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comparison pyGenomeTracks.xml @ 7:d691445a7d2e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
author iuc
date Fri, 17 Apr 2020 15:57:09 +0000
parents ad2e499da28f
children 345d24273a58
comparison
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6:ad2e499da28f 7:d691445a7d2e
28 @BINARY@ 28 @BINARY@
29 --tracks '$tracks_config' 29 --tracks '$tracks_config'
30 #if $region and $region is not None: 30 #if $region and $region is not None:
31 --region '$region' 31 --region '$region'
32 #end if 32 #end if
33 #if $global_args.title is not None:
34 --title '$global_args.title'
35 #end if
36 --fontSize $global_args.fontsize
37 --dpi $global_args.dpi
38 --trackLabelFraction $global_args.trackLabelFraction
39 --trackLabelHAlign $global_args.trackLabelHAlign
33 --outFileName plot.$image_file_format 40 --outFileName plot.$image_file_format
34 && mv plot.$image_file_format plot 41 && mv plot.$image_file_format plot
35 ]]> 42 ]]>
36 </command> 43 </command>
37 <configfiles> 44 <configfiles>
38 <configfile name="tracks_config"> 45 <configfile name="tracks_config">
39 ## First the xaxis if where = top 46 ## Each track:
40 #if $x_axis.x_axis_select == "true":
41 #if $x_axis.where == 'top':
42 [x-axis]
43 #if $x_axis.fontsize:
44 fontsize = $x_axis.fontsize
45 #end if
46 where = top
47 #end if
48 #end if
49
50 ## Then each track:
51 #for $counter, $track in enumerate($tracks): 47 #for $counter, $track in enumerate($tracks):
52 ## Hi-C Track 48 ## Hi-C Track
53 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": 49 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
54 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): 50 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
55 [hic_section_${counter}_${counter_matrix}] 51 [hic_section_${counter}_${counter_matrix}]
122 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": 118 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
123 color = bed_rgb 119 color = bed_rgb
124 #elif $track.track_file_style_conditional.color_bed.color: 120 #elif $track.track_file_style_conditional.color_bed.color:
125 color = $track.track_file_style_conditional.color_bed.color 121 color = $track.track_file_style_conditional.color_bed.color
126 #end if 122 #end if
127 #if $track.track_file_style_conditional.border_color: 123 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually':
128 border_color = $track.track_file_style_conditional.border_color 124 border_color = $track.track_file_style_conditional.border_color_bed.color
125 #else
126 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select
129 #end if 127 #end if
130 display = collapsed 128 display = collapsed
131 #if $track.track_file_style_conditional.height_chrom: 129 #if $track.track_file_style_conditional.height_chrom:
132 height = $track.track_file_style_conditional.height_chrom 130 height = $track.track_file_style_conditional.height_chrom
133 #end if 131 #end if
146 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): 144 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
147 [genes_${counter}_${counter_bed}] 145 [genes_${counter}_${counter_bed}]
148 #set ext = $data_bed.extension 146 #set ext = $data_bed.extension
149 file = ${counter}_${counter_bed}.$ext 147 file = ${counter}_${counter_bed}.$ext
150 #if $ext == 'gtf': 148 #if $ext == 'gtf':
151 prefered_name = $track.track_file_style_conditional.bed_advanced.gtf.prefered_name 149 prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name
152 merge_transcripts = $track.track_file_style_conditional.bed_advanced.gtf.merge_transcripts 150 merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts
153 #end if 151 #end if
154 #if $track.track_file_style_conditional.title: 152 #if $track.track_file_style_conditional.title:
155 title = $track.track_file_style_conditional.title 153 title = $track.track_file_style_conditional.title
156 #elif $track.track_file_style_conditional.overlay_select == 'no': 154 #elif $track.track_file_style_conditional.overlay_select == 'no':
157 title = $data_bed.name 155 title = $data_bed.name
159 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": 157 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
160 color = bed_rgb 158 color = bed_rgb
161 #elif $track.track_file_style_conditional.color_bed.color: 159 #elif $track.track_file_style_conditional.color_bed.color:
162 color = $track.track_file_style_conditional.color_bed.color 160 color = $track.track_file_style_conditional.color_bed.color
163 #end if 161 #end if
164 #if $track.track_file_style_conditional.border_color: 162 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually':
165 border_color = $track.track_file_style_conditional.border_color 163 border_color = $track.track_file_style_conditional.border_color_bed.color
166 #end if
167 #if $track.track_file_style_conditional.flybase:
168 style = flybase
169 height_utr = $track.track_file_style_conditional.bed_advanced.flybase.height_utr
170 color_utr = $track.track_file_style_conditional.bed_advanced.flybase.color_utr
171 #else 164 #else
172 style = UCSC 165 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select
173 arrow_interval = $track.track_file_style_conditional.bed_advanced.ucsc.arrow_interval 166 #end if
167 style = $track.track_file_style_conditional.bed_style.bed_style_select
168 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'UCSC':
169 arrow_interval = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_interval
170 #else:
171 height_utr = $track.track_file_style_conditional.bed_style.bed_advanced.height_utr
172 #if $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'manually':
173 color_utr = $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color
174 #elif $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb':
175 color_utr = bed_rgb
176 #else:
177 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
178 color_utr = bed_rgb
179 #else:
180 color_utr = $track.track_file_style_conditional.color_bed.color
181 #end if
182 #end if
183 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length != '':
184 arrow_length = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length
185 #end if
186 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'flybase':
187 arrowhead_included = $track.track_file_style_conditional.bed_style.arrowhead_included
188 #end if
174 #end if 189 #end if
175 display = $track.track_file_style_conditional.display 190 display = $track.track_file_style_conditional.display
176 #if $track.track_file_style_conditional.height_bed: 191 #if $track.track_file_style_conditional.height_bed:
177 height = $track.track_file_style_conditional.height_bed 192 height = $track.track_file_style_conditional.height_bed
178 #end if 193 #end if
179 labels = $track.track_file_style_conditional.labels 194 labels = $track.track_file_style_conditional.labels.plot_labels
195 #if $track.track_file_style_conditional.labels.plot_labels == 'true':
196 all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside
197 labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin
198 #end if
180 file_type = bed 199 file_type = bed
181 #if $track.track_file_style_conditional.fontsize: 200 #if $track.track_file_style_conditional.fontsize:
182 fontsize = $track.track_file_style_conditional.fontsize 201 fontsize = $track.track_file_style_conditional.fontsize
183 #end if 202 #end if
184 #if $track.track_file_style_conditional.bed_advanced.gene_rows: 203 #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows:
185 gene_rows = $track.track_file_style_conditional.bed_advanced.gene_rows 204 gene_rows = $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows
186 #end if 205 #end if
187 global_max_row = $track.track_file_style_conditional.bed_advanced.global_max_row 206 global_max_row = $track.track_file_style_conditional.bed_style.bed_advanced.global_max_row
188 max_labels = $track.track_file_style_conditional.bed_advanced.max_labels 207 max_labels = $track.track_file_style_conditional.bed_style.bed_advanced.max_labels
189 line_width = $track.track_file_style_conditional.bed_advanced.line_width 208 line_width = $track.track_file_style_conditional.bed_style.bed_advanced.line_width
190 arrowhead_included = $track.track_file_style_conditional.arrowhead_included
