Mercurial > repos > iuc > pygenometracks
comparison pyGenomeTracks.xml @ 0:2074627b0f83 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
| author | iuc |
|---|---|
| date | Sat, 23 Jun 2018 02:28:35 -0400 |
| parents | |
| children | 0ea86f6bf2a1 |
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| -1:000000000000 | 0:2074627b0f83 |
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| 1 <tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | |
| 2 <description>plot genomic data tracks</description> | |
| 3 <macros> | |
| 4 <token name="@BINARY@">pyGenomeTracks</token> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements" /> | |
| 8 <command detect_errors="exit_code"> | |
| 9 <![CDATA[ | |
| 10 | |
| 11 sed '/^$/d' '$tracks_config' && | |
| 12 @BINARY@ | |
| 13 --tracks '$tracks_config' | |
| 14 #if $region and $region is not None: | |
| 15 --region '$region' | |
| 16 #end if | |
| 17 --outFileName plot.$image_file_format | |
| 18 && mv plot.$image_file_format plot | |
| 19 ]]> | |
| 20 </command> | |
| 21 <configfiles> | |
| 22 <configfile name="tracks_config"> | |
| 23 #if $x_axis.x_axis_select == "yes": | |
| 24 [x-axis] | |
| 25 #if $x_axis.fontsize: | |
| 26 fontsize = $x_axis.fontsize | |
| 27 #end if | |
| 28 #if $x_axis.where: | |
| 29 where = $x_axis.where | |
| 30 #end if | |
| 31 #end if | |
| 32 #for $counter, $track in enumerate($tracks): | |
| 33 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": | |
| 34 | |
| 35 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): | |
| 36 [hic_section_$counter] | |
| 37 file = $data_matrix | |
| 38 file_type = hic_matrix | |
| 39 #if $track.track_file_style_conditional.title: | |
| 40 title = $track.track_file_style_conditional.title | |
| 41 #else: | |
| 42 title = $data_matrix.name | |
| 43 #end if | |
| 44 #if $track.track_file_style_conditional.depth: | |
| 45 depth = $track.track_file_style_conditional.depth | |
| 46 #end if | |
| 47 #if $track.track_file_style_conditional.colormap: | |
| 48 colormap = $track.track_file_style_conditional.colormap | |
| 49 #end if | |
| 50 #if $track.track_file_style_conditional.min_value: | |
| 51 min_value = $track.track_file_style_conditional.min_value | |
| 52 #end if | |
| 53 #if $track.track_file_style_conditional.max_value: | |
| 54 max_value = $track.track_file_style_conditional.max_value | |
| 55 #end if | |
| 56 transform = $track.track_file_style_conditional.transform | |
| 57 height = $track.track_file_style_conditional.height_matrix | |
| 58 | |
| 59 #if $track.track_file_style_conditional.boundaries_file is not None: | |
| 60 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix] | |
| 61 boundaries_file = $boundary_file | |
| 62 #end if | |
| 63 | |
| 64 #if $track.track_file_style_conditional.x_labels: | |
| 65 x labels = $track.track_file_style_conditional.x_labels | |
| 66 #end if | |
| 67 #if $track.track_file_style_conditional.type: | |
| 68 type = $track.track_file_style_conditional.type | |
| 69 #end if | |
| 70 #if $track.track_file_style_conditional.show_masked_bins: | |
| 71 show_masked_bins = $track.track_file_style_conditional.show_masked_bins | |
| 72 #end if | |
| 73 #if $track.track_file_style_conditional.scale_factor: | |
| 74 scale factor = $track.track_file_style_conditional.scale_factor | |
| 75 #end if | |
| 76 | |
| 77 [spacer] | |
| 78 #if $track.track_file_style_conditional.spacer_height: | |
| 79 height = $track.track_file_style_conditional.spacer_height | |
| 80 #end if | |
| 81 #end for | |
| 82 | |
| 83 #end if | |
| 84 | |
| 85 | |
| 86 | |
| 87 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option": | |
| 88 | |
| 89 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: | |
| 90 [tad_score_$counter] | |
| 91 file = $data_bedgraph | |
| 92 #if $track.track_file_style_conditional.title: | |
| 93 title = $track.track_file_style_conditional.title | |
| 94 #else: | |
| 95 title = $data_bedgraph.name | |
| 96 #end if | |
| 97 #if $track.track_file_style_conditional.color: | |
| 98 color = $track.track_file_style_conditional.color | |
| 99 #end if | |
| 100 #if $track.track_file_style_conditional.height_tad: | |
