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comparison pyGenomeTracks.xml @ 2:c171f2b7d76e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
author iuc
date Fri, 23 Aug 2019 07:24:20 -0400
parents 0ea86f6bf2a1
children feab9265552d
comparison
equal deleted inserted replaced
1:0ea86f6bf2a1 2:c171f2b7d76e
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10 #for $counter, $track in enumerate($tracks):
11 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
12 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
13 #set ext = $data_matrix.extension
14 ln -s $data_matrix ${counter}_${counter_matrix}.$ext &&
15 #end for
16 #end if
17 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
18 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
19 #set ext = $data_bed.extension
20 ln -s $data_bed ${counter}_${counter_bed}.$ext &&
21 #end for
22 #end if
23 #end for
24
10 25
11 sed '/^$/d' '$tracks_config' && 26 sed '/^$/d' '$tracks_config' &&
12 @BINARY@ 27 @BINARY@
13 --tracks '$tracks_config' 28 --tracks '$tracks_config'
14 #if $region and $region is not None: 29 #if $region and $region is not None:
33 #end if 48 #end if
34 #for $counter, $track in enumerate($tracks): 49 #for $counter, $track in enumerate($tracks):
35 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": 50 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
36 51
37 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): 52 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
38 [hic_section_$counter] 53 [hic_section_${counter}_${counter_matrix}]
39 file = $data_matrix 54 #set ext = $data_matrix.extension
55 file = ${counter}_${counter_matrix}.$ext
40 file_type = hic_matrix 56 file_type = hic_matrix
41 #if $track.track_file_style_conditional.title: 57 #if $track.track_file_style_conditional.title:
42 title = $track.track_file_style_conditional.title 58 title = $track.track_file_style_conditional.title
43 #else: 59 #else:
44 title = $data_matrix.name 60 title = $data_matrix.name
53 min_value = $track.track_file_style_conditional.min_value 69 min_value = $track.track_file_style_conditional.min_value
54 #end if 70 #end if
55 #if $track.track_file_style_conditional.max_value: 71 #if $track.track_file_style_conditional.max_value:
56 max_value = $track.track_file_style_conditional.max_value 72 max_value = $track.track_file_style_conditional.max_value
57 #end if 73 #end if
74 #if $track.track_file_style_conditional.transform != "":
58 transform = $track.track_file_style_conditional.transform 75 transform = $track.track_file_style_conditional.transform
76 #end if
77 #if $track.track_file_style_conditional.height_matrix != "":
59 height = $track.track_file_style_conditional.height_matrix 78 height = $track.track_file_style_conditional.height_matrix
60 79 #end if
61 #if $track.track_file_style_conditional.boundaries_file is not None: 80
62 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]
63 boundaries_file = $boundary_file
64 #end if
65
66 #if $track.track_file_style_conditional.x_labels:
67 x labels = $track.track_file_style_conditional.x_labels
68 #end if
69 #if $track.track_file_style_conditional.type:
70 type = $track.track_file_style_conditional.type
71 #end if
72 #if $track.track_file_style_conditional.show_masked_bins: 81 #if $track.track_file_style_conditional.show_masked_bins:
73 show_masked_bins = $track.track_file_style_conditional.show_masked_bins 82 show_masked_bins = $track.track_file_style_conditional.show_masked_bins
74 #end if 83 #end if
84 #if $track.track_file_style_conditional.invert_orientation:
85 orientation = inverted
86 #end if
75 #if $track.track_file_style_conditional.scale_factor: 87 #if $track.track_file_style_conditional.scale_factor:
76 scale factor = $track.track_file_style_conditional.scale_factor 88 scale factor = $track.track_file_style_conditional.scale_factor
77 #end if 89 #end if
78 90
91 #if str($track.track_file_style_conditional.boundaries_file) != "None":
92 #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix:
93 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]
94 #else:
95 #set boundary_file = $track.track_file_style_conditional.boundaries_file[0]
96 #end if
97 [tads_${counter}_${counter_matrix}]
98 file = $boundary_file
99 file_type = domains
100 border color = black
101 color = none
102 overlay previous = share-y
103 #end if
104
105
106 #if $track.track_file_style_conditional.spacer_height != "":
79 [spacer] 107 [spacer]
80 #if $track.track_file_style_conditional.spacer_height:
81 height = $track.track_file_style_conditional.spacer_height 108 height = $track.track_file_style_conditional.spacer_height
82 #end if 109 #end if
83 #end for 110 #end for
84 111
85 #end if 112 #end if
88 115
89 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option": 116 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":
90 117
91 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: 118 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
92 [tad_score_$counter] 119 [tad_score_$counter]
93 file = $data_bedgraph 120 file = $data_bedgraph
94 #if $track.track_file_style_conditional.title: 121 #if $track.track_file_style_conditional.title:
95 title = $track.track_file_style_conditional.title 122 title = $track.track_file_style_conditional.title
96 #else: 123 #else:
97 title = $data_bedgraph.name 124 title = $data_bedgraph.name
98 #end if 125 #end if
100 color = $track.track_file_style_conditional.color 127 color = $track.track_file_style_conditional.color
101 #end if 128 #end if
102 #if $track.track_file_style_conditional.height_tad: 129 #if $track.track_file_style_conditional.height_tad:
103 height = $track.track_file_style_conditional.height_tad 130 height = $track.track_file_style_conditional.height_tad
104 #end if 131 #end if
132 #if $track.track_file_style_conditional.show_data:
133 show data range = $track.track_file_style_conditional.show_data
134 #end if
135
136 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
137 #if $columns > 4:
138 file_type = bedgraph_matrix
105 #if $track.track_file_style_conditional.type_lines: 139 #if $track.track_file_style_conditional.type_lines:
106 type = $track.track_file_style_conditional.type_lines 140 type = $track.track_file_style_conditional.type_lines