191 #if $track.track_file_style_conditional.invert_orientation: 209 #if $track.track_file_style_conditional.invert_orientation:
192 orientation = inverted 210 orientation = inverted
193 #end if 211 #end if
194 overlay_previous = $track.track_file_style_conditional.overlay_select 212 overlay_previous = $track.track_file_style_conditional.overlay_select
195 ## If spacer is asked a new section is created: 213 ## If spacer is asked a new section is created:
221 color = $track.track_file_style_conditional.color_link.color 239 color = $track.track_file_style_conditional.color_link.color
222 alpha = $track.track_file_style_conditional.alpha 240 alpha = $track.track_file_style_conditional.alpha
223 line_width = $track.track_file_style_conditional.line_width 241 line_width = $track.track_file_style_conditional.line_width
224 line_style = $track.track_file_style_conditional.line_style 242 line_style = $track.track_file_style_conditional.line_style
225 links_type = $track.track_file_style_conditional.links_type 243 links_type = $track.track_file_style_conditional.links_type
244 compact_arcs_level = $track.track_file_style_conditional.compact_arcs_level
245 #if $track.track_file_style_conditional.ylim != "":
246 ylim = $track.track_file_style_conditional.ylim
247 #end if
226 #if $track.track_file_style_conditional.invert_orientation: 248 #if $track.track_file_style_conditional.invert_orientation:
227 orientation = inverted 249 orientation = inverted
228 #end if 250 #end if
229 overlay_previous = $track.track_file_style_conditional.overlay_select 251 overlay_previous = $track.track_file_style_conditional.overlay_select
230 file_type = links 252 file_type = links
261 #end if 283 #end if
262 #end if 284 #end if
263 #if $track.track_file_style_conditional.height_narrow_peak: 285 #if $track.track_file_style_conditional.height_narrow_peak:
264 height = $track.track_file_style_conditional.height_narrow_peak 286 height = $track.track_file_style_conditional.height_narrow_peak
265 #end if 287 #end if
288 line_width = $track.track_file_style_conditional.line_width
266 show_labels = $track.track_file_style_conditional.show_labels 289 show_labels = $track.track_file_style_conditional.show_labels
267 file_type = narrow_peak 290 file_type = narrow_peak
268 #if $track.track_file_style_conditional.fontsize: 291 #if $track.track_file_style_conditional.fontsize:
269 fontsize = $track.track_file_style_conditional.fontsize 292 fontsize = $track.track_file_style_conditional.fontsize
270 #end if 293 #end if
402 min_value = $track.track_file_style_conditional.min_value 425 min_value = $track.track_file_style_conditional.min_value
403 #end if 426 #end if
404 #if $track.track_file_style_conditional.max_value != "": 427 #if $track.track_file_style_conditional.max_value != "":
405 max_value = $track.track_file_style_conditional.max_value 428 max_value = $track.track_file_style_conditional.max_value
406 #end if 429 #end if
407 #if $track.track_file_style_conditional.type_lines: 430 type = $track.track_file_style_conditional.type.type_selector
408 type = $track.track_file_style_conditional.type_lines
409 #end if
410 file_type = bedgraph_matrix 431 file_type = bedgraph_matrix
411 show_data_range = $track.track_file_style_conditional.show_data 432 #if $track.track_file_style_conditional.type.type_selector == 'lines':
412 plot_horizontal_lines = $track.track_file_style_conditional.plot_horizontal_lines 433 show_data_range = $track.track_file_style_conditional.type.show_data
413 pos_score_in_bin = $track.track_file_style_conditional.pos_score_in_bin 434 plot_horizontal_lines = $track.track_file_style_conditional.type.plot_horizontal_lines
435 pos_score_in_bin = $track.track_file_style_conditional.type.pos_score_in_bin
436 #else
437 colormap = $track.track_file_style_conditional.type.colormap
438 #end if
414 #if $track.track_file_style_conditional.invert_orientation: 439 #if $track.track_file_style_conditional.invert_orientation:
415 orientation = inverted 440 orientation = inverted
416 #end if 441 #end if
417 ## If spacer is asked a new section is created: 442 ## If spacer is asked a new section is created:
418 #if $track.track_file_style_conditional.spacer_height != "": 443 #if $track.track_file_style_conditional.spacer_height != "":
463 #end if 488 #end if
464 489
465 ## Spacer 490 ## Spacer
466 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": 491 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
467 [spacer] 492 [spacer]
493 #if $track.track_file_style_conditional.title:
494 title = $track.track_file_style_conditional.title
495 #end if
468 #if $track.track_file_style_conditional.spacer_height != "": 496 #if $track.track_file_style_conditional.spacer_height != "":
469 height = $track.track_file_style_conditional.spacer_height 497 height = $track.track_file_style_conditional.spacer_height
470 #end if 498 #end if
471 #end if 499 #end if
500
501 ## Xaxis:
502 #if $track.track_file_style_conditional.track_file_style_selector == "xaxis_option":
503 [x-axis]
504 #if $track.track_file_style_conditional.title:
505 title = $track.track_file_style_conditional.title
506 #end if
507 #if $track.track_file_style_conditional.fontsize != "":
508 fontsize = $track.track_file_style_conditional.fontsize
509 #end if
510 where = $track.track_file_style_conditional.xaxis_where
511 ## If spacer is asked a new section is created:
512 #if $track.track_file_style_conditional.spacer_height != "":
513 [spacer]
514 height = $track.track_file_style_conditional.spacer_height
515 #end if
516 #end if
517
518 ## Scale bar:
519 #if $track.track_file_style_conditional.track_file_style_selector == "scale_bar_option":
520 [scale_bar]
521 #if $track.track_file_style_conditional.title:
522 title = $track.track_file_style_conditional.title
523 #end if
524 #if $track.track_file_style_conditional.color != "":
525 color = $track.track_file_style_conditional.color
526 #end if
527 alpha = $track.track_file_style_conditional.alpha
528 line_width = $track.track_file_style_conditional.line_width
529 #if $track.track_file_style_conditional.x_center != "":
530 x_center = $track.track_file_style_conditional.x_center
531 #end if
532 #if $track.track_file_style_conditional.size != "":
533 size = $track.track_file_style_conditional.size
534 #end if
535 where = $track.track_file_style_conditional.sb_where
536 #if $track.track_file_style_conditional.fontsize != "":
537 fontsize = $track.track_file_style_conditional.fontsize
538 #end if
539 file_type = scalebar
540 ## If spacer is asked a new section is created:
541 #if $track.track_file_style_conditional.spacer_height != "":
542 [spacer]
543 height = $track.track_file_style_conditional.spacer_height
544 #end if
545 #end if
472 #end for 546 #end for
473
474 #if $x_axis.x_axis_select == "true":
475 #if $x_axis.where == 'bottom':
476 [x-axis]
477 #if $x_axis.fontsize:
478 fontsize = $x_axis.fontsize
479 #end if
480 where = bottom
481 #end if
482 #end if
483 </configfile> 547 </configfile>
484 </configfiles> 548 </configfiles>
485 <inputs> 549 <inputs>
486 <expand macro="region" /> 550 <!--Arguments for pgt-->
487 551 <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false"
552 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" />
553 <section name="global_args" title="Configure figure parameters" expanded="False">
554 <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/>
555 <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/>
556 <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72"
557 help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/>
558 <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05"
559 min="0" max="1"/>
560 <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels">
561 <option value="left" selected="True">left</option>
562 <option value="right">right</option>
563 <option value="center">center</option>
564 </param>
565 </section>
566 <!--Info to build the config file-->
488 <repeat name="tracks" min="1" title="Include tracks in your plot" 567 <repeat name="tracks" min="1" title="Include tracks in your plot"
489 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph"> 568 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph.