| 101 height = $track.track_file_style_conditional.height_tad | |
| 102 #end if | |
| 103 #if $track.track_file_style_conditional.type_lines: | |
| 104 type = $track.track_file_style_conditional.type_lines | |
| 105 #end if | |
| 106 #if $track.track_file_style_conditional.show_data: | |
| 107 show data range = $track.track_file_style_conditional.show_data | |
| 108 #end if | |
| 109 | |
| 110 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) | |
| 111 #if $columns > 5: | |
| 112 file_type = bedgraph_matrix | |
| 113 #else: | |
| 114 file_type = bedgraph | |
| 115 #end if | |
| 116 type = lines | |
| 117 [spacer] | |
| 118 #if $track.track_file_style_conditional.spacer_height: | |
| 119 height = $track.track_file_style_conditional.spacer_height | |
| 120 #end if | |
| 121 #end for | |
| 122 #end if | |
| 123 | |
| 124 | |
| 125 | |
| 126 | |
| 127 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option": | |
| 128 #for $data_bed in $track.track_file_style_conditional.track_input_bed: | |
| 129 | |
| 130 [chrom states_$counter] | |
| 131 file = $data_bed | |
| 132 #if $track.track_file_style_conditional.title: | |
| 133 title = $track.track_file_style_conditional.title | |
| 134 #else: | |
| 135 title = $data_bed.name | |
| 136 #end if | |
| 137 #if $track.track_file_style_conditional.color: | |
| 138 color = $track.track_file_style_conditional.color | |
| 139 #end if | |
| 140 display = collapsed | |
| 141 #if $track.track_file_style_conditional.height_chrom: | |
| 142 height = $track.track_file_style_conditional.height_chrom | |
| 143 #end if | |
| 144 #if $track.track_file_style_conditional.border_color: | |
| 145 border_color = $track.track_file_style_conditional.border_color | |
| 146 #end if | |
| 147 file_type = bed | |
| 148 [spacer] | |
| 149 #if $track.track_file_style_conditional.spacer_height: | |
| 150 height = $track.track_file_style_conditional.spacer_height | |
| 151 #end if | |
| 152 #end for | |
| 153 | |
| 154 #end if | |
| 155 | |
| 156 | |
| 157 | |
| 158 | |
| 159 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": | |
| 160 #for $data_bed in $track.track_file_style_conditional.track_input_bed: | |
| 161 | |
| 162 [genes_$counter] | |
| 163 file = $data_bed | |
| 164 #if $track.track_file_style_conditional.title: | |
| 165 title = $track.track_file_style_conditional.title | |
| 166 #else: | |
| 167 title = $data_bed.name | |
| 168 #end if | |
| 169 #if $track.track_file_style_conditional.color: | |
| 170 color = $track.track_file_style_conditional.color | |
| 171 #end if | |
| 172 | |
| 173 #if $track.track_file_style_conditional.height_bed: | |
| 174 height = $track.track_file_style_conditional.height_bed | |
| 175 #end if | |
| 176 | |
| 177 #if $track.track_file_style_conditional.labels: | |
| 178 labels = $track.track_file_style_conditional.labels | |
| 179 #end if | |
| 180 | |
| 181 #if $track.track_file_style_conditional.type: | |
| 182 type = $track.track_file_style_conditional.type | |
| 183 #end if | |
| 184 | |
| 185 file_type = bed | |
| 186 #if $track.track_file_style_conditional.fontsize: | |
| 187 fontsize = $track.track_file_style_conditional.fontsize | |
| 188 #end if | |
| 189 | |
| 190 #if $track.track_file_style_conditional.gene_rows: | |
| 191 gene rows = $track.track_file_style_conditional.gene_rows | |
| 192 #end if | |
| 193 | |
| 194 #if $track.track_file_style_conditional.global_max_row: | |
| 195 global max row = $track.track_file_style_conditional.global_max_row | |
| 196 #end if | |
| 197 [spacer] | |
| 198 #if $track.track_file_style_conditional.spacer_height: | |
| 199 height = $track.track_file_style_conditional.spacer_height | |
| 200 #end if | |
| 201 #end for | |
| 202 #end if | |
| 203 | |
| 204 | |
| 205 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option": | |
| 206 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: | |
| 207 | |
| 208 [bedgraph_$counter] | |
| 209 file = $data_bedgraph | |
| 210 #if $track.track_file_style_conditional.title: | |
| 211 title = $track.track_file_style_conditional.title | |
| 212 #else: | |
