option">TAD score</option> 252 <option value="tad_score_track_option">TAD score</option>
253 <option value="gene_track_option">Gene track / Bed track</option> 253 <option value="gene_track_option">Gene track / Bed track</option>
254 <option value="bigwig_track_option">Bigwig track</option> 254 <option value="bigwig_track_option">Bigwig track</option>
255 <option value="bedgraph_track_option">Bedgraph track </option> 255 <option value="bedgraph_track_option">Bedgraph track </option>
256 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option> 256 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
257 <option value="vlines_track_option">Vlines track</option> 257 <option value="vlines_track_option">Vlines track</option>
258 <option value="spacer_option">Spacer</option> 258 <option value="spacer_option">Spacer</option>
259 </param> 259 </param>
260 <when value="hic_matrix_option"> 260 <when value="hic_matrix_option">
261 <expand macro="plot_title" /> 261 <expand macro="plot_title" />
262 <expand macro="matrix_h5_cooler_macro" /> 262 <expand macro="matrix_h5_cooler_macro" />
263 263
264 <expand macro="colormap" /> 264 <expand macro="colormap" />
265 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> 265 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
266 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> 266 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
267 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/> 267 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
268 <param name="transform" type="select" label="Plot the transformed value"> 268 <param name="transform" type="select" label="Plot the transformed value">
269 <option value="log1p" selected="True" >log1p</option> 269 <option value="log1p" selected="True" >log1p</option>
270 <option value="log">log</option> 270 <option value="log">log</option>
271 <option value="-log">-log</option> 271 <option value="-log">-log</option>
272 272
273 </param> 273 </param>
274 <param name="width_matrix" type="float" value="1.5" optional="True" label="Width"/> 274 <param name="width_matrix" type="float" value="1.5" optional="True" label="Width"/>
275 275
276 <param name="type" type="select" optional="True" label="Plotting type"> 276 <param name="type" type="select" optional="True" label="Plotting type">
277 <option value="arcplot">arcplot</option> 277 <option value="arcplot">arcplot</option>
278 <option value="interaction">interaction</option> 278 <option value="interaction">interaction</option>
279 </param> 279 </param>
280 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false" 280 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false"
290 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 290 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
291 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" 291 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
292 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead 292 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
293 of the matrix set to lines if a heatmap representing the matrix is not wanted"/> 293 of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
294 <param name="width_tad" type="float" value="0.2" optional="True" label="Width"/> 294 <param name="width_tad" type="float" value="0.2" optional="True" label="Width"/>
295 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> 295 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
296 </when> 296 </when>
297 <when value="chrom_states_option"> 297 <when value="chrom_states_option">
298 <expand macro="plot_title" /> 298 <expand macro="plot_title" />
299 299
300 <expand macro="track_input_bed_macro" /> 300 <expand macro="track_input_bed_macro" />
301 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 301 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
302 302
303 <param name="border_color" type="color" value="#000000" label="Border color" optional="True" /> 303 <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
304 <param name="width_chrom" type="float" value="1.5" optional="True" label="Width"/> 304 <param name="width_chrom" type="float" value="1.5" optional="True" label="Width"/>
305 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" 305 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
306 label="Plot labels" /> 306 label="Plot labels" />
307 </when> 307 </when>
308 <when value="gene_track_option"> 308 <when value="gene_track_option">
309 <expand macro="plot_title" /> 309 <expand macro="plot_title" />
310 310
311 <expand macro="track_input_bed_macro" /> 311 <expand macro="track_input_bed_macro" />
312 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 312 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
313 <param name="width_bed" type="float" value="1.5" optional="True" label="Width"/> 313 <param name="width_bed" type="float" value="1.5" optional="True" label="Width"/>
314 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" 314 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