107 #end if 141 #end if
108 #if $track.track_file_style_conditional.show_data:
109 show data range = $track.track_file_style_conditional.show_data
110 #end if
111
112 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
113 #if $columns > 5:
114 file_type = bedgraph_matrix
115 #else: 142 #else:
116 file_type = bedgraph 143 file_type = bedgraph
117 #end if 144 #end if
118 type = lines 145 #if $track.track_file_style_conditional.spacer_height != "":
119 [spacer] 146 [spacer]
120 #if $track.track_file_style_conditional.spacer_height:
121 height = $track.track_file_style_conditional.spacer_height 147 height = $track.track_file_style_conditional.spacer_height
122 #end if 148 #end if
123 #end for 149 #end for
124 #end if 150 #end if
125 151
134 #if $track.track_file_style_conditional.title: 160 #if $track.track_file_style_conditional.title:
135 title = $track.track_file_style_conditional.title 161 title = $track.track_file_style_conditional.title
136 #else: 162 #else:
137 title = $data_bed.name 163 title = $data_bed.name
138 #end if 164 #end if
139 #if $track.track_file_style_conditional.color: 165 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
140 color = $track.track_file_style_conditional.color 166 color = bed_rgb
167 #elif $track.track_file_style_conditional.color_bed.color:
168 color = $track.track_file_style_conditional.color_bed.color
169 #end if
170 #if $track.track_file_style_conditional.border_color:
171 border color = $track.track_file_style_conditional.border_color
141 #end if 172 #end if
142 display = collapsed 173 display = collapsed
143 #if $track.track_file_style_conditional.height_chrom: 174 #if $track.track_file_style_conditional.height_chrom:
144 height = $track.track_file_style_conditional.height_chrom 175 height = $track.track_file_style_conditional.height_chrom
145 #end if 176 #end if
146 #if $track.track_file_style_conditional.border_color:
147 border_color = $track.track_file_style_conditional.border_color
148 #end if
149 file_type = bed 177 file_type = bed
178 #if $track.track_file_style_conditional.spacer_height != "":
150 [spacer] 179 [spacer]
151 #if $track.track_file_style_conditional.spacer_height:
152 height = $track.track_file_style_conditional.spacer_height 180 height = $track.track_file_style_conditional.spacer_height
153 #end if 181 #end if
154 #end for 182 #end for
155 183
156 #end if 184 #end if
157 185
158 186
159 187
160 188
161 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": 189 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
162 #for $data_bed in $track.track_file_style_conditional.track_input_bed: 190 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
163 191
164 [genes_$counter] 192 [genes_${counter}_${counter_bed}]
165 file = $data_bed 193 #set ext = $data_bed.extension
194 file = ${counter}_${counter_bed}.$ext
166 #if $track.track_file_style_conditional.title: 195 #if $track.track_file_style_conditional.title:
167 title = $track.track_file_style_conditional.title 196 title = $track.track_file_style_conditional.title
168 #else: 197 #else:
169 title = $data_bed.name 198 title = $data_bed.name
170 #end if 199 #end if
171 #if $track.track_file_style_conditional.color: 200 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
172 color = $track.track_file_style_conditional.color 201 color = bed_rgb
173 #end if 202 #elif $track.track_file_style_conditional.color_bed.color:
203 color = $track.track_file_style_conditional.color_bed.color
204 #end if
205 #if $track.track_file_style_conditional.border_color:
206 border color = $track.track_file_style_conditional.border_color
207 #end if
208
209 #if $track.track_file_style_conditional.flybase:
210 style = flybase
211 #else
212 style = UCSC
213 #end if
214
215 display = $track.track_file_style_conditional.display
174 216
175 #if $track.track_file_style_conditional.height_bed: 217 #if $track.track_file_style_conditional.height_bed:
176 height = $track.track_file_style_conditional.height_bed 218 height = $track.track_file_style_conditional.height_bed
177 #end if 219 #end if
178 220
179 #if $track.track_file_style_conditional.labels: 221 #if $track.track_file_style_conditional.labels:
180 labels = $track.track_file_style_conditional.labels 222 labels = $track.track_file_style_conditional.labels
181 #end if
182
183 #if $track.track_file_style_conditional.type:
184 type = $track.track_file_style_conditional.type
185 #end if 223 #end if
186 224
187 file_type = bed 225 file_type = bed
188 #if $track.track_file_style_conditional.fontsize: 226 #if $track.track_file_style_conditional.fontsize:
189 fontsize = $track.track_file_style_conditional.fontsize 227 fontsize = $track.track_file_style_conditional.fontsize
194 #end if 232 #end if
195 233
196 #if $track.track_file_style_conditional.global_max_row: 234 #if $track.track_file_style_conditional.global_max_row:
197 global max row = $track.track_file_style_conditional.global_max_row 235 global max row = $track.track_file_style_conditional.global_max_row
198 #end if 236 #end if
237 #if $track.track_file_style_conditional.spacer_height != "":
199 [spacer] 238 [spacer]
200 #if $track.track_file_style_conditional.spacer_height:
201 height = $track.track_file_style_conditional.spacer_height 239 height = $track.track_file_style_conditional.spacer_height
202 #end if 240 #end if
203 #end for 241 #end for
204 #end if 242 #end if
205 243
209 247
210 [bedgraph_$counter] 248 [bedgraph_$counter]
211 file = $data_bedgraph 249 file = $data_bedgraph
212 #if $track.track_file_style_conditional.title: 250 #if $track.track_file_style_conditional.title:
213 title = $track.track_file_style_conditional.title 251 title = $track.track_file_style_conditional.title
214 #else: 252 #elif $track.track_file_style_conditional.overlay_select == "no":
215 title = $data_bedgraph.name 253 title = $data_bedgraph.name
216 #end if 254 #end if
217 #if $track.track_file_style_conditional.color: 255 #if $track.track_file_style_conditional.color:
218 color = $track.track_file_style_conditional.color 256 color = $track.track_file_style_conditional.color
219 #end if 257 #end if
258 alpha = $track.track_file_style_conditional.alpha
