Mercurial > repos > iuc > pygenometracks
comparison pyGenomeTracks.xml @ 14:59fd173ac850 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b
author | iuc |
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date | Fri, 26 May 2023 07:54:55 +0000 |
parents | 360df4999907 |
children | 36b848d5f3ec |
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13:360df4999907 | 14:59fd173ac850 |
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186 #end if | 186 #end if |
187 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": | 187 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": |
188 color = bed_rgb | 188 color = bed_rgb |
189 #elif $track.track_file_style_conditional.color_bed.color: | 189 #elif $track.track_file_style_conditional.color_bed.color: |
190 color = $track.track_file_style_conditional.color_bed.color | 190 color = $track.track_file_style_conditional.color_bed.color |
191 #if $track.track_file_style_conditional.color_bed.color_bed_select == "colormap": | |
192 #if str($track.track_file_style_conditional.color_bed.min_value) != '': | |
193 min_value = $track.track_file_style_conditional.color_bed.min_value | |
194 #end if | |
195 #if str($track.track_file_style_conditional.color_bed.max_value) != '': | |
196 max_value = $track.track_file_style_conditional.color_bed.max_value | |
197 #end if | |
198 #end if | |
191 #end if | 199 #end if |
192 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': | 200 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': |
193 border_color = $track.track_file_style_conditional.border_color_bed.color | 201 border_color = $track.track_file_style_conditional.border_color_bed.color |
194 #else | 202 #else |
195 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select | 203 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select |
228 #end if | 236 #end if |
229 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": | 237 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": |
230 color = bed_rgb | 238 color = bed_rgb |
231 #elif $track.track_file_style_conditional.color_bed.color: | 239 #elif $track.track_file_style_conditional.color_bed.color: |
232 color = $track.track_file_style_conditional.color_bed.color | 240 color = $track.track_file_style_conditional.color_bed.color |
241 #if $track.track_file_style_conditional.color_bed.color_bed_select == "colormap": | |
242 #if str($track.track_file_style_conditional.color_bed.min_value) != '': | |
243 min_value = $track.track_file_style_conditional.color_bed.min_value | |
244 #end if | |
245 #if str($track.track_file_style_conditional.color_bed.max_value) != '': | |
246 max_value = $track.track_file_style_conditional.color_bed.max_value | |
247 #end if | |
248 #end if | |
233 #end if | 249 #end if |
234 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': | 250 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': |
235 border_color = $track.track_file_style_conditional.border_color_bed.color | 251 border_color = $track.track_file_style_conditional.border_color_bed.color |
236 #else | 252 #else |
237 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select | 253 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select |
303 #end for | 319 #end for |
304 #end if | 320 #end if |
305 | 321 |
306 ## Link | 322 ## Link |
307 #if $track.track_file_style_conditional.track_file_style_selector == "link_track_option": | 323 #if $track.track_file_style_conditional.track_file_style_selector == "link_track_option": |
308 [links_$counter] | 324 #for $counter_link, $data_link in enumerate($track.track_file_style_conditional.track_input_link): |
309 file = $track.track_file_style_conditional.track_input_link | 325 [links_${counter}_${counter_link}] |
310 #if $track.track_file_style_conditional.title: | 326 file = $data_link |
327 #if $track.track_file_style_conditional.title: | |
311 title = $track.track_file_style_conditional.title | 328 title = $track.track_file_style_conditional.title |
312 #elif $track.track_file_style_conditional.overlay_select == 'no': | 329 #elif $track.track_file_style_conditional.overlay_select == 'no': |
313 title = $track.track_file_style_conditional.track_input_link.element_identifier | 330 title = $data_link.element_identifier |
314 #end if | 331 #end if |
315 #if $track.track_file_style_conditional.height: | 332 #if $track.track_file_style_conditional.height: |
316 height = $track.track_file_style_conditional.height | 333 height = $track.track_file_style_conditional.height |
317 #end if | 334 #end if |
318 #if $track.track_file_style_conditional.min_value != "": | 335 #if $track.track_file_style_conditional.min_value != "": |
319 min_value = $track.track_file_style_conditional.min_value | 336 min_value = $track.track_file_style_conditional.min_value |
320 #end if | 337 #end if |
321 #if $track.track_file_style_conditional.max_value != "": | 338 #if $track.track_file_style_conditional.max_value != "": |
322 max_value = $track.track_file_style_conditional.max_value | 339 max_value = $track.track_file_style_conditional.max_value |
323 #end if | 340 #end if |
324 color = $track.track_file_style_conditional.color_link.color | 341 color = $track.track_file_style_conditional.color_link.color |
325 alpha = $track.track_file_style_conditional.alpha | 342 alpha = $track.track_file_style_conditional.alpha |
326 line_width = $track.track_file_style_conditional.line_width | 343 line_width = $track.track_file_style_conditional.line_width |
327 line_style = $track.track_file_style_conditional.line_style | 344 line_style = $track.track_file_style_conditional.line_style |
328 links_type = $track.track_file_style_conditional.display.links_type | 345 links_type = $track.track_file_style_conditional.display.links_type |
329 #if $track.track_file_style_conditional.display.links_type in ['arcs', 'triangles']: | 346 #if $track.track_file_style_conditional.display.links_type in ['arcs', 'triangles']: |