315 label="Plot labels" /> 315 label="Plot labels" />
319 </param> 319 </param>
320 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false" 320 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false"
321 label="Global max rows" /> 321 label="Global max rows" />
322 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" /> 322 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" />
323 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> 323 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
324 324
325 </when> 325 </when>
326 <when value="bedgraph_track_option"> 326 <when value="bedgraph_track_option">
327 <expand macro="plot_title" /> 327 <expand macro="plot_title" />
328 <expand macro="track_input_bedgraph_macro" /> 328 <expand macro="track_input_bedgraph_macro" />
329 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 329 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
330 330
331 <param name="width_bedgraph" type="float" value="0.2" optional="True" label="Width"/> 331 <param name="width_bedgraph" type="float" value="0.2" optional="True" label="Width"/>
332 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> 332 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
333 </when> 333 </when>
334 <when value="bigwig_track_option"> 334 <when value="bigwig_track_option">
335 <expand macro="plot_title" /> 335 <expand macro="plot_title" />
336 336
337 <expand macro="track_input_bigwig_macro" /> 337 <expand macro="track_input_bigwig_macro" />
338 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 338 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
339 339
340 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> 340 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
341 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/> 341 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
342 342
343 <param name="width_bigwig" type="float" value="1.5" optional="True" label="Width"/> 343 <param name="width_bigwig" type="float" value="1.5" optional="True" label="Width"/>
344 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" /> 344 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
345 <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false" 345 <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false"
346 label="NAN's to zeros" /> 346 label="NAN's to zeros" />
347 <conditional name="type_conditional"> 347 <conditional name="type_conditional">
358 </when> 358 </when>
359 <when value="fill_option" /> 359 <when value="fill_option" />
360 </conditional> 360 </conditional>
361 <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" /> 361 <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" />
362 </when> 362 </when>
363 363
364 364
365 <when value="bedgraph_matrix_track_option"> 365 <when value="bedgraph_matrix_track_option">
366 <expand macro="plot_title" /> 366 <expand macro="plot_title" />
367 367
368 <expand macro="track_input_bedgraph_matrix_macro" /> 368 <expand macro="track_input_bedgraph_matrix_macro" />
369 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> 369 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
370 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/> 370 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
371 371
372 <param name="width_bedgraph" type="float" value="1.5" optional="True" label="Width"/> 372 <param name="width_bedgraph" type="float" value="1.5" optional="True" label="Width"/>
380 </when> 380 </when>
381 <when value="spacer_option"> 381 <when value="spacer_option">
382 <expand macro="spacer_macro" /> 382 <expand macro="spacer_macro" />
383 </when> 383 </when>
384 </conditional> 384 </conditional>
385 385
386 </repeat> 386 </repeat>
387 387
388 388
389 <conditional name="x_axis"> 389 <conditional name="x_axis">
390 <param name="x_axis_select" type="select" label="Configure x-axis"> 390 <param name="x_axis_select" type="select" label="Configure x-axis">
391 <option value="no" selected="True">No</option> 391 <option value="no" selected="True">No</option>
392 <option value="yes">Yes</option> 392 <option value="yes">Yes</option>
393 </param> 393 </param>
404 <option value="png">png</option> 404 <option value="png">png</option>
405 <option value="svg">svg</option> 405 <option value="svg">svg</option>
406 </param> 406 </param>
407 </inputs> 407 </inputs>
408 <outputs> 408 <outputs>
409 <data format="png" name="outFileName" from_work_dir="plot"> 409 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on [${on_string}]: Plot">
410 <change_format> 410 <change_format>
411 <when input="image_file_format" value="png" format="png" /> 411 <when input="image_file_format" value="png" format="png" />
412 <when input="image_file_format" value="svg" format="svg" /> 412 <when input="image_file_format" value="svg" format="svg" />
413 </change_format> 413 </change_format>
414 </data> 414 </data>
416 <tests> 416 <tests>
417 <test> 417 <test>
418 <param name="region" value="chrX:3000000-3500000"/> 418 <param name="region" value="chrX:3000000-3500000"/>
419 <conditional name="x_axis"> 419 <conditional name="x_axis">