259 #if $track.track_file_style_conditional.color_negative.color_negative_select == "yes":
260 negative color = $track.track_file_style_conditional.color_negative.color
261 #end if
220 #if $track.track_file_style_conditional.height_bedgraph: 262 #if $track.track_file_style_conditional.height_bedgraph:
221 height = $track.track_file_style_conditional.height_bedgraph 263 height = $track.track_file_style_conditional.height_bedgraph
222 #end if 264 #end if
265 #if $track.track_file_style_conditional.min_value:
266 min_value = $track.track_file_style_conditional.min_value
267 #else:
268 min_value = auto
269 #end if
270 #if $track.track_file_style_conditional.max_value:
271 max_value = $track.track_file_style_conditional.max_value
272 #else:
273 max_value = auto
274 #end if
275
223 #if $track.track_file_style_conditional.show_data: 276 #if $track.track_file_style_conditional.show_data:
224 show data range = $track.track_file_style_conditional.show_data 277 show data range = $track.track_file_style_conditional.show_data
225 #end if 278 #end if
226 279
227 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) 280 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
228 #if $columns > 5: 281 #if $columns > 4:
229 file_type = bedgraph_matrix 282 file_type = bedgraph_matrix
283 type = lines
230 #else: 284 #else:
231 file_type = bedgraph 285 file_type = bedgraph
232 #end if 286 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
233 type = lines 287 type = fill
288 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
289 type = line:$track.track_file_style_conditional.type_conditional.width_line
290 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
291 type = points:$track.track_file_style_conditional.type_conditional.width_point
292 #end if
293 #end if
294 #if $track.track_file_style_conditional.invert_orientation:
295 orientation = inverted
296 #end if
297 overlay previous = $track.track_file_style_conditional.overlay_select
298 #if $track.track_file_style_conditional.spacer_height != "":
234 [spacer] 299 [spacer]
235 #if $track.track_file_style_conditional.spacer_height:
236 height = $track.track_file_style_conditional.spacer_height 300 height = $track.track_file_style_conditional.spacer_height
237 #end if 301 #end if
238 #end for 302 #end for
239 #end if 303 #end if
240 304
242 #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig: 306 #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig:
243 [bigwig_$counter] 307 [bigwig_$counter]
244 file = $data_bigwig 308 file = $data_bigwig
245 #if $track.track_file_style_conditional.title: 309 #if $track.track_file_style_conditional.title:
246 title = $track.track_file_style_conditional.title 310 title = $track.track_file_style_conditional.title
247 #else: 311 #elif $track.track_file_style_conditional.overlay_select == "no":
248 title = $data_bigwig.name 312 title = $data_bigwig.name
249 #end if 313 #end if
314 #if $track.track_file_style_conditional.color:
250 color = $track.track_file_style_conditional.color 315 color = $track.track_file_style_conditional.color
316 #end if
317 alpha = $track.track_file_style_conditional.alpha
318 #if $track.track_file_style_conditional.color_negative.color_negative_select == "yes":
319 negative color = $track.track_file_style_conditional.color_negative.color
320 #end if
251 #if $track.track_file_style_conditional.min_value: 321 #if $track.track_file_style_conditional.min_value:
252 min_value = $track.track_file_style_conditional.min_value 322 min_value = $track.track_file_style_conditional.min_value
253 #else: 323 #else:
254 min_value = 0 324 min_value = 0
255 #end if 325 #end if
257 max_value = $track.track_file_style_conditional.max_value 327 max_value = $track.track_file_style_conditional.max_value
258 #else: 328 #else:
259 max_value = auto 329 max_value = auto
260 #end if 330 #end if
261 height = $track.track_file_style_conditional.height_bigwig 331 height = $track.track_file_style_conditional.height_bigwig
262 #if $track.track_file_style_conditional.number_of_bins: 332 summary method = $track.track_file_style_conditional.reading_bw_conditional.summary
263 number of bins = $track.track_file_style_conditional.number_of_bins 333 nans to zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros
264 #end if 334 #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins:
265 nans to zeros = $track.track_file_style_conditional.nans_to_zeros 335 number of bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins
266 #if $track.track_file_style_conditional.type_conditional == 'fill_option': 336 #end if
337 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
267 type = fill 338 type = fill
268 #elif $track.track_file_style_conditional.type_conditional == 'line_option': 339 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
269 type = line:$track.track_file_style_conditional.type_conditional.height_line 340 type = line:$track.track_file_style_conditional.type_conditional.width_line
270 #elif $track.track_file_style_conditional.type_conditional == 'point_option': 341 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
271 type = points:$track.track_file_style_conditional.type_conditional.width_point 342 type = points:$track.track_file_style_conditional.type_conditional.width_point
272 #end if 343 #end if
273 #if $track.track_file_style_conditional.data_range: 344 #if $track.track_file_style_conditional.data_range:
274 show data range = $track.track_file_style_conditional.data_range 345 show data range = $track.track_file_style_conditional.data_range
275 #end if 346 #end if
276 file_type = bigwig 347 file_type = bigwig
348 #if $track.track_file_style_conditional.invert_orientation:
349 orientation = inverted
350 #end if
351 overlay previous = $track.track_file_style_conditional.overlay_select
352 #if $track.track_file_style_conditional.spacer_height != "":
277 [spacer] 353 [spacer]
278 #if $track.track_file_style_conditional.spacer_height:
279 height = $track.track_file_style_conditional.spacer_height 354 height = $track.track_file_style_conditional.spacer_height
280 #end if 355 #end if
281 #end for 356 #end for
282 #end if 357 #end if
283 358