| 213 title = $data_bedgraph.name | |
| 214 #end if | |
| 215 #if $track.track_file_style_conditional.color: | |
| 216 color = $track.track_file_style_conditional.color | |
| 217 #end if | |
| 218 #if $track.track_file_style_conditional.height_bedgraph: | |
| 219 height = $track.track_file_style_conditional.height_bedgraph | |
| 220 #end if | |
| 221 #if $track.track_file_style_conditional.show_data: | |
| 222 show data range = $track.track_file_style_conditional.show_data | |
| 223 #end if | |
| 224 | |
| 225 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) | |
| 226 #if $columns > 5: | |
| 227 file_type = bedgraph_matrix | |
| 228 #else: | |
| 229 file_type = bedgraph | |
| 230 #end if | |
| 231 type = lines | |
| 232 [spacer] | |
| 233 #if $track.track_file_style_conditional.spacer_height: | |
| 234 height = $track.track_file_style_conditional.spacer_height | |
| 235 #end if | |
| 236 #end for | |
| 237 #end if | |
| 238 | |
| 239 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option": | |
| 240 #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig: | |
| 241 [bigwig_$counter] | |
| 242 file = $data_bigwig | |
| 243 #if $track.track_file_style_conditional.title: | |
| 244 title = $track.track_file_style_conditional.title | |
| 245 #else: | |
| 246 title = $data_bigwig.name | |
| 247 #end if | |
| 248 color = $track.track_file_style_conditional.color | |
| 249 #if $track.track_file_style_conditional.min_value: | |
| 250 min_value = $track.track_file_style_conditional.min_value | |
| 251 #else: | |
| 252 min_value = 0 | |
| 253 #end if | |
| 254 #if $track.track_file_style_conditional.max_value: | |
| 255 max_value = $track.track_file_style_conditional.max_value | |
| 256 #else: | |
| 257 max_value = auto | |
| 258 #end if | |
| 259 height = $track.track_file_style_conditional.height_bigwig | |
| 260 #if $track.track_file_style_conditional.number_of_bins: | |
| 261 number of bins = $track.track_file_style_conditional.number_of_bins | |
| 262 #end if | |
| 263 nans to zeros = $track.track_file_style_conditional.nans_to_zeros | |
| 264 #if $track.track_file_style_conditional.type_conditional == 'fill_option': | |
| 265 type = fill | |
| 266 #elif $track.track_file_style_conditional.type_conditional == 'line_option': | |
| 267 type = line:$track.track_file_style_conditional.type_conditional.height_line | |
| 268 #elif $track.track_file_style_conditional.type_conditional == 'point_option': | |
| 269 type = points:$track.track_file_style_conditional.type_conditional.width_point | |
| 270 #end if | |
| 271 #if $track.track_file_style_conditional.data_range: | |
| 272 show data range = $track.track_file_style_conditional.data_range | |
| 273 #end if | |
| 274 file_type = bigwig | |
| 275 [spacer] | |
| 276 #if $track.track_file_style_conditional.spacer_height: | |
| 277 height = $track.track_file_style_conditional.spacer_height | |
| 278 #end if | |
| 279 #end for | |
| 280 #end if | |
| 281 | |
| 282 | |
| 283 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option": | |
| 284 #for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix: | |
| 285 | |
| 286 [bedgraph_matrix_$counter] | |
| 287 file = $data_bedgraph_matrix | |
| 288 #if $track.track_file_style_conditional.title: | |
| 289 title = $track.track_file_style_conditional.title | |
| 290 #else: | |
| 291 title = $data_bedgraph_matrix.name | |
| 292 #end if | |
| 293 #if $track.track_file_style_conditional.height_bedgraph: | |
| 294 height = $track.track_file_style_conditional.height_bedgraph | |
| 295 #end if | |
| 296 orientation = inverted | |
| 297 #if $track.track_file_style_conditional.min_value: | |
| 298 min_value = $track.track_file_style_conditional.min_value | |
| 299 #end if | |
| 300 #if $track.track_file_style_conditional.max_value: | |
| 301 max_value = $track.track_file_style_conditional.max_value | |
| 302 #end if | |
| 303 #if $track.track_file_style_conditional.type_lines: | |
| 304 type = $track.track_file_style_conditional.type_lines | |
| 305 #end if | |
| 306 file_type = bedgraph_matrix | |
| 307 plot horizontal lines=False | |
| 308 [spacer] | |