330 compact_arcs_level = $track.track_file_style_conditional.display.compact_arcs_level | 347 compact_arcs_level = $track.track_file_style_conditional.display.compact_arcs_level |
331 use_middle = $track.track_file_style_conditional.display.use_middle | 348 use_middle = $track.track_file_style_conditional.display.use_middle |
332 #end if | 349 #end if |
333 #if $track.track_file_style_conditional.display.links_type != 'squares' and $track.track_file_style_conditional.display.ylim != "": | 350 #if $track.track_file_style_conditional.display.links_type != 'squares' and $track.track_file_style_conditional.display.ylim != "": |
334 ylim = $track.track_file_style_conditional.display.ylim | 351 ylim = $track.track_file_style_conditional.display.ylim |
335 #end if | 352 #end if |
336 #if $track.track_file_style_conditional.display.links_type == 'squares' and $track.track_file_style_conditional.display.region2 != "": | 353 #if $track.track_file_style_conditional.display.links_type == 'squares' and $track.track_file_style_conditional.display.region2 != "": |
337 region2 = $track.track_file_style_conditional.display.region2 | 354 region2 = $track.track_file_style_conditional.display.region2 |
338 #end if | 355 #end if |
339 #if $track.track_file_style_conditional.invert_orientation: | 356 #if $track.track_file_style_conditional.invert_orientation: |
340 orientation = inverted | 357 orientation = inverted |
341 #end if | 358 #end if |
342 overlay_previous = $track.track_file_style_conditional.overlay_select | 359 overlay_previous = $track.track_file_style_conditional.overlay_select |
343 file_type = links | 360 file_type = links |
344 ## If spacer is asked a new section is created: | 361 ## If spacer is asked a new section is created: |
345 #if $track.track_file_style_conditional.spacer_height != "": | 362 #if $track.track_file_style_conditional.spacer_height != "": |
346 [spacer] | 363 [spacer] |
347 height = $track.track_file_style_conditional.spacer_height | 364 height = $track.track_file_style_conditional.spacer_height |
348 #end if | 365 #end if |
366 #end for | |
349 #end if | 367 #end if |
350 | 368 |
351 ## Narrow peak | 369 ## Narrow peak |
352 #if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option": | 370 #if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option": |
353 #for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak): | 371 #for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak): |
887 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> | 905 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> |
888 <option value="RdYlBu_r">RdYlBu reversed</option> | 906 <option value="RdYlBu_r">RdYlBu reversed</option> |
889 <option value="viridis">viridis</option> | 907 <option value="viridis">viridis</option> |
890 <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> | 908 <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> |
891 </param> | 909 </param> |
910 <expand macro="minmax_macro" /> | |
892 </when> | 911 </when> |
893 </conditional> | 912 </conditional> |
894 <expand macro="border_color_bed_macro" /> | 913 <expand macro="border_color_bed_macro" /> |
895 <param name="line_width" type="float" value="0.5" label="width of lines" /> | 914 <param name="line_width" type="float" value="0.5" label="width of lines" /> |
896 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/> | 915 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/> |
917 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> | 936 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> |
918 <option value="RdYlBu_r">RdYlBu reversed</option> | 937 <option value="RdYlBu_r">RdYlBu reversed</option> |
919 <option value="viridis">viridis</option> | 938 <option value="viridis">viridis</option> |
920 <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> | 939 <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> |
921 </param> | 940 </param> |
941 <expand macro="minmax_macro" /> | |
922 </when> | 942 </when> |
923 </conditional> | 943 </conditional> |
924 <expand macro="border_color_bed_macro" /> | 944 <expand macro="border_color_bed_macro" /> |
925 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> | 945 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> |
926 <conditional name="labels"> | 946 <conditional name="labels"> |
1746 </section> | 1766 </section> |
1747 </conditional> | 1767 </conditional> |
1748 <conditional name="color_bed"> | 1768 <conditional name="color_bed"> |
1749 <param name="color_bed_select" value="colormap" /> | 1769 <param name="color_bed_select" value="colormap" /> |
1750 <param name="color" value="RdYlBu_r" /> | 1770 <param name="color" value="RdYlBu_r" /> |
1771 <param name="min_value" value="0" /> | |
1772 <param name="max_value" value="2" /> | |
1751 </conditional> | 1773 </conditional> |
1752 </conditional> | 1774 </conditional> |
1753 </repeat> | 1775 </repeat> |
1754 <repeat name="tracks"> | 1776 <repeat name="tracks"> |
1755 <conditional name="track_file_style_conditional"> | 1777 <conditional name="track_file_style_conditional"> |
2426 </conditional> | 2448 </conditional> |
2427 </repeat> | 2449 </repeat> |
2428 <repeat name="tracks"> | 2450 <repeat name="tracks"> |
2429 <conditional name="track_file_style_conditional"> | 2451 <conditional name="track_file_style_conditional"> |
2430 <param name="track_file_style_selector" value="link_track_option" /> | 2452 <param name="track_file_style_selector" value="link_track_option" /> |
2431 <param name="track_input_link" value="test.arcs" ftype="bed" /> | 2453 <param name="track_input_link" value="test.arcs,test.arcs" ftype="bed" /> |
2432 <param name="title" value="highly compacted" /> | 2454 <param name="title" value="highly compacted" /> |
2433 <conditional name="color_link"> | 2455 <conditional name="color_link"> |
2434 <param name="color_link_select" value="manually" /> | 2456 <param name="color_link_select" value="manually" /> |
2435 <param name="color" value="#000000" /> | 2457 <param name="color" value="#000000" /> |
2436 </conditional> | 2458 </conditional> |