305 #if $track.track_file_style_conditional.type_lines: 380 #if $track.track_file_style_conditional.type_lines:
306 type = $track.track_file_style_conditional.type_lines 381 type = $track.track_file_style_conditional.type_lines
307 #end if 382 #end if
308 file_type = bedgraph_matrix 383 file_type = bedgraph_matrix
309 plot horizontal lines=False 384 plot horizontal lines=False
385 #if $track.track_file_style_conditional.invert_orientation:
386 orientation = inverted
387 #end if
388 #if $track.track_file_style_conditional.spacer_height != "":
310 [spacer] 389 [spacer]
311 #if $track.track_file_style_conditional.spacer_height:
312 height = $track.track_file_style_conditional.spacer_height 390 height = $track.track_file_style_conditional.spacer_height
313 #end if 391 #end if
314 #end for 392 #end for
315 #end if 393 #end if
316 394
321 type = vlines 399 type = vlines
322 file_type = bed 400 file_type = bed
323 #end if 401 #end if
324 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": 402 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
325 403
404 #if $track.track_file_style_conditional.spacer_height != "":
326 [spacer] 405 [spacer]
327 #if $track.track_file_style_conditional.spacer_height:
328 height = $track.track_file_style_conditional.spacer_height 406 height = $track.track_file_style_conditional.spacer_height
329 #end if 407 #end if
330 #end if 408 #end if
331 #end for 409 #end for
332 410
364 <expand macro="plot_title" /> 442 <expand macro="plot_title" />
365 <expand macro="matrix_h5_cooler_multiple_macro" /> 443 <expand macro="matrix_h5_cooler_multiple_macro" />
366 444
367 <expand macro="colormap" /> 445 <expand macro="colormap" />
368 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> 446 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
369 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> 447 <expand macro="minmax_macro" />
370 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
371 <param name="transform" type="select" label="Plot the transformed value"> 448 <param name="transform" type="select" label="Plot the transformed value">
372 <option value="log1p" selected="True" >log1p</option> 449 <option value="log1p" selected="True" >log1p</option>
373 <option value="log">log</option> 450 <option value="log">log</option>
374 <option value="-log">-log</option> 451 <option value="-log">-log</option>
452 <option value="">no transformation</option>
375 453
376 </param> 454 </param>
377 <param name="height_matrix" type="float" value="1.5" optional="True" label="height"/> 455 <param name="height_matrix" type="float" value="" optional="True" label="height"/>
378
379 <param name="type" type="select" optional="True" label="Plotting type">
380 <option value="arcplot">arcplot</option>
381 <option value="interaction">interaction</option>
382 </param>
383 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false" 456 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false"
384 label="Show masked bins" /> 457 label="Show masked bins" />
385 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple='True'/> <!-- multiple='True'--> 458 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple='True'/> <!-- multiple='True'-->
386 <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" /> 459 <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" />
387 <param name="x_labels" type="boolean" truevalue="yes" falsevalue="no" optional="True" label="Show x labels" /> 460 <expand macro="inverted_macro" />
388 <expand macro="spacer_macro" /> 461 <expand macro="spacer_macro" />
389 462
390 </when> 463 </when>
391 <when value="tad_score_track_option"> 464 <when value="tad_score_track_option">
392 <expand macro="plot_title" /> 465 <expand macro="plot_title" />
402 </when> 475 </when>
403 <when value="chrom_states_option"> 476 <when value="chrom_states_option">
404 <expand macro="plot_title" /> 477 <expand macro="plot_title" />
405 478
406 <expand macro="track_input_bed_macro" /> 479 <expand macro="track_input_bed_macro" />
407 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 480 <expand macro="color_bed_macro" />
408
409 <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
410 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/> 481 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/>
411 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" 482 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
412 label="Plot labels" /> 483 label="Plot labels" />
413 <expand macro="spacer_macro" /> 484 <expand macro="spacer_macro" />
414 485
415 </when> 486 </when>
416 <when value="gene_track_option"> 487 <when value="gene_track_option">
417 <expand macro="plot_title" /> 488 <expand macro="plot_title" />
418 489
419 <expand macro="track_input_bed_macro" /> 490 <expand macro="track_input_bed_gtf_macro" />
420 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 491 <expand macro="color_bed_macro" />
421 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> 492 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/>
422 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" 493 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
423 label="Plot labels" /> 494 label="Plot labels" />
424 <param name="type" type="select" optional="True" label="Type"> 495 <param name="flybase" type="boolean" checked="true" label="Use flybase style" help="This will be only used for bed with 12 columns"/>
425 <option value="genes">genes</option> 496 <param name="display" type="select" label="display to use">
426 <option value="domains">domains</option> 497 <option value="stacked" selected="True">stacked (no overlap even with the label)</option>
498 <option value="interlaced">interlaced (everything on 2 lines)</option>
499 <option value="collapsed">collapsed (everything on 1 line)</option>
500 <option value="domain">domain (only the first line of stacked)</option>
427 </param> 501 </param>
428 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false" 502 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false"
429 label="Global max rows" /> 503 label="Global max rows" />
430 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" /> 504 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" />