| 309 #if $track.track_file_style_conditional.spacer_height: | |
| 310 height = $track.track_file_style_conditional.spacer_height | |
| 311 #end if | |
| 312 #end for | |
| 313 #end if | |
| 314 | |
| 315 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option": | |
| 316 | |
| 317 [vlines_$counter] | |
| 318 file = $track.track_file_style_conditional.track_input_bed_single | |
| 319 type = vlines | |
| 320 file_type = bed | |
| 321 #end if | |
| 322 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": | |
| 323 | |
| 324 [spacer] | |
| 325 #if $track.track_file_style_conditional.spacer_height: | |
| 326 height = $track.track_file_style_conditional.spacer_height | |
| 327 #end if | |
| 328 #end if | |
| 329 #end for</configfile> | |
| 330 </configfiles> | |
| 331 <inputs> | |
| 332 <expand macro="region" /> | |
| 333 | |
| 334 <repeat name="tracks" min="1" title="Include tracks in your plot" | |
| 335 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph"> | |
| 336 <conditional name="track_file_style_conditional"> | |
| 337 <param name="track_file_style_selector" type="select" label="Choose style of the track"> | |
| 338 <option value="hic_matrix_option">TAD visualization</option> | |
| 339 <option value="chrom_states_option">Chromatine states</option> | |
| 340 <option value="tad_score_track_option">TAD score</option> | |
| 341 <option value="gene_track_option">Gene track / Bed track</option> | |
| 342 <option value="bigwig_track_option">Bigwig track</option> | |
| 343 <option value="bedgraph_track_option">Bedgraph track </option> | |
| 344 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option> | |
| 345 <option value="vlines_track_option">Vlines track</option> | |
| 346 <option value="spacer_option">Spacer</option> | |
| 347 </param> | |
| 348 <when value="hic_matrix_option"> | |
| 349 <expand macro="plot_title" /> | |
| 350 <expand macro="matrix_h5_cooler_multiple_macro" /> | |
| 351 | |
| 352 <expand macro="colormap" /> | |
| 353 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> | |
| 354 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> | |
| 355 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/> | |
| 356 <param name="transform" type="select" label="Plot the transformed value"> | |
| 357 <option value="log1p" selected="True" >log1p</option> | |
| 358 <option value="log">log</option> | |
| 359 <option value="-log">-log</option> | |
| 360 | |
| 361 </param> | |
| 362 <param name="height_matrix" type="float" value="1.5" optional="True" label="height"/> | |
| 363 | |
| 364 <param name="type" type="select" optional="True" label="Plotting type"> | |
| 365 <option value="arcplot">arcplot</option> | |
| 366 <option value="interaction">interaction</option> | |
| 367 </param> | |
| 368 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false" | |
| 369 label="Show masked bins" /> | |
| 370 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple='True'/> <!-- multiple='True'--> | |
| 371 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" /> | |
| 372 <param name="x_labels" type="boolean" truevalue="yes" falsevalue="no" optional="True" label="Show x labels" /> | |
| 373 <expand macro="spacer_macro" /> | |
| 374 | |
| 375 </when> | |
| 376 <when value="tad_score_track_option"> | |
| 377 <expand macro="plot_title" /> | |
| 378 <expand macro="track_input_bedgraph_macro" /> | |
| 379 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> | |
| 380 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" | |
| 381 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead | |
| 382 of the matrix set to lines if a heatmap representing the matrix is not wanted"/> | |
| 383 <param name="height_tad" type="float" value="0.2" optional="True" label="height"/> | |
| 384 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> | |
| 385 <expand macro="spacer_macro" /> | |
| 386 | |
| 387 </when> | |
| 388 <when value="chrom_states_option"> | |
| 389 <expand macro="plot_title" /> | |
| 390 | |
| 391 <expand macro="track_input_bed_macro" /> | |
| 392 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> | |
| 393 | |