569 The order you add them represent the order they will be plotted from top to bottom.">
490 <conditional name="track_file_style_conditional"> 570 <conditional name="track_file_style_conditional">
491 <param name="track_file_style_selector" type="select" label="Choose style of the track"> 571 <param name="track_file_style_selector" type="select" label="Choose style of the track">
492 <option value="hic_matrix_option">TAD visualization</option> 572 <option value="hic_matrix_option">TAD visualization</option>
493 <option value="chrom_states_option">Chromatine states</option> 573 <option value="chrom_states_option">Chromatine states</option>
494 <option value="bedgraph_matrix_track_option">TAD score</option> 574 <option value="bedgraph_matrix_track_option">TAD score</option>
499 <option value="bedgraph_track_option">Bedgraph track </option> 579 <option value="bedgraph_track_option">Bedgraph track </option>
500 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option> 580 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
501 <option value="vlines_track_option">Vlines track</option> 581 <option value="vlines_track_option">Vlines track</option>
502 <option value="hlines_track_option">Hlines track</option> 582 <option value="hlines_track_option">Hlines track</option>
503 <option value="spacer_option">Spacer</option> 583 <option value="spacer_option">Spacer</option>
584 <option value="xaxis_option">X-axis</option>
585 <option value="scale_bar_option">Scale bar track</option>
504 </param> 586 </param>
505 <when value="hic_matrix_option"> 587 <when value="hic_matrix_option">
506 <expand macro="plot_title" /> 588 <expand macro="plot_title" />
507 <expand macro="matrix_h5_cooler_multiple_macro" /> 589 <expand macro="matrix_h5_cooler_multiple_macro" />
508 590
509 <expand macro="colormap" /> 591 <param name="colormap" type="select" label="Color map to use for the heatmap" help="Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
592 <option value="RdYlBu_r">RdYlBu reversed</option>
593 <expand macro="colormap_macro"/>
594 </param>
510 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> 595 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
511 <expand macro="minmax_macro" /> 596 <expand macro="minmax_macro" />
512 <param name="transform" type="select" label="Plot the transformed value"> 597 <param name="transform" type="select" label="Plot the transformed value">
513 <option value="log1p" selected="True" >log1p</option> 598 <option value="log1p" selected="True" >log1p</option>
514 <option value="log">log</option> 599 <option value="log">log</option>
528 613
529 </when> 614 </when>
530 <when value="chrom_states_option"> 615 <when value="chrom_states_option">
531 <expand macro="plot_title" /> 616 <expand macro="plot_title" />
532 <expand macro="track_input_bed_macro" /> 617 <expand macro="track_input_bed_macro" />
533 <expand macro="color_bed_macro" /> 618 <conditional name="color_bed">
619 <param name="color_bed_select" type="select" label="Define color:">
620 <option value="manually" selected="True">manually</option>
621 <option value="bed_rgb">From the 9th field</option>
622 <option value="colormap">From the 5th field (score)</option>
623 </param>
624 <when value="manually">
625 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
626 </when>
627 <when value="bed_rgb" />
628 <when value="colormap">
629 <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">
630 <expand macro="colormap_macro" />
631 </param>
632 </when>
633 </conditional>
634 <expand macro="border_color_bed_macro" />
534 <param name="line_width" type="float" value="0.5" label="width of lines" /> 635 <param name="line_width" type="float" value="0.5" label="width of lines" />
535 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/> 636 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/>
536 <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true" 637 <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true"
537 label="Plot labels" /> 638 label="Plot labels" />
538 <expand macro="spacer_macro" /> 639 <expand macro="spacer_macro" />
540 </when> 641 </when>
541 <when value="gene_track_option"> 642 <when value="gene_track_option">
542 <expand macro="plot_title" /> 643 <expand macro="plot_title" />
543 644
544 <expand macro="track_input_bed_gtf_macro" /> 645 <expand macro="track_input_bed_gtf_macro" />
545 <expand macro="color_bed_macro" /> 646 <conditional name="color_bed">
647 <param name="color_bed_select" type="select" label="Define color:">
648 <option value="manually" selected="True">manually</option>
649 <option value="bed_rgb">From the 9th field</option>
650 <option value="colormap">From the 5th field (score)</option>
651 </param>
652 <when value="manually">
653 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
654 </when>
655 <when value="bed_rgb" />
656 <when value="colormap">
657 <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">
658 <expand macro="colormap_macro" />
659 </param>
660 </when>
661 </conditional>
662 <expand macro="border_color_bed_macro" />
546 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> 663 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/>
547 <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true" 664 <conditional name="labels">
548 label="Plot labels" /> 665 <param name="plot_labels" type="select" label="Plot labels">
549 <param name="flybase" type="boolean" checked="true" label="Use flybase style" help="This will be only used for bed with 12 columns"/> 666 <option value="true" selected="True">yes</option>
667 <option value="false">no</option>
668 </param>
669 <when value="true">
670 <param name="all_labels_inside" type="boolean" truevalue="true" falsevalue="false" checked="false"
671 label="Put all labels inside the plotted region"
672 help="Put labels on the left of the region if the region ends after the plotted region."/>
673 <param name="labels_in_margin" type="boolean" truevalue="true" falsevalue="false" checked="false"
674 label="Allow to put labels in the right margin"
675 help="Put labels in the margin if the region ends after the plotted region."/>
676 </when>
677 <when value="false"/>
678 </conditional>
550 <param name="display" type="select" label="display to use"> 679 <param name="display" type="select" label="display to use">
551 <option value="stacked" selected="True">stacked (no overlap even with the label)</option> 680 <option value="stacked" selected="True">stacked (no overlap even with the label)</option>
552 <option value="interleaved">interleaved (everything on 2 lines)</option> 681 <option value="interleaved">interleaved (everything on 2 lines)</option>
553 <option value="collapsed">collapsed (everything on 1 line)</option> 682 <option value="collapsed">collapsed (everything on 1 line)</option>
554 <option value="triangles">triangles (plot triangles between start and end)</option> 683 <option value="triangles">triangles (plot triangles between start and end)</option>