420 <param name="x_axis_select" value="yes" /> 420 <param name="x_axis_select" value="yes" />
421 </conditional> 421 </conditional>
422 <repeat name="tracks"> 422 <repeat name="tracks">
423 <conditional name="track_file_style_conditional"> 423 <conditional name="track_file_style_conditional">
424 <param name="track_file_style_selector" value="hic_matrix_option" /> 424 <param name="track_file_style_selector" value="hic_matrix_option" />
425 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/> 425 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
426 426
428 <param name="colormap" value="RdYlBu_r" /> 428 <param name="colormap" value="RdYlBu_r" />
429 <param name="depth" value="200000" /> 429 <param name="depth" value="200000" />
430 <param name="transform" value="log1p" /> 430 <param name="transform" value="log1p" />
431 <param name="boundaries_file" value="domains.bed" /> 431 <param name="boundaries_file" value="domains.bed" />
432 <param name="x_labels" value="True" /> 432 <param name="x_labels" value="True" />
433 </conditional> 433 </conditional>
434 </repeat> 434 </repeat>
435 <repeat name="tracks"> 435 <repeat name="tracks">
436 <conditional name="track_file_style_conditional"> 436 <conditional name="track_file_style_conditional">
437 <param name="track_file_style_selector" value="spacer_option" /> 437 <param name="track_file_style_selector" value="spacer_option" />
438 <param name="spacer_width" value="0.05" /> 438 <param name="spacer_width" value="0.05" />
439 </conditional> 439 </conditional>
440 </repeat> 440 </repeat>
443 <param name="track_file_style_selector" value="chrom_states_option" /> 443 <param name="track_file_style_selector" value="chrom_states_option" />
444 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> 444 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
445 <param name="title" value="TAD state" /> 445 <param name="title" value="TAD state" />
446 <param name="width_chrom" value="0.5" /> 446 <param name="width_chrom" value="0.5" />
447 <param name="labels" value="off" /> 447 <param name="labels" value="off" />
448 </conditional> 448 </conditional>
449 </repeat> 449 </repeat>
450 <repeat name="tracks"> 450 <repeat name="tracks">
451 <conditional name="track_file_style_conditional"> 451 <conditional name="track_file_style_conditional">
452 <param name="track_file_style_selector" value="tad_score_track_option" /> 452 <param name="track_file_style_selector" value="tad_score_track_option" />
453 <param name="track_input_bedgraph" value="tad_score.gz" ftype="bedgraph" /> 453 <param name="track_input_bedgraph" value="tad_score.gz" ftype="bedgraph" />
454 <param name="title" value="TAD separation score (Ramirez et al.)" /> 454 <param name="title" value="TAD separation score (Ramirez et al.)" />
455 <param name="width_tad" value="10" /> 455 <param name="width_tad" value="10" />
456 </conditional> 456 </conditional>
457 </repeat> 457 </repeat>
458 <repeat name="tracks"> 458 <repeat name="tracks">
459 <conditional name="track_file_style_conditional"> 459 <conditional name="track_file_style_conditional">
460 <param name="track_file_style_selector" value="spacer_option" /> 460 <param name="track_file_style_selector" value="spacer_option" />
461 <param name="spacer_width" value="1" /> 461 <param name="spacer_width" value="1" />
462 </conditional> 462 </conditional>
463 </repeat> 463 </repeat>
466 <param name="track_file_style_selector" value="bedgraph_track_option" /> 466 <param name="track_file_style_selector" value="bedgraph_track_option" />
467 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> 467 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
468 <param name="title" value="bedgraph" /> 468 <param name="title" value="bedgraph" />
469 <param name="width_bedgraph" value="4" /> 469 <param name="width_bedgraph" value="4" />
470 <param name="color" value="blue" /> 470 <param name="color" value="blue" />
471 </conditional> 471 </conditional>
472 </repeat> 472 </repeat>
473 <repeat name="tracks"> 473 <repeat name="tracks">
474 <conditional name="track_file_style_conditional"> 474 <conditional name="track_file_style_conditional">
475 <param name="track_file_style_selector" value="bigwig_track_option" /> 475 <param name="track_file_style_selector" value="bigwig_track_option" />
476 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 476 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
478 <param name="width_bigwig" value="4" /> 478 <param name="width_bigwig" value="4" />
479 <param name="color" value="blue" /> 479 <param name="color" value="blue" />
480 <conditional name="type_conditional"> 480 <conditional name="type_conditional">
481 <param name="type_selector" value="fill_option" /> 481 <param name="type_selector" value="fill_option" />
482 </conditional> 482 </conditional>
483 </conditional> 483 </conditional>
484 </repeat> 484 </repeat>
485 485
486 <repeat name="tracks"> 486 <repeat name="tracks">
487 <conditional name="track_file_style_conditional"> 487 <conditional name="track_file_style_conditional">