| 394 <param name="border_color" type="color" value="#000000" label="Border color" optional="True" /> | |
| 395 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/> | |
| 396 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" | |
| 397 label="Plot labels" /> | |
| 398 <expand macro="spacer_macro" /> | |
| 399 | |
| 400 </when> | |
| 401 <when value="gene_track_option"> | |
| 402 <expand macro="plot_title" /> | |
| 403 | |
| 404 <expand macro="track_input_bed_macro" /> | |
| 405 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> | |
| 406 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> | |
| 407 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" | |
| 408 label="Plot labels" /> | |
| 409 <param name="type" type="select" optional="True" label="Type"> | |
| 410 <option value="genes">genes</option> | |
| 411 <option value="domains">domains</option> | |
| 412 </param> | |
| 413 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false" | |
| 414 label="Global max rows" /> | |
| 415 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" /> | |
| 416 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> | |
| 417 <expand macro="spacer_macro" /> | |
| 418 | |
| 419 </when> | |
| 420 <when value="bedgraph_track_option"> | |
| 421 <expand macro="plot_title" /> | |
| 422 <expand macro="track_input_bedgraph_macro" /> | |
| 423 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> | |
| 424 | |
| 425 <param name="height_bedgraph" type="float" value="0.2" optional="True" label="height"/> | |
| 426 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> | |
| 427 <expand macro="spacer_macro" /> | |
| 428 | |
| 429 </when> | |
| 430 <when value="bigwig_track_option"> | |
| 431 <expand macro="plot_title" /> | |
| 432 | |
| 433 <expand macro="track_input_bigwig_macro" /> | |
| 434 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> | |
| 435 | |
| 436 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> | |
| 437 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/> | |
| 438 | |
| 439 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> | |
| 440 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" /> | |
| 441 <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false" | |
| 442 label="NAN's to zeros" /> | |
| 443 <conditional name="type_conditional"> | |
| 444 <param name="type_selector" type="select" label="Choose style of the plot."> | |
| 445 <option value="fill_option">fill</option> | |
| 446 <option value="line_option">line</option> | |
| 447 <option value="point_option">point</option> | |
| 448 </param> | |
| 449 <when value="line_option"> | |
| 450 <param name="width_line" type="float" value="0.5" optional="True" label="Width"/> | |
| 451 </when> | |
| 452 <when value="point_option"> | |
| 453 <param name="width_point" type="float" value="0.5" optional="True" label="Width"/> | |
| 454 </when> | |
| 455 <when value="fill_option" /> | |
| 456 </conditional> | |
| 457 <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" /> | |
| 458 <expand macro="spacer_macro" /> | |
| 459 | |
| 460 </when> | |
| 461 | |
| 462 | |
| 463 <when value="bedgraph_matrix_track_option"> | |
| 464 <expand macro="plot_title" /> | |
| 465 | |
| 466 <expand macro="track_input_bedgraph_matrix_macro" /> | |
| 467 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> | |
| 468 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/> | |
| 469 | |
| 470 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> | |
| 471 | |
| 472 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" | |
| 473 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead | |
| 474 of the matrix set to lines if a heatmap representing the matrix is not wanted"/> | |
| 475 <expand macro="spacer_macro" /> | |
| 476 | |
| 477 </when> | |
| 478 <when value="vlines_track_option"> | |
| 479 <expand macro="track_input_bed_single_macro" /> | |
| 480 </when> | |
| 481 <when value="spacer_option"> | |
| 482 <expand macro="spacer_macro" /> | |
| 483 </when> | |
| 484 </conditional> | |
| 485 | |
| 486 </repeat> | |
| 487 | |
| 488 | |
| 489 <conditional name="x_axis"> | |
| 490 <param name="x_axis_select" type="select" label="Configure x-axis"> | |
