Mercurial > repos > iuc > pygenometracks
comparison pyGenomeTracks.xml @ 2:c171f2b7d76e draft
"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 |
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| 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 |