555 </param> 684 </param>
556 <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false"
557 label="Include the arrowhead in the bed interval:"
558 help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/>
559 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> 685 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
560 <expand macro="bed_advanced_macro" /> 686 <conditional name="bed_style">
687 <param name="bed_style_select" type="select" label="Bed style">
688 <option value="flybase" selected="True">flybase (blocks with arrow at extremities)</option>
689 <option value="UCSC">UCSC (blocks with arrows in introns)</option>
690 <option value="tssarrow">tssarrow (blocks with arrow above at beginning)</option>
691 </param>
692 <when value="flybase">
693 <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false"
694 label="Include the arrowhead in the bed interval:"
695 help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/>
696 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
697 <expand macro="utr_macro" />
698 <expand macro="bed_advanced_macro" />
699 </section>
700 </when>
701 <when value="UCSC">
702 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
703 <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/>
704 <expand macro="bed_advanced_macro" />
705 </section>
706 </when>
707 <when value="tssarrow">
708 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
709 <param name="arrow_length" type="integer" optional="true" label="arrow length" help="the length of the arrow in bp (default is 4% of the plotted region)"/>
710 <expand macro="utr_macro" />
711 <expand macro="bed_advanced_macro" />
712 </section>
713 </when>
714 </conditional>
561 <expand macro="overlay_macro" /> 715 <expand macro="overlay_macro" />
562 <expand macro="inverted_macro" /> 716 <expand macro="inverted_macro" />
563 <expand macro="spacer_macro" /> 717 <expand macro="spacer_macro" />
564 718
565 </when> 719 </when>
566 <when value="link_track_option"> 720 <when value="link_track_option">
567 <expand macro="plot_title" /> 721 <expand macro="plot_title" />
568 <expand macro="track_input_link_macro" /> 722 <expand macro="track_input_link_macro" />
569 <expand macro="links_color_macro" /> 723 <conditional name="color_link">
724 <param name="color_link_select" type="select" label="Define color:">
725 <option value="manually" selected="True">manually</option>
726 <option value="colormap">From the 7th field (score)</option>
727 </param>
728 <when value="manually">
729 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
730 </when>
731 <when value="colormap">
732 <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">
733 <expand macro="colormap_macro" />
734 </param>
735 </when>
736 </conditional>
570 <expand macro="lines_macro" /> 737 <expand macro="lines_macro" />
571 <param name="links_type" type="select" label="Representation of the link:"> 738 <param name="links_type" type="select" label="Representation of the link:">
572 <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option> 739 <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option>
573 <option value="triangles">triangles</option> 740 <option value="triangles">triangles</option>
574 <option value="loops">loops (a rectangle highlighting the intersection)</option> 741 <option value="loops">loops (a rectangle highlighting the intersection)</option>
575 </param> 742 </param>
743 <param name="compact_arcs_level" type="select" label="Height of arcs and triangles:">
744 <option value="0" selected="True">default (proportional to distance)</option>
745 <option value="1">compacted (the height is proportional to the square root of the distance)</option>
746 <option value="2">highly compacted (the height is the same for all distances)</option>
747 </param>
748 <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/>
576 <param name="height" type="float" value="1.5" optional="True" label="height"/> 749 <param name="height" type="float" value="1.5" optional="True" label="height"/>
577 <expand macro="minmax_macro" /> 750 <expand macro="minmax_macro" />
578 <expand macro="overlay_macro" /> 751 <expand macro="overlay_macro" />
579 <expand macro="inverted_macro" /> 752 <expand macro="inverted_macro" />
580 <expand macro="spacer_macro" /> 753 <expand macro="spacer_macro" />
601 <when value="box"> 774 <when value="box">
602 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true" 775 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true"
603 optional="True" label="Plot a vertical bar at the summit position." /> 776 optional="True" label="Plot a vertical bar at the summit position." />
604 </when> 777 </when>
605 </conditional> 778 </conditional>
779 <param name="line_width" type="float" value="1" label="width of lines" />
606 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="true" 780 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="true"
607 label="Plot labels (name, p-val, q-val)" /> 781 label="Plot labels (name, p-val, q-val)" />
608 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> 782 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
609 <expand macro="overlay_macro" /> 783 <expand macro="overlay_macro" />
610 <expand macro="inverted_macro" /> 784 <expand macro="inverted_macro" />
634 <expand macro="color_coverage_macro" /> 808 <expand macro="color_coverage_macro" />
635 809
636 <expand macro="minmax_macro" /> 810 <expand macro="minmax_macro" />
637 811
638 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> 812 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/>
639 <expand macro="reading_bw_macro" /> 813 <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False">
640 <expand macro="type_coverage_macro" /> 814 <param name="summary" type="select" label="Summary method">
815 <option value="mean" selected="True">mean=mean value</option>
816 <option value="min">min=minimum value</option>
817 <option value="max">max=maximum value</option>
818 <option value="coverage">coverage=number of covered bases</option>
819 <option value="std">std=standard deviation</option>
820 </param>
821 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
822 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
823 label="NAN's to zeros" />
824 </section>
641 <expand macro="type_coverage_macro" /> 825 <expand macro="type_coverage_macro" />
642 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> 826 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/>
643 <expand macro="inverted_macro" /> 827 <expand macro="inverted_macro" />
644 <expand macro="overlay_macro" /> 828 <expand macro="overlay_macro" />
645 <expand macro="spacer_macro" /> 829 <expand macro="spacer_macro" />
652 <expand macro="track_input_bedgraph_matrix_macro" /> 836 <expand macro="track_input_bedgraph_matrix_macro" />
653 <expand macro="minmax_macro" /> 837 <expand macro="minmax_macro" />
654 838