431 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> 505 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
433 507
434 </when> 508 </when>
435 <when value="bedgraph_track_option"> 509 <when value="bedgraph_track_option">
436 <expand macro="plot_title" /> 510 <expand macro="plot_title" />
437 <expand macro="track_input_bedgraph_macro" /> 511 <expand macro="track_input_bedgraph_macro" />
438 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 512 <expand macro="color_coverage_macro" />
439 513 <expand macro="minmax_macro" />
440 <param name="height_bedgraph" type="float" value="0.2" optional="True" label="height"/> 514 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
515 <expand macro="type_coverage_macro" />
441 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> 516 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
517 <expand macro="inverted_macro" />
518 <expand macro="overlay_macro" />
442 <expand macro="spacer_macro" /> 519 <expand macro="spacer_macro" />
443 520
444 </when> 521 </when>
445 <when value="bigwig_track_option"> 522 <when value="bigwig_track_option">
446 <expand macro="plot_title" /> 523 <expand macro="plot_title" />
447 524
448 <expand macro="track_input_bigwig_macro" /> 525 <expand macro="track_input_bigwig_macro" />
449 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 526 <expand macro="color_coverage_macro" />
450 527
451 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> 528 <expand macro="minmax_macro" />
452 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
453 529
454 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> 530 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/>
455 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" /> 531 <expand macro="reading_bw_macro" />
456 <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false" 532 <expand macro="type_coverage_macro" />
457 label="NAN's to zeros" /> 533 <expand macro="type_coverage_macro" />
458 <conditional name="type_conditional"> 534 <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" label="Show visualization of data range"/>
459 <param name="type_selector" type="select" label="Choose style of the plot."> 535 <expand macro="inverted_macro" />
460 <option value="fill_option">fill</option> 536 <expand macro="overlay_macro" />
461 <option value="line_option">line</option>
462 <option value="point_option">point</option>
463 </param>
464 <when value="line_option">
465 <param name="width_line" type="float" value="0.5" optional="True" label="Width"/>
466 </when>
467 <when value="point_option">
468 <param name="width_point" type="float" value="0.5" optional="True" label="Width"/>
469 </when>
470 <when value="fill_option" />
471 </conditional>
472 <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" />
473 <expand macro="spacer_macro" /> 537 <expand macro="spacer_macro" />
474 538
475 </when> 539 </when>
476 540
477 541
478 <when value="bedgraph_matrix_track_option"> 542 <when value="bedgraph_matrix_track_option">
479 <expand macro="plot_title" /> 543 <expand macro="plot_title" />
480 544
481 <expand macro="track_input_bedgraph_matrix_macro" /> 545 <expand macro="track_input_bedgraph_matrix_macro" />
482 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> 546 <expand macro="minmax_macro" />
483 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
484 547
485 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> 548 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
486 549
487 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" 550 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
488 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead 551 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
489 of the matrix set to lines if a heatmap representing the matrix is not wanted"/> 552 of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
553 <expand macro="inverted_macro" />
490 <expand macro="spacer_macro" /> 554 <expand macro="spacer_macro" />
491 555
492 </when> 556 </when>
493 <when value="vlines_track_option"> 557 <when value="vlines_track_option">
494 <expand macro="track_input_bed_single_macro" /> 558 <expand macro="track_input_bed_single_macro" />
506 <option value="no" selected="True">No</option> 570 <option value="no" selected="True">No</option>
507 <option value="yes">Yes</option> 571 <option value="yes">Yes</option>
508 </param> 572 </param>
509 <when value="yes"> 573 <when value="yes">
510 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> 574 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
511 <param name="where" type="select" optional="True" label="Where to place the x-axis"> 575 <param name="where" type="select" label="Where to place the x-axis">
512 <option value="top" >Top</option> 576 <option value="top" selected="True">Top</option>
513 <option value="bottom">Bottom</option> 577 <option value="bottom">Bottom</option>
514 </param> 578 </param>
515 </when> 579 </when>
516 <when value="no" /> 580 <when value="no" />
517 </conditional> 581 </conditional>
536 </conditional> 600 </conditional>
537 <repeat name="tracks"> 601 <repeat name="tracks">
538 <conditional name="track_file_style_conditional"> 602 <conditional name="track_file_style_conditional">
539 <param name="track_file_style_selector" value="hic_matrix_option" /> 603 <param name="track_file_style_selector" value="hic_matrix_option" />
540 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> 604 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
541
542 <param name="title" value="Kc DpnII (Li et al. 2015)" /> 605 <param name="title" value="Kc DpnII (Li et al. 2015)" />
543 <param name="colormap" value="RdYlBu_r" /> 606 <param name="colormap" value="RdYlBu_r" />
544 <param name="depth" value="200000" /> 607 <param name="depth" value="200000" />
545 <param name="transform" value="log1p" /> 608 <param name="transform" value="log1p" />
546 <param name="boundaries_file" value="domains.bed" /> 609 <param name="boundaries_file" value="domains.bed" />
558 <param name="track_file_style_selector" value="chrom_states_option" /> 621 <param name="track_file_style_selector" value="chrom_states_option" />
559 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> 622 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