| 491 <option value="no" selected="True">No</option> | |
| 492 <option value="yes">Yes</option> | |
| 493 </param> | |
| 494 <when value="yes"> | |
| 495 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> | |
| 496 <param name="where" type="select" optional="True" label="Where to place the x-axis"> | |
| 497 <option value="top">Top</option> | |
| 498 <option value="bottom">Bottom</option> | |
| 499 </param> | |
| 500 </when> | |
| 501 <when value="no" /> | |
| 502 </conditional> | |
| 503 <param name="image_file_format" type="select" label="Image output format"> | |
| 504 <option value="png">png</option> | |
| 505 <option value="svg">svg</option> | |
| 506 </param> | |
| 507 </inputs> | |
| 508 <outputs> | |
| 509 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on [${on_string}]: Plot"> | |
| 510 <change_format> | |
| 511 <when input="image_file_format" value="png" format="png" /> | |
| 512 <when input="image_file_format" value="svg" format="svg" /> | |
| 513 </change_format> | |
| 514 </data> | |
| 515 </outputs> | |
| 516 <tests> | |
| 517 <test> | |
| 518 <param name="region" value="chrX:3000000-3500000"/> | |
| 519 <conditional name="x_axis"> | |
| 520 <param name="x_axis_select" value="yes" /> | |
| 521 </conditional> | |
| 522 <repeat name="tracks"> | |
| 523 <conditional name="track_file_style_conditional"> | |
| 524 <param name="track_file_style_selector" value="hic_matrix_option" /> | |
| 525 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> | |
| 526 | |
| 527 <param name="title" value="Kc DpnII (Li et al. 2015)" /> | |
| 528 <param name="colormap" value="RdYlBu_r" /> | |
| 529 <param name="depth" value="200000" /> | |
| 530 <param name="transform" value="log1p" /> | |
| 531 <param name="boundaries_file" value="domains.bed" /> | |
| 532 <param name="x_labels" value="True" /> | |
| 533 </conditional> | |
| 534 </repeat> | |
| 535 <repeat name="tracks"> | |
| 536 <conditional name="track_file_style_conditional"> | |
| 537 <param name="track_file_style_selector" value="spacer_option" /> | |
| 538 <param name="spacer_height" value="0.05" /> | |
| 539 </conditional> | |
| 540 </repeat> | |
| 541 <repeat name="tracks"> | |
| 542 <conditional name="track_file_style_conditional"> | |
| 543 <param name="track_file_style_selector" value="chrom_states_option" /> | |
| 544 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> | |
| 545 <param name="title" value="TAD state" /> | |
| 546 <param name="height_chrom" value="0.5" /> | |
| 547 <param name="labels" value="off" /> | |
| 548 </conditional> | |
| 549 </repeat> | |
| 550 <repeat name="tracks"> | |
| 551 <conditional name="track_file_style_conditional"> | |
| 552 <param name="track_file_style_selector" value="tad_score_track_option" /> | |
| 553 <param name="track_input_bedgraph" value="tad_score.gz" ftype="bedgraph" /> | |
| 554 <param name="title" value="TAD separation score (Ramirez et al.)" /> | |
| 555 <param name="height_tad" value="10" /> | |
| 556 </conditional> | |
| 557 </repeat> | |
| 558 <repeat name="tracks"> | |
| 559 <conditional name="track_file_style_conditional"> | |
| 560 <param name="track_file_style_selector" value="spacer_option" /> | |
| 561 <param name="spacer_height" value="1" /> | |
| 562 </conditional> | |
| 563 </repeat> | |
| 564 <repeat name="tracks"> | |
| 565 <conditional name="track_file_style_conditional"> | |
| 566 <param name="track_file_style_selector" value="bedgraph_track_option" /> | |
| 567 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> | |
| 568 <param name="title" value="bedgraph" /> | |
| 569 <param name="height_bedgraph" value="4" /> | |
| 570 <param name="color" value="blue" /> | |
| 571 </conditional> | |
| 572 </repeat> | |
| 573 <repeat name="tracks"> | |
| 574 <conditional name="track_file_style_conditional"> | |
| 575 <param name="track_file_style_selector" value="bigwig_track_option" /> | |
| 576 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> | |
| 577 <param name="title" value="rep 1 test fill" /> | |
| 578 <param name="height_bigwig" value="4" /> | |
| 579 <param name="color" value="blue" /> | |