488 <param name="track_file_style_selector" value="bigwig_track_option" /> 488 <param name="track_file_style_selector" value="bigwig_track_option" />
489 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 489 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
490 <param name="title" value="rep 1 test line" /> 490 <param name="title" value="rep 1 test line" />
492 <param name="color" value="red" /> 492 <param name="color" value="red" />
493 <conditional name="type_conditional"> 493 <conditional name="type_conditional">
494 <param name="type_selector" value="line_option" /> 494 <param name="type_selector" value="line_option" />
495 <param name="width_line" value="1" /> 495 <param name="width_line" value="1" />
496 </conditional> 496 </conditional>
497 </conditional> 497 </conditional>
498 </repeat> 498 </repeat>
499 499
500 <repeat name="tracks"> 500 <repeat name="tracks">
501 <conditional name="track_file_style_conditional"> 501 <conditional name="track_file_style_conditional">
502 <param name="track_file_style_selector" value="bigwig_track_option" /> 502 <param name="track_file_style_selector" value="bigwig_track_option" />
505 <param name="width_bigwig" value="4" /> 505 <param name="width_bigwig" value="4" />
506 <param name="color" value="red" /> 506 <param name="color" value="red" />
507 <conditional name="type_conditional"> 507 <conditional name="type_conditional">
508 <param name="type_selector" value="line_option" /> 508 <param name="type_selector" value="line_option" />
509 <param name="width_line" value="0.1" /> 509 <param name="width_line" value="0.1" />
510 510
511 </conditional> 511 </conditional>
512 </conditional> 512 </conditional>
513 </repeat> 513 </repeat>
514 514
515 <repeat name="tracks"> 515 <repeat name="tracks">
516 <conditional name="track_file_style_conditional"> 516 <conditional name="track_file_style_conditional">
517 <param name="track_file_style_selector" value="bigwig_track_option" /> 517 <param name="track_file_style_selector" value="bigwig_track_option" />
518 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 518 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
519 <param name="title" value="rep 1 test point:0.5" /> 519 <param name="title" value="rep 1 test point:0.5" />
520 <param name="width_bigwig" value="4" /> 520 <param name="width_bigwig" value="4" />
521 <param name="color" value="black" /> 521 <param name="color" value="black" />
522 <conditional name="type_conditional"> 522 <conditional name="type_conditional">
523 <param name="type_selector" value="point_option" /> 523 <param name="type_selector" value="point_option" />
524 <param name="width_point" value="0.5" /> 524 <param name="width_point" value="0.5" />
525 525
526 </conditional> 526 </conditional>
527 </conditional> 527 </conditional>
528 </repeat> 528 </repeat>
529 529
530 <repeat name="tracks"> 530 <repeat name="tracks">
531 <conditional name="track_file_style_conditional"> 531 <conditional name="track_file_style_conditional">
532 <param name="track_file_style_selector" value="spacer_option" /> 532 <param name="track_file_style_selector" value="spacer_option" />
533 <param name="spacer_width" value="0.5" /> 533 <param name="spacer_width" value="0.5" />
534 </conditional> 534 </conditional>
535 </repeat> 535 </repeat>
538 <param name="track_file_style_selector" value="gene_track_option" /> 538 <param name="track_file_style_selector" value="gene_track_option" />
539 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 539 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
540 <param name="title" value="genes" /> 540 <param name="title" value="genes" />
541 <param name="width_bed" value="5" /> 541 <param name="width_bed" value="5" />
542 <param name="fontsize" value="10" /> 542 <param name="fontsize" value="10" />
543 </conditional> 543 </conditional>
544 </repeat> 544 </repeat>
545 <repeat name="tracks"> 545 <repeat name="tracks">
546 <conditional name="track_file_style_conditional"> 546 <conditional name="track_file_style_conditional">
547 <param name="track_file_style_selector" value="spacer_option" /> 547 <param name="track_file_style_selector" value="spacer_option" />
548 <param name="spacer_width" value="1" /> 548 <param name="spacer_width" value="1" />
549 </conditional> 549 </conditional>
550 </repeat> 550 </repeat>
554 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 554 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
555 <param name="title" value="max num rows 3" /> 555 <param name="title" value="max num rows 3" />
556 <param name="width_bed" value="3" /> 556 <param name="width_bed" value="3" />
557 <param name="fontsize" value="8" /> 557 <param name="fontsize" value="8" />
558 <param name="gene_rows" value="3" /> 558 <param name="gene_rows" value="3" />
559 </conditional> 559 </conditional>
560 </repeat> 560 </repeat>
561 <repeat name="tracks"> 561 <repeat name="tracks">
562 <conditional name="track_file_style_conditional"> 562 <conditional name="track_file_style_conditional">