560 <param name="title" value="TAD state" /> 623 <param name="title" value="TAD state" />
561 <param name="height_chrom" value="0.5" /> 624 <param name="height_chrom" value="0.5" />
562 <param name="labels" value="off" /> 625 <param name="labels" value="off" />
626 <conditional name="color_bed">
627 <param name="color_bed_select" value="bed_rgb" />
628 </conditional>
563 </conditional> 629 </conditional>
564 </repeat> 630 </repeat>
565 <repeat name="tracks"> 631 <repeat name="tracks">
566 <conditional name="track_file_style_conditional"> 632 <conditional name="track_file_style_conditional">
567 <param name="track_file_style_selector" value="tad_score_track_option" /> 633 <param name="track_file_style_selector" value="tad_score_track_option" />
595 <conditional name="type_conditional"> 661 <conditional name="type_conditional">
596 <param name="type_selector" value="fill_option" /> 662 <param name="type_selector" value="fill_option" />
597 </conditional> 663 </conditional>
598 </conditional> 664 </conditional>
599 </repeat> 665 </repeat>
600
601 <repeat name="tracks"> 666 <repeat name="tracks">
602 <conditional name="track_file_style_conditional"> 667 <conditional name="track_file_style_conditional">
603 <param name="track_file_style_selector" value="bigwig_track_option" /> 668 <param name="track_file_style_selector" value="bigwig_track_option" />
604 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 669 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
605 <param name="title" value="rep 1 test line" /> 670 <param name="title" value="rep 1 test line" />
609 <param name="type_selector" value="line_option" /> 674 <param name="type_selector" value="line_option" />
610 <param name="width_line" value="1" /> 675 <param name="width_line" value="1" />
611 </conditional> 676 </conditional>
612 </conditional> 677 </conditional>
613 </repeat> 678 </repeat>
614
615 <repeat name="tracks"> 679 <repeat name="tracks">
616 <conditional name="track_file_style_conditional"> 680 <conditional name="track_file_style_conditional">
617 <param name="track_file_style_selector" value="bigwig_track_option" /> 681 <param name="track_file_style_selector" value="bigwig_track_option" />
618 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 682 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
619 <param name="title" value="rep 1 test lw=0.2" /> 683 <param name="title" value="rep 1 test lw=0.2" />
624 <param name="width_line" value="0.1" /> 688 <param name="width_line" value="0.1" />
625 689
626 </conditional> 690 </conditional>
627 </conditional> 691 </conditional>
628 </repeat> 692 </repeat>
629
630 <repeat name="tracks"> 693 <repeat name="tracks">
631 <conditional name="track_file_style_conditional"> 694 <conditional name="track_file_style_conditional">
632 <param name="track_file_style_selector" value="bigwig_track_option" /> 695 <param name="track_file_style_selector" value="bigwig_track_option" />
633 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 696 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
634 <param name="title" value="rep 1 test point:0.5" /> 697 <param name="title" value="rep 1 test point:0.5" />
639 <param name="width_point" value="0.5" /> 702 <param name="width_point" value="0.5" />
640 703
641 </conditional> 704 </conditional>
642 </conditional> 705 </conditional>
643 </repeat> 706 </repeat>
644
645 <repeat name="tracks"> 707 <repeat name="tracks">
646 <conditional name="track_file_style_conditional"> 708 <conditional name="track_file_style_conditional">
647 <param name="track_file_style_selector" value="spacer_option" /> 709 <param name="track_file_style_selector" value="spacer_option" />
648 <param name="spacer_height" value="0.5" /> 710 <param name="spacer_height" value="0.5" />
649 </conditional> 711 </conditional>
676 <repeat name="tracks"> 738 <repeat name="tracks">
677 <conditional name="track_file_style_conditional"> 739 <conditional name="track_file_style_conditional">
678 <param name="track_file_style_selector" value="spacer_option" /> 740 <param name="track_file_style_selector" value="spacer_option" />
679 <param name="spacer_height" value="1" /> 741 <param name="spacer_height" value="1" />
680 </conditional> 742 </conditional>
681 </repeat> 743 </repeat>
682 <repeat name="tracks"> 744 <repeat name="tracks">
683 <conditional name="track_file_style_conditional"> 745 <conditional name="track_file_style_conditional">
684 <param name="track_file_style_selector" value="gene_track_option" /> 746 <param name="track_file_style_selector" value="gene_track_option" />
685 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> 747 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
686 <param name="title" value="bed6 global max row" /> 748 <param name="title" value="bed6 global max row" />
698 </repeat> 760 </repeat>
699 <param name="image_file_format" value="png" /> 761 <param name="image_file_format" value="png" />
700 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> 762 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
701 </test> 763 </test>
702 <test> 764 <test>
703 <param name="region" value="chrX:3000000-3500000"/> 765 <param name="region" value="chrX:3000000-3500000"/>
704 <conditional name="x_axis"> 766 <conditional name="x_axis">
705 <param name="x_axis_select" value="yes" /> 767 <param name="x_axis_select" value="yes" />
706 </conditional>
707 <repeat name="tracks">
708 <conditional name="track_file_style_conditional">
709 <param name="track_file_style_selector" value="bigwig_track_option" />
710 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
711 <param name="title" value="rep 1 test line" />
712 <param name="height_bigwig" value="4" />
713 <param name="color" value="red" />
714 <conditional name="type_conditional">
715 <param name="type_selector" value="line_option" />
716 <param name="width_line" value="1" />
717 </conditional>
718 </conditional> 768 </conditional>
769 <repeat name="tracks">
770 <conditional name="track_file_style_conditional">
771 <param name="track_file_style_selector" value="bigwig_track_option" />
772 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