| 580 <conditional name="type_conditional"> | |
| 581 <param name="type_selector" value="fill_option" /> | |
| 582 </conditional> | |
| 583 </conditional> | |
| 584 </repeat> | |
| 585 | |
| 586 <repeat name="tracks"> | |
| 587 <conditional name="track_file_style_conditional"> | |
| 588 <param name="track_file_style_selector" value="bigwig_track_option" /> | |
| 589 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> | |
| 590 <param name="title" value="rep 1 test line" /> | |
| 591 <param name="height_bigwig" value="4" /> | |
| 592 <param name="color" value="red" /> | |
| 593 <conditional name="type_conditional"> | |
| 594 <param name="type_selector" value="line_option" /> | |
| 595 <param name="width_line" value="1" /> | |
| 596 </conditional> | |
| 597 </conditional> | |
| 598 </repeat> | |
| 599 | |
| 600 <repeat name="tracks"> | |
| 601 <conditional name="track_file_style_conditional"> | |
| 602 <param name="track_file_style_selector" value="bigwig_track_option" /> | |
| 603 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> | |
| 604 <param name="title" value="rep 1 test lw=0.2" /> | |
| 605 <param name="height_bigwig" value="4" /> | |
| 606 <param name="color" value="red" /> | |
| 607 <conditional name="type_conditional"> | |
| 608 <param name="type_selector" value="line_option" /> | |
| 609 <param name="width_line" value="0.1" /> | |
| 610 | |
| 611 </conditional> | |
| 612 </conditional> | |
| 613 </repeat> | |
| 614 | |
| 615 <repeat name="tracks"> | |
| 616 <conditional name="track_file_style_conditional"> | |
| 617 <param name="track_file_style_selector" value="bigwig_track_option" /> | |
| 618 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> | |
| 619 <param name="title" value="rep 1 test point:0.5" /> | |
| 620 <param name="height_bigwig" value="4" /> | |
| 621 <param name="color" value="black" /> | |
| 622 <conditional name="type_conditional"> | |
| 623 <param name="type_selector" value="point_option" /> | |
| 624 <param name="width_point" value="0.5" /> | |
| 625 | |
| 626 </conditional> | |
| 627 </conditional> | |
| 628 </repeat> | |
| 629 | |
| 630 <repeat name="tracks"> | |
| 631 <conditional name="track_file_style_conditional"> | |
| 632 <param name="track_file_style_selector" value="spacer_option" /> | |
| 633 <param name="spacer_height" value="0.5" /> | |
| 634 </conditional> | |
| 635 </repeat> | |
| 636 <repeat name="tracks"> | |
| 637 <conditional name="track_file_style_conditional"> | |
| 638 <param name="track_file_style_selector" value="gene_track_option" /> | |
| 639 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> | |
| 640 <param name="title" value="genes" /> | |
| 641 <param name="height_bed" value="5" /> | |
| 642 <param name="fontsize" value="10" /> | |
| 643 </conditional> | |
| 644 </repeat> | |
| 645 <repeat name="tracks"> | |
| 646 <conditional name="track_file_style_conditional"> | |
| 647 <param name="track_file_style_selector" value="spacer_option" /> | |
| 648 <param name="spacer_height" value="1" /> | |
| 649 </conditional> | |
| 650 </repeat> | |
| 651 <repeat name="tracks"> | |
| 652 <conditional name="track_file_style_conditional"> | |
| 653 <param name="track_file_style_selector" value="gene_track_option" /> | |
| 654 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> | |
| 655 <param name="title" value="max num rows 3" /> | |
| 656 <param name="height_bed" value="3" /> | |
| 657 <param name="fontsize" value="8" /> | |
| 658 <param name="gene_rows" value="3" /> | |
| 659 </conditional> | |
| 660 </repeat> | |
| 661 <repeat name="tracks"> | |
| 662 <conditional name="track_file_style_conditional"> | |
| 663 <param name="track_file_style_selector" value="spacer_option" /> | |
| 664 <param name="spacer_height" value="1" /> | |
| 665 </conditional> | |
| 666 </repeat> | |
| 667 <repeat name="tracks"> | |
| 668 <conditional name="track_file_style_conditional"> | |
| 669 <param name="track_file_style_selector" value="gene_track_option" /> | |
| 670 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> | |
| 671 <param name="title" value="bed6 global max row" /> | |