655 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> 839 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
656 840
657 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" 841 <conditional name="type">
658 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead 842 <param name="type_selector" type="select" label="type of plotting">
659 of the matrix."/> 843 <option value="lines" selected="True">lines: each column in the bedgraph will be a line and a mean line will be added</option>
660 <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end" help="Only used when type is lines"> 844 <option value="matrix">matrix: each column in the bedgraph will be a raw in the matrix</option>
661 <option value="center" selected="True">Center</option> 845 </param>
662 <option value="block">Block (draw a horizontal line between start and end)</option> 846 <when value="lines">
663 </param> 847 <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false"
664 <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Plot an horizontal line at 0 when type is lines" /> 848 label="Plot an horizontal line at 0 when type is lines" />
665 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" /> 849 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false"
850 label="Show visualization of data range" />
851 <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end">
852 <option value="center" selected="True">Center</option>
853 <option value="block">Block (draw a horizontal line between start and end)</option>
854 </param>
855 </when>
856 <when value="matrix">
857 <param name="colormap" type="select" label="colormap">
858 <option value="viridis">Viridis</option>
859 <expand macro="colormap_macro" />
860 </param>
861 </when>
862 </conditional>
863
864
666 <expand macro="inverted_macro" /> 865 <expand macro="inverted_macro" />
667 <expand macro="spacer_macro" /> 866 <expand macro="spacer_macro" />
668 867
669 </when> 868 </when>
670 <when value="vlines_track_option"> 869 <when value="vlines_track_option">
681 <expand macro="inverted_macro" /> 880 <expand macro="inverted_macro" />
682 <expand macro="overlay_macro" /> 881 <expand macro="overlay_macro" />
683 <expand macro="spacer_macro" /> 882 <expand macro="spacer_macro" />
684 </when> 883 </when>
685 <when value="spacer_option"> 884 <when value="spacer_option">
885 <expand macro="plot_title" />
686 <param name="spacer_height" type="float" value="" optional="True" 886 <param name="spacer_height" type="float" value="" optional="True"
687 label="Height of the spacer."/> 887 label="Height of the spacer."/>
688 </when> 888 </when>
889 <when value="xaxis_option">
890 <expand macro="plot_title" />
891 <param name="fontsize" type="float" optional="True"
892 label="Fontsize of the x-axis."/>
893 <param name="xaxis_where" type="select" label="chromosome name and coordinates position relative to the axis">
894 <option value="bottom" selected="True">below</option>
895 <option value="top">above</option>
896 </param>
897 <expand macro="spacer_macro" />
898 </when>
899 <when value="scale_bar_option">
900 <expand macro="plot_title" />
901 <param name="color" type="color" label="Color of the scale bar" optional="True" />
902 <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
903 <param name="line_width" type="float" value="0.5" label="width of lines"/>
904 <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True"
905 help="If not set it will be in the middle of the plotted area."/>
906 <param name="size" type="integer" label="size of the scale bar" optional="True"
907 help="If not set it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/>
908 <param name="sb_where" type="select" label="where the size of the scale bar should appear relative to the bar">
909 <option value="left" selected="True">left</option>
910 <option value="right">right</option>
911 <option value="bottom">below</option>
912 <option value="top">above</option>
913 </param>
914 <param name="fontsize" type="float" optional="True"
915 label="Fontsize of the size of the scale bar."/>
916 <expand macro="spacer_macro" />
917 </when>
689 </conditional> 918 </conditional>
690
691 </repeat> 919 </repeat>
692
693
694 <conditional name="x_axis">
695 <param name="x_axis_select" type="select" label="Configure x-axis">
696 <option value="false" selected="True">No</option>
697 <option value="true">Yes</option>
698 </param>
699 <when value="true">
700 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
701 <param name="where" type="select" label="Where to place the x-axis">
702 <option value="top" selected="True">Top</option>
703 <option value="bottom">Bottom</option>
704 </param>
705 </when>
706 <when value="false" />
707 </conditional>
708 <param name="image_file_format" type="select" label="Image output format"> 920 <param name="image_file_format" type="select" label="Image output format">
709 <option value="png">png</option> 921 <option value="png">png</option>
710 <option value="svg">svg</option> 922 <option value="svg">svg</option>
711 </param> 923 </param>
712 </inputs> 924 </inputs>
717 <when input="image_file_format" value="svg" format="svg" /> 929 <when input="image_file_format" value="svg" format="svg" />
718 </change_format> 930 </change_format>
719 </data> 931 </data>
720 </outputs> 932 </outputs>
721 <tests> 933 <tests>
934 <!--test 1-->
722 <test> 935 <test>
723 <param name="region" value="chrX:3000000-3500000"/> 936 <param name="region" value="chrX:3000000-3500000"/>
724 <conditional name="x_axis"> 937 <repeat name="tracks">
725 <param name="x_axis_select" value="true" /> 938 <conditional name="track_file_style_conditional">
726 </conditional> 939 <param name="track_file_style_selector" value="xaxis_option" />
940 <param name="xaxis_where" value="top" />
941 </conditional>
942 </repeat>
727 <repeat name="tracks"> 943 <repeat name="tracks">
728 <conditional name="track_file_style_conditional"> 944 <conditional name="track_file_style_conditional">
729 <param name="track_file_style_selector" value="hic_matrix_option" /> 945 <param name="track_file_style_selector" value="hic_matrix_option" />
730 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> 946 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
731 <param name="title" value="Kc DpnII (Li et al. 2015)" /> 947 <param name="title" value="Kc DpnII (Li et al. 2015)" />
732 <param name="colormap" value="RdYlBu_r" /> 948 <!--<param name="colormap" value="RdYlBu_r" />-->
733 <param name="depth" value="200000" /> 949 <param name="depth" value="200000" />
734 <param name="transform" value="log1p" /> 950 <param name="transform" value="log1p" />
735 <param name="boundaries_file" value="domains.bed" /> 951 <param name="boundaries_file" value="domains.bed" />
736 </conditional> 952 </conditional>
737 </repeat> 953 </repeat>
756 <repeat name="tracks"> 972 <repeat name="tracks">
757 <conditional name="track_file_style_conditional"> 973 <conditional name="track_file_style_conditional">