773 <param name="title" value="rep 1 test line" />
774 <param name="height_bigwig" value="4" />
775 <param name="color" value="red" />
776 <conditional name="type_conditional">
777 <param name="type_selector" value="line_option" />
778 <param name="width_line" value="1" />
779 </conditional>
780 </conditional>
719 </repeat> 781 </repeat>
720 <param name="image_file_format" value="png" /> 782 <param name="image_file_format" value="png" />
721 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" /> 783 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" />
722 </test> 784 </test>
785 <test>
786 <param name="region" value="chrX:3000000-3500000"/>
787 <conditional name="x_axis">
788 <param name="x_axis_select" value="yes" />
789 </conditional>
790 <repeat name="tracks">
791 <conditional name="track_file_style_conditional">
792 <param name="track_file_style_selector" value="hic_matrix_option" />
793 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
794 <param name="title" value="Kc DpnII (Li et al. 2015) log1p" />
795 <param name="colormap" value="RdYlBu_r" />
796 <param name="depth" value="200000" />
797 <param name="transform" value="log1p" />
798 <param name="boundaries_file" value="domains.bed" />
799 </conditional>
800 </repeat>
801 <repeat name="tracks">
802 <conditional name="track_file_style_conditional">
803 <param name="track_file_style_selector" value="chrom_states_option" />
804 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
805 <param name="title" value="TAD state" />
806 <param name="height_chrom" value="0.5" />
807 <param name="labels" value="off" />
808 <conditional name="color_bed">
809 <param name="color_bed_select" value="bed_rgb" />
810 </conditional>
811 </conditional>
812 </repeat>
813 <repeat name="tracks">
814 <conditional name="track_file_style_conditional">
815 <param name="track_file_style_selector" value="hic_matrix_option" />
816 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
817 <param name="title" value="Kc DpnII (Li et al. 2015) inverted no transform" />
818 <param name="colormap" value="Reds" />
819 <param name="depth" value="200000" />
820 <param name="transform" value="" />
821 <param name="invert_orientation" value="yes" />
822 <param name="min_value" value="5" />
823 <param name="max_value" value="70" />
824 </conditional>
825 </repeat>
826 <repeat name="tracks">
827 <conditional name="track_file_style_conditional">
828 <param name="track_file_style_selector" value="spacer_option" />
829 <param name="spacer_height" value="1" />
830 </conditional>
831 </repeat>
832 <repeat name="tracks">
833 <conditional name="track_file_style_conditional">
834 <param name="track_file_style_selector" value="bedgraph_track_option" />
835 <param name="track_input_bedgraph" value="test_with_neg_values.bg.gz" ftype="bedgraph" />
836 <param name="title" value="bedgraph with negative values" />
837 <param name="height_bedgraph" value="4" />
838 <param name="color" value="black" />
839 <conditional name="color_negative">
840 <param name="color_negative_select" value="yes" />
841 <param name="color" value="red" />
842 </conditional>
843 <conditional name="type_conditional">
844 <param name="type_selector" value="fill_option" />
845 </conditional>
846 </conditional>
847 </repeat>
848 <repeat name="tracks">
849 <conditional name="track_file_style_conditional">
850 <param name="track_file_style_selector" value="bedgraph_track_option" />
851 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
852 <param name="title" value="bedgraph" />
853 <param name="height_bedgraph" value="4" />
854 <param name="color" value="blue" />
855 <conditional name="type_conditional">
856 <param name="type_selector" value="fill_option" />
857 </conditional>
858 </conditional>
859 </repeat>
860 <repeat name="tracks">
861 <conditional name="track_file_style_conditional">
862 <param name="track_file_style_selector" value="bigwig_track_option" />
863 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
864 <param name="title" value="rep 1 test fill" />
865 <param name="height_bigwig" value="4" />
866 <param name="color" value="blue" />
867 <conditional name="type_conditional">
868 <param name="type_selector" value="fill_option" />
869 </conditional>
870 </conditional>
871 </repeat>
872 <repeat name="tracks">
873 <conditional name="track_file_style_conditional">
874 <param name="track_file_style_selector" value="bigwig_track_option" />
875 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
876 <param name="title" value="(red points/width=5/max value/100 bins) overlayed with (dark red line/min value/30000 bins) overlayed with (black line/min value)" />
877 <param name="height_bigwig" value="10" />
878 <param name="color" value="red" />
879 <conditional name="type_conditional">
880 <param name="type_selector" value="point_option" />
881 <param name="width_point" value="5" />
882 </conditional>
883 <section name="reading_bw_conditional">
884 <param name="summary" value="max"/>
885 <param name="number_of_bins" value="100"/>
886 </section>
887 </conditional>
888 </repeat>
889 <repeat name="tracks">
890 <conditional name="track_file_style_conditional">
891 <param name="track_file_style_selector" value="bigwig_track_option" />
892 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
893 <param name="height_bigwig" value="10" />
894 <param name="color" value="#c00000" />
895 <conditional name="type_conditional">
896 <param name="type_selector" value="line_option" />
897 </conditional>
898 <section name="reading_bw_conditional">
899 <param name="summary" value="min"/>
900 </section>
901 <param name="overlay_select" value="share-y" />
902 </conditional>
903 </repeat>
904 <repeat name="tracks">
905 <conditional name="track_file_style_conditional">
906 <param name="track_file_style_selector" value="bigwig_track_option" />
907 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
908 <param name="height_bigwig" value="10" />
909 <param name="color" value="black" />
910 <conditional name="type_conditional">
911 <param name="type_selector" value="line_option" />
912 </conditional>
913 <section name="reading_bw_conditional">
914 <param name="summary" value="min"/>
915 <param name="number_of_bins" value="30000"/>
