Mercurial > repos > iuc > pygenometracks

comparison pyGenomeTracks.xml @ 14:d640aa8a24ab draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b
author iuc
date Fri, 26 May 2023 07:54:18 +0000
parents e0c00f68067f
children c7af51147b55
comparison
equal deleted inserted replaced
13:e0c00f68067f 14:d640aa8a24ab
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>