758 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> 974 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
759 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> 975 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
760 <param name="title" value="TAD separation score (Ramirez et al.)" /> 976 <param name="title" value="TAD separation score (Ramirez et al.)" />
977 <conditional name="type">
978 <param name="type_selector" value="matrix" />
979 <!--<param name="colormap" value="viridis" />-->
980 </conditional>
761 <param name="height_bedgraph" value="10" /> 981 <param name="height_bedgraph" value="10" />
762 </conditional> 982 </conditional>
763 </repeat> 983 </repeat>
764 <repeat name="tracks"> 984 <repeat name="tracks">
765 <conditional name="track_file_style_conditional"> 985 <conditional name="track_file_style_conditional">
855 <param name="track_file_style_selector" value="gene_track_option" /> 1075 <param name="track_file_style_selector" value="gene_track_option" />
856 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 1076 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
857 <param name="title" value="max num rows 3" /> 1077 <param name="title" value="max num rows 3" />
858 <param name="height_bed" value="3" /> 1078 <param name="height_bed" value="3" />
859 <param name="fontsize" value="8" /> 1079 <param name="fontsize" value="8" />
860 <section name="bed_advanced"> 1080 <conditional name="bed_style">
861 <param name="gene_rows" value="3" /> 1081 <section name="bed_advanced">
862 </section> 1082 <param name="gene_rows" value="3" />
1083 </section>
1084 </conditional>
863 </conditional> 1085 </conditional>
864 </repeat> 1086 </repeat>
865 <repeat name="tracks"> 1087 <repeat name="tracks">
866 <conditional name="track_file_style_conditional"> 1088 <conditional name="track_file_style_conditional">
867 <param name="track_file_style_selector" value="spacer_option" /> 1089 <param name="track_file_style_selector" value="spacer_option" />
873 <param name="track_file_style_selector" value="gene_track_option" /> 1095 <param name="track_file_style_selector" value="gene_track_option" />
874 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> 1096 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
875 <param name="title" value="bed6 global max row" /> 1097 <param name="title" value="bed6 global max row" />
876 <param name="height_bed" value="20" /> 1098 <param name="height_bed" value="20" />
877 <param name="fontsize" value="10" /> 1099 <param name="fontsize" value="10" />
878 <section name="bed_advanced"> 1100 <conditional name="bed_style">
879 <param name="global_max_row" value="true" /> 1101 <section name="bed_advanced">
880 </section> 1102 <param name="global_max_row" value="true" />
1103 </section>
1104 </conditional>
881 </conditional> 1105 </conditional>
882 </repeat> 1106 </repeat>
883 <repeat name="tracks"> 1107 <repeat name="tracks">
884 <conditional name="track_file_style_conditional"> 1108 <conditional name="track_file_style_conditional">
885 <param name="track_file_style_selector" value="vlines_track_option" /> 1109 <param name="track_file_style_selector" value="vlines_track_option" />
887 </conditional> 1111 </conditional>
888 </repeat> 1112 </repeat>
889 <param name="image_file_format" value="png" /> 1113 <param name="image_file_format" value="png" />
890 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> 1114 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
891 </test> 1115 </test>
1116 <!--test 2-->
892 <test> 1117 <test>
893 <param name="region" value="chrX:3000000-3500000"/> 1118 <param name="region" value="chrX:3000000-3500000"/>
894 <conditional name="x_axis"> 1119 <repeat name="tracks">
895 <param name="x_axis_select" value="true" /> 1120 <conditional name="track_file_style_conditional">
896 </conditional> 1121 <param name="track_file_style_selector" value="xaxis_option" />
1122 <param name="xaxis_where" value="top" />
1123 </conditional>
1124 </repeat>
897 <repeat name="tracks"> 1125 <repeat name="tracks">
898 <conditional name="track_file_style_conditional"> 1126 <conditional name="track_file_style_conditional">
899 <param name="track_file_style_selector" value="bigwig_track_option" /> 1127 <param name="track_file_style_selector" value="bigwig_track_option" />
900 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 1128 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
901 <param name="title" value="rep 1 test line" /> 1129 <param name="title" value="rep 1 test line" />
947 </conditional> 1175 </conditional>
948 </repeat> 1176 </repeat>
949 <param name="image_file_format" value="png" /> 1177 <param name="image_file_format" value="png" />
950 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" /> 1178 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" />
951 </test> 1179 </test>
1180 <!--test 3-->
952 <test> 1181 <test>
953 <param name="region" value="chrX:3000000-3500000"/> 1182 <param name="region" value="chrX:3000000-3500000"/>
954 <conditional name="x_axis"> 1183 <repeat name="tracks">
955 <param name="x_axis_select" value="true" /> 1184 <conditional name="track_file_style_conditional">
956 </conditional> 1185 <param name="track_file_style_selector" value="xaxis_option" />
1186 <param name="xaxis_where" value="top" />
1187 </conditional>
1188 </repeat>
957 <repeat name="tracks"> 1189 <repeat name="tracks">
958 <conditional name="track_file_style_conditional"> 1190 <conditional name="track_file_style_conditional">
959 <param name="track_file_style_selector" value="hic_matrix_option" /> 1191 <param name="track_file_style_selector" value="hic_matrix_option" />
960 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> 1192 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
961 <param name="title" value="Kc DpnII (Li et al. 2015) log1p" /> 1193 <param name="title" value="Kc DpnII (Li et al. 2015) log1p" />
1090 <param name="track_file_style_selector" value="gene_track_option" /> 1322 <param name="track_file_style_selector" value="gene_track_option" />
1091 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 1323 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
1092 <param name="title" value="genes in ucsc" /> 1324 <param name="title" value="genes in ucsc" />
1093 <param name="height_bed" value="5" /> 1325 <param name="height_bed" value="5" />
1094 <param name="fontsize" value="10" /> 1326 <param name="fontsize" value="10" />
1095 <param name="flybase" value="false"/> 1327 <conditional name="bed_style">
1328 <param name="bed_style_select" value="UCSC"/>
1329 </conditional>
1096 </conditional> 1330 </conditional>
1097 </repeat> 1331 </repeat>
1098 <repeat name="tracks"> 1332 <repeat name="tracks">
1099 <conditional name="track_file_style_conditional"> 1333 <conditional name="track_file_style_conditional">
1100 <param name="track_file_style_selector" value="gene_track_option" /> 1334 <param name="track_file_style_selector" value="gene_track_option" />