916 </section>
917 <param name="overlay_select" value="share-y" />
918 <param name="spacer_height" value="1" />
919 </conditional>
920 </repeat>
921 <repeat name="tracks">
922 <conditional name="track_file_style_conditional">
923 <param name="track_file_style_selector" value="gene_track_option" />
924 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
925 <param name="title" value="genes in ucsc" />
926 <param name="height_bed" value="5" />
927 <param name="fontsize" value="10" />
928 <param name="flybase" value="false"/>
929 </conditional>
930 </repeat>
931 <repeat name="tracks">
932 <conditional name="track_file_style_conditional">
933 <param name="track_file_style_selector" value="gene_track_option" />
934 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
935 <param name="title" value="bed6 global max row color from score" />
936 <param name="height_bed" value="20" />
937 <param name="fontsize" value="10" />
938 <param name="global_max_row" value="True" />
939 <conditional name="color_bed">
940 <param name="color_bed_select" value="colormap" />
941 <param name="color" value="RdYlBu_r" />
942 </conditional>
943 </conditional>
944 </repeat>
945 <repeat name="tracks">
946 <conditional name="track_file_style_conditional">
947 <param name="track_file_style_selector" value="gene_track_option" />
948 <param name="track_input_bed" value="domains.bed" ftype="bed" />
949 <param name="title" value="domains.bed using the 9th field for colors interlaced" />
950 <param name="height_bed" value="2" />
951 <param name="fontsize" value="10" />
952 <conditional name="color_bed">
953 <param name="color_bed_select" value="bed_rgb" />
954 </conditional>
955 <param name="display" value="interlaced" />
956 </conditional>
957 </repeat>
958 <param name="image_file_format" value="png" />
959 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" />
960 </test>
961 <test>
962 <param name="region" value="X:2700000-3100000"/>
963 <conditional name="x_axis">
964 <param name="x_axis_select" value="yes" />
965 <param name="where" value="bottom" />
966 </conditional>
967 <repeat name="tracks">
968 <conditional name="track_file_style_conditional">
969 <param name="track_file_style_selector" value="bigwig_track_option" />
970 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
971 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" />
972 <param name="height_bigwig" value="7" />
973 <param name="color" value="#00b0f0" />
974 <param name="number_of_bins" value="2000"/>
975 </conditional>
976 </repeat>
977 <repeat name="tracks">
978 <conditional name="track_file_style_conditional">
979 <param name="track_file_style_selector" value="bigwig_track_option" />
980 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
981 <param name="title" value="" />
982 <param name="color" value="#ff0000" />
983 <param name="alpha" value="0.5" />
984 <param name="summary" value="max" />
985 <param name="number_of_bins" value="300"/>
986 <param name="overlay_select" value="share-y"/>
987 </conditional>
988 </repeat>
989 <param name="image_file_format" value="png" />
990 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" />
991 </test>
992 <test>
993 <param name="region" value="X:3000000-3300000"/>
994 <conditional name="x_axis">
995 <param name="x_axis_select" value="yes" />
996 </conditional>
997 <repeat name="tracks">
998 <conditional name="track_file_style_conditional">
999 <param name="track_file_style_selector" value="gene_track_option" />
1000 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
1001 <param name="title" value="test" />
1002 <param name="height_bed" value="10" />
1003 <param name="color" value="#000000" />
1004 <param name="flybase" value="false" />
1005 <param name="spacer_height" value="1"/>
1006 </conditional>
1007 </repeat>
1008 <repeat name="tracks">
1009 <conditional name="track_file_style_conditional">
1010 <param name="track_file_style_selector" value="gene_track_option" />
1011 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
1012 <param name="title" value="test" />
1013 <param name="height_bed" value="10" />
1014 <param name="color" value="#000000" />
1015 <param name="flybase" value="false" />
1016 <param name="spacer_height" value="1"/>
1017 </conditional>
1018 </repeat>
1019 <param name="image_file_format" value="png" />
1020 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" />
1021 </test>
723 </tests> 1022 </tests>
724 <help><![CDATA[ 1023 <help><![CDATA[
725 1024
726 pyGenomeTracks 1025 pyGenomeTracks
727 ============== 1026 ==============
728 1027
729 **pyGenomeTracks** is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable. 1028 **pyGenomeTracks** is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable.
730 Currently, it is possible to plot: 1029 Currently, it is possible to plot:
731 1030
732 - bigwig 1031 - bigwig
733 - bed (many options) 1032 - bed (many options)
734 - bedgraph 1033 - bedgraph
735 - links (represented as arcs) 1034 - links (represented as arcs)
759 _________________ 1058 _________________
760 1059
761 Output 1060 Output
762 ------ 1061 ------
763 1062
764 **pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) 1063 **pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files)
765 also contains Hi-C data. The plot is composed of tracks that need to be specified. 1064 also contains Hi-C data. The plot is composed of tracks that need to be specified.
766 Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**. 1065 Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**.
767 TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to: 1066 TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to:
768 TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states, 1067 TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states,
769 principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. 1068 principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track.
770 Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_. 1069 Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_.
771 1070
772 .. image:: $PATH_TO_IMAGES/pyGenomeTracks.png 1071 .. image:: $PATH_TO_IMAGES/pyGenomeTracks.png
773 :width: 70 % 1072 :width: 70 %
774 1073