563 <param name="track_file_style_selector" value="spacer_option" /> 563 <param name="track_file_style_selector" value="spacer_option" />
564 <param name="spacer_width" value="1" /> 564 <param name="spacer_width" value="1" />
565 </conditional> 565 </conditional>
566 </repeat> 566 </repeat>
570 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> 570 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
571 <param name="title" value="bed6 global max row" /> 571 <param name="title" value="bed6 global max row" />
572 <param name="width_bed" value="20" /> 572 <param name="width_bed" value="20" />
573 <param name="fontsize" value="10" /> 573 <param name="fontsize" value="10" />
574 <param name="global_max_row" value="True" /> 574 <param name="global_max_row" value="True" />
575 </conditional> 575 </conditional>
576 </repeat> 576 </repeat>
577 <repeat name="tracks"> 577 <repeat name="tracks">
578 <conditional name="track_file_style_conditional"> 578 <conditional name="track_file_style_conditional">
579 <param name="track_file_style_selector" value="vlines_track_option" /> 579 <param name="track_file_style_selector" value="vlines_track_option" />
580 <param name="track_input_bed" value="domains.bed" ftype="bed" /> 580 <param name="track_input_bed" value="domains.bed" ftype="bed" />
581 <param name="type" value="vlines" /> 581 <param name="type" value="vlines" />
582 </conditional> 582 </conditional>
583 </repeat> 583 </repeat>
584 <param name="image_file_format" value="png" /> 584 <param name="image_file_format" value="png" />
585 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> 585 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
586 </test> 586 </test>
587 </tests> 587 </tests>
588 <help><![CDATA[ 588 <help><![CDATA[
589 589
590 Plot TADs 590 Plot Topologic Associated Domains
591 ========= 591 =================================
592 592
593 ``hicPlotTADs`` is a visualization tool to plot the topologically associating domains (TADs) in a given region. Additional tracks can be added to enable the comparisons with other data like gene tracks. 593 **hicPlotTADs** is a visualization tool to plot the topologically associating domains (TADs) in a given region. Additional tracks can be added to enable the comparisons with other data like gene, ChIP-seq, RNA-seq or other tracks, including TAD seperation scores computed by ``hicFindTADs``.
594 594
595 Input 595 _________________
596
597 Usage
596 ----- 598 -----
597 - the region to plot: chr1:1000-2000 599
598 - the tracks: 600 This tool takes various types of tracks as input:
599 - the contact matrix 601
600 - Boundaries file: The result of ``hicFindTADs``. 602 - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap.
601 - different tracks for comparison: 603 - **Chromatin states:** display blocks of different colors following a bed file.
602 - Chromatine states: 604 - **TAD score:** display TAD seperation score computed by ``hicFindTADs``.
603 - TAD score 605 - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off.
604 - gene tracks 606 - **Bigwig track:** generic bigwig track plotting.
605 - Generic bigwig, bedgraph or bedgraph matrix files 607 - **Bedgraph track:** generic bedgraph track plotting.
606 - Vlines: vertical lines as a visual support where regions start / end over all tracks 608 - **Bedgraph matrix track** is used to specifically plot bm files computed by ``hicFindTADs`` (TAD seperation scores).
607 - Spacer: Add some space between the different tracks 609 - **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 ``hicFindTADs``.
608 610 - **Spacer:** Add some space between two tracks.
609 For each track parameters for the color, the width or the font size can be defined. 611
612 For each track, parameters for the color, the width or the font size can be defined.
613
614 _________________
610 615
611 Output 616 Output
612 ------ 617 ------
613 An output looks like this: 618
614 619 **hicPlotTADs** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) also contains Hi-C data. The plot is composed of tracks that need to be specified.
615 620 Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **hicPlotTADs**. TADs were computed by ``hicFindTADs``. The additional tracks added correspond to: TAD-separation score (as reported by ``hicFindTADs``), chromatin states, principal component 1 (A/B compartment) computed using ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_.
616 .. image:: $PATH_TO_IMAGES/master_TADs_plot.png 621
617 :width: 80 % 622 .. image:: $PATH_TO_IMAGES/hicPlotTADs.png
623 :width: 70 %
624
625 _________________
618 626
619 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 627 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
620 628
621 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 629 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
630 .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9
622 ]]></help> 631 ]]></help>
623 <expand macro="citations" /> 632 <expand macro="citations" />
624 </tool> 633 </tool>