1101 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> 1335 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
1102 <param name="title" value="bed6 global max row color from score" /> 1336 <param name="title" value="bed6 global max row color from score" />
1103 <param name="height_bed" value="20" /> 1337 <param name="height_bed" value="20" />
1104 <param name="fontsize" value="10" /> 1338 <param name="fontsize" value="10" />
1105 <section name="bed_advanced"> 1339 <conditional name="bed_style">
1106 <param name="global_max_row" value="true" /> 1340 <section name="bed_advanced">
1107 </section> 1341 <param name="global_max_row" value="true" />
1342 </section>
1343 </conditional>
1108 <conditional name="color_bed"> 1344 <conditional name="color_bed">
1109 <param name="color_bed_select" value="colormap" /> 1345 <param name="color_bed_select" value="colormap" />
1110 <param name="color" value="RdYlBu_r" /> 1346 <param name="color" value="RdYlBu_r" />
1111 </conditional> 1347 </conditional>
1112 </conditional> 1348 </conditional>
1113 </repeat> 1349 </repeat>
1114 <repeat name="tracks"> 1350 <repeat name="tracks">
1115 <conditional name="track_file_style_conditional"> 1351 <conditional name="track_file_style_conditional">
1116 <param name="track_file_style_selector" value="gene_track_option" /> 1352 <param name="track_file_style_selector" value="gene_track_option" />
1117 <param name="track_input_bed" value="domains.bed" ftype="bed" /> 1353 <param name="track_input_bed" value="domains.bed" ftype="bed" />
1118 <param name="title" value="domains.bed using the 9th field for colors interleaved" /> 1354 <param name="title" value="domains.bed using the 9th field for colors interleaved border=red" />
1119 <param name="height_bed" value="2" /> 1355 <param name="height_bed" value="2" />
1120 <param name="fontsize" value="10" /> 1356 <param name="fontsize" value="10" />
1121 <conditional name="color_bed"> 1357 <conditional name="color_bed">
1122 <param name="color_bed_select" value="bed_rgb" /> 1358 <param name="color_bed_select" value="bed_rgb" />
1123 </conditional> 1359 </conditional>
1124 <param name="border_color" value="red" /> 1360 <conditional name="border_color_bed">
1125 <param name="labels" value="false" /> 1361 <param name="border_color_bed_select" value="manually" />
1362 <param name="color" value="red" />
1363 </conditional>
1364 <conditional name="labels">
1365 <param name="plot_labels" value="false" />
1366 </conditional>
1367 <param name="display" value="interleaved" />
1368 </conditional>
1369 </repeat>
1370 <repeat name="tracks">
1371 <conditional name="track_file_style_conditional">
1372 <param name="track_file_style_selector" value="gene_track_option" />
1373 <param name="track_input_bed" value="domains.bed" ftype="bed" />
1374 <param name="title" value="domains.bed using the 9th field for colors interleaved border=bed_rgb" />
1375 <param name="height_bed" value="2" />
1376 <param name="fontsize" value="10" />
1377 <conditional name="color_bed">
1378 <param name="color_bed_select" value="bed_rgb" />
1379 </conditional>
1380 <conditional name="border_color_bed">
1381 <param name="border_color_bed_select" value="bed_rgb" />
1382 </conditional>
1383 <conditional name="labels">
1384 <param name="plot_labels" value="false" />
1385 </conditional>
1386 <param name="display" value="interleaved" />
1387 </conditional>
1388 </repeat>
1389 <repeat name="tracks">
1390 <conditional name="track_file_style_conditional">
1391 <param name="track_file_style_selector" value="gene_track_option" />
1392 <param name="track_input_bed" value="domains.bed" ftype="bed" />
1393 <param name="title" value="domains.bed using the 9th field for colors interleaved border=none" />
1394 <param name="height_bed" value="2" />
1395 <param name="fontsize" value="10" />
1396 <conditional name="color_bed">
1397 <param name="color_bed_select" value="bed_rgb" />
1398 </conditional>
1399 <conditional name="border_color_bed">
1400 <param name="border_color_bed_select" value="none" />
1401 </conditional>
1402 <conditional name="labels">
1403 <param name="plot_labels" value="false" />
1404 </conditional>
1126 <param name="display" value="interleaved" /> 1405 <param name="display" value="interleaved" />
1127 </conditional> 1406 </conditional>
1128 </repeat> 1407 </repeat>
1129 <param name="image_file_format" value="png" /> 1408 <param name="image_file_format" value="png" />
1130 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" /> 1409 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" />
1131 </test> 1410 </test>
1411 <!--test 4-->
1132 <test> 1412 <test>
1133 <param name="region" value="X:2700000-3100000"/> 1413 <param name="region" value="X:2700000-3100000"/>
1134 <conditional name="x_axis">
1135 <param name="x_axis_select" value="true" />
1136 <param name="where" value="bottom" />
1137 </conditional>
1138 <repeat name="tracks"> 1414 <repeat name="tracks">
1139 <conditional name="track_file_style_conditional"> 1415 <conditional name="track_file_style_conditional">
1140 <param name="track_file_style_selector" value="bigwig_track_option" /> 1416 <param name="track_file_style_selector" value="bigwig_track_option" />
1141 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 1417 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
1142 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" /> 1418 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" />
1159 <param name="number_of_bins" value="300"/> 1435 <param name="number_of_bins" value="300"/>
1160 </section> 1436 </section>
1161 <param name="overlay_select" value="share-y"/> 1437 <param name="overlay_select" value="share-y"/>
1162 </conditional> 1438 </conditional>
1163 </repeat> 1439 </repeat>
1440 <repeat name="tracks">
1441 <conditional name="track_file_style_conditional">
1442 <param name="track_file_style_selector" value="xaxis_option" />
1443 <param name="xaxis_where" value="bottom" />
1444 </conditional>
1445 </repeat>
1164 <param name="image_file_format" value="png" /> 1446 <param name="image_file_format" value="png" />
1165 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" /> 1447 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" />
1166 </test> 1448 </test>
1449 <!--test 5-->
1167 <test> 1450 <test>
1168 <param name="region" value="X:3000000-3300000"/> 1451 <param name="region" value="X:3000000-3300000"/>
1169 <conditional name="x_axis"> 1452 <repeat name="tracks">
1170 <param name="x_axis_select" value="true" /> 1453 <conditional name="track_file_style_conditional">
1171 </conditional> 1454 <param name="track_file_style_selector" value="xaxis_option" />
1455 <param name="xaxis_where" value="top" />
1456 </conditional>
1457 </repeat>
1172 <repeat name="tracks"> 1458 <repeat name="tracks">
1173 <conditional name="track_file_style_conditional"> 1459 <conditional name="track_file_style_conditional">