| 672 <param name="height_bed" value="20" /> | |
| 673 <param name="fontsize" value="10" /> | |
| 674 <param name="global_max_row" value="True" /> | |
| 675 </conditional> | |
| 676 </repeat> | |
| 677 <repeat name="tracks"> | |
| 678 <conditional name="track_file_style_conditional"> | |
| 679 <param name="track_file_style_selector" value="vlines_track_option" /> | |
| 680 <param name="track_input_bed_single" value="domains.bed" ftype="bed" /> | |
| 681 <param name="type" value="vlines" /> | |
| 682 </conditional> | |
| 683 </repeat> | |
| 684 <param name="image_file_format" value="png" /> | |
| 685 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> | |
| 686 </test> | |
| 687 <test> | |
| 688 <param name="region" value="chrX:3000000-3500000"/> | |
| 689 <conditional name="x_axis"> | |
| 690 <param name="x_axis_select" value="yes" /> | |
| 691 </conditional> | |
| 692 <repeat name="tracks"> | |
| 693 <conditional name="track_file_style_conditional"> | |
| 694 <param name="track_file_style_selector" value="bigwig_track_option" /> | |
| 695 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> | |
| 696 <param name="title" value="rep 1 test line" /> | |
| 697 <param name="height_bigwig" value="4" /> | |
| 698 <param name="color" value="red" /> | |
| 699 <conditional name="type_conditional"> | |
| 700 <param name="type_selector" value="line_option" /> | |
| 701 <param name="width_line" value="1" /> | |
| 702 </conditional> | |
| 703 </conditional> | |
| 704 </repeat> | |
| 705 <param name="image_file_format" value="png" /> | |
| 706 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" /> | |
| 707 </test> | |
| 708 </tests> | |
| 709 <help><![CDATA[ | |
| 710 | |
| 711 pyGenomeTracks | |
| 712 ============== | |
| 713 | |
| 714 **pyGenomeTracks** is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable. | |
| 715 Currently, it is possible to plot: | |
| 716 | |
| 717 - bigwig | |
| 718 - bed (many options) | |
| 719 - bedgraph | |
| 720 - links (represented as arcs) | |
| 721 - Hi-C matrices | |
| 722 | |
| 723 _________________ | |
| 724 | |
| 725 Usage | |
| 726 ----- | |
| 727 | |
| 728 This tool takes various types of tracks as input: | |
| 729 | |
| 730 - **Chromatin states:** display blocks of different colors following a bed file. | |
| 731 - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off. | |
| 732 - **Bigwig track:** generic bigwig track plotting. | |
| 733 - **Bedgraph track:** generic bedgraph track plotting. | |
| 734 - **Bedgraph matrix track** is used to specifically plot bm files computed by HiCExplorer's ``hicFindTADs`` (TAD seperation scores). | |
| 735 - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer's ``hicFindTADs``. | |
| 736 - **Spacer:** Add some space between two tracks. | |
| 737 - **Hi-C tracks:** | |
| 738 - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap. | |
| 739 - **TAD score:** display TAD seperation score computed by HiCExplorer's ``hicFindTADs``. | |
| 740 | |
| 741 | |
| 742 For each track, parameters for the color, the width or the font size can be defined. | |
| 743 | |
| 744 _________________ | |
| 745 | |
| 746 Output | |
| 747 ------ | |
| 748 | |
| 749 **pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) | |
| 750 also contains Hi-C data. The plot is composed of tracks that need to be specified. | |
| 751 Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**. | |
| 752 TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to: | |
| 753 TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states, | |
| 754 principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. | |
| 755 Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_. | |
| 756 | |
| 757 .. image:: $PATH_TO_IMAGES/pyGenomeTracks.png | |
| 758 :width: 70 % | |
| 759 | |
| 760 _________________ | |
| 761 | |
| 762 | For more information about pyGenomeTracks please consider our documentation on github_ | |
| 763 | |
| 764 .. _github: https://github.com/deeptools/pyGenomeTracks | |
| 765 .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9 | |
| 766 ]]></help> | |
| 767 <expand macro="citations" /> | |
| 768 </tool> |