1174 <param name="track_file_style_selector" value="gene_track_option" /> 1460 <param name="track_file_style_selector" value="gene_track_option" />
1175 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> 1461 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
1176 <param name="title" value="test" /> 1462 <param name="title" value="test" />
1177 <param name="height_bed" value="10" /> 1463 <param name="height_bed" value="10" />
1178 <param name="color" value="#000000" /> 1464 <param name="color" value="#000000" />
1179 <param name="flybase" value="false" /> 1465 <conditional name="bed_style">
1466 <param name="bed_style_select" value="UCSC"/>
1467 </conditional>
1180 <param name="spacer_height" value="1"/> 1468 <param name="spacer_height" value="1"/>
1181 </conditional> 1469 </conditional>
1182 </repeat> 1470 </repeat>
1183 <repeat name="tracks"> 1471 <repeat name="tracks">
1184 <conditional name="track_file_style_conditional"> 1472 <conditional name="track_file_style_conditional">
1185 <param name="track_file_style_selector" value="gene_track_option" /> 1473 <param name="track_file_style_selector" value="gene_track_option" />
1186 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> 1474 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
1187 <param name="title" value="test" /> 1475 <param name="title" value="test" />
1188 <param name="height_bed" value="10" /> 1476 <param name="height_bed" value="10" />
1189 <param name="color" value="#000000" /> 1477 <param name="color" value="#000000" />
1190 <param name="flybase" value="false" /> 1478 <conditional name="bed_style">
1479 <param name="bed_style_select" value="UCSC"/>
1480 </conditional>
1191 <param name="spacer_height" value="1"/> 1481 <param name="spacer_height" value="1"/>
1192 </conditional> 1482 </conditional>
1193 </repeat> 1483 </repeat>
1194 <param name="image_file_format" value="png" /> 1484 <param name="image_file_format" value="png" />
1195 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" /> 1485 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" />
1196 </test> 1486 </test>
1487 <!--test 6-->
1197 <test> 1488 <test>
1198 <param name="region" value="X:2760000-2802000"/> 1489 <param name="region" value="X:2760000-2802000"/>
1199 <conditional name="x_axis">
1200 <param name="x_axis_select" value="true" />
1201 <param name="where" value="bottom" />
1202 </conditional>
1203 <repeat name="tracks"> 1490 <repeat name="tracks">
1204 <conditional name="track_file_style_conditional"> 1491 <conditional name="track_file_style_conditional">
1205 <param name="track_file_style_selector" value="narrow_peak_track_option" /> 1492 <param name="track_file_style_selector" value="narrow_peak_track_option" />
1206 <param name="title" value="box" /> 1493 <param name="title" value="box" />
1207 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> 1494 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
1208 <param name="color" value="#9bbb59" /> 1495 <param name="color" value="#9bbb59" />
1209 <param name="height_narrow_peak" value="4" /> 1496 <param name="height_narrow_peak" value="4" />
1497 <conditional name="display">
1498 <param name="display_selector" value="box" />
1499 <param name="use_summit" value="true" />
1500 </conditional>
1501 <param name="show_labels" value="true" />
1502 </conditional>
1503 </repeat>
1504 <repeat name="tracks">
1505 <conditional name="track_file_style_conditional">
1506 <param name="track_file_style_selector" value="narrow_peak_track_option" />
1507 <param name="title" value="box line_width = 2" />
1508 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
1509 <param name="color" value="#9bbb59" />
1510 <param name="height_narrow_peak" value="4" />
1511 <param name="line_width" value="2" />
1210 <conditional name="display"> 1512 <conditional name="display">
1211 <param name="display_selector" value="box" /> 1513 <param name="display_selector" value="box" />
1212 <param name="use_summit" value="true" /> 1514 <param name="use_summit" value="true" />
1213 </conditional> 1515 </conditional>
1214 <param name="show_labels" value="true" /> 1516 <param name="show_labels" value="true" />
1245 <param name="show_data" value="false" /> 1547 <param name="show_data" value="false" />
1246 </conditional> 1548 </conditional>
1247 <param name="show_labels" value="true" /> 1549 <param name="show_labels" value="true" />
1248 </conditional> 1550 </conditional>
1249 </repeat> 1551 </repeat>
1552 <repeat name="tracks">
1553 <conditional name="track_file_style_conditional">
1554 <param name="track_file_style_selector" value="xaxis_option" />
1555 <param name="xaxis_where" value="bottom" />
1556 </conditional>
1557 </repeat>
1250 <param name="image_file_format" value="png" /> 1558 <param name="image_file_format" value="png" />
1251 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" /> 1559 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" />
1252 </test> 1560 </test>
1561 <!--test 7-->
1253 <test> 1562 <test>
1254 <param name="region" value="chrX:3300000-3500000"/> 1563 <param name="region" value="chrX:3300000-3500000"/>
1255 <conditional name="x_axis"> 1564 <repeat name="tracks">
1256 <param name="x_axis_select" value="true" /> 1565 <conditional name="track_file_style_conditional">
1257 </conditional> 1566 <param name="track_file_style_selector" value="xaxis_option" />
1567 <param name="xaxis_where" value="top" />
1568 </conditional>
1569 </repeat>
1258 <repeat name="tracks"> 1570 <repeat name="tracks">
1259 <conditional name="track_file_style_conditional"> 1571 <conditional name="track_file_style_conditional">
1260 <param name="track_file_style_selector" value="gene_track_option" /> 1572 <param name="track_file_style_selector" value="gene_track_option" />
1261 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 1573 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
1262 <param name="title" value="genes" /> 1574 <param name="title" value="genes" />
1267 <conditional name="track_file_style_conditional"> 1579 <conditional name="track_file_style_conditional">
1268 <param name="track_file_style_selector" value="gene_track_option" /> 1580 <param name="track_file_style_selector" value="gene_track_option" />
1269 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> 1581 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
1270 <param name="title" value="gtf" /> 1582 <param name="title" value="gtf" />
1271 <param name="height_bed" value="10" /> 1583 <param name="height_bed" value="10" />
1272 <section name="bed_advanced"> 1584 <conditional name="bed_style">
1273 <section name ="flybase"> 1585 <section name="bed_advanced">
1274 <param name="height_utr" value="0.75"/> 1586 <param name="height_utr" value="0.75"/>
1275 <param name="color_utr" value="#ff0000"/> 1587 <conditional name="color_utr">
1588 <param name="color_utr_select" value="manually"/>
1589 <param name="color" value="#ff0000"/>
1590 </conditional>
1591 <section name ="gtf">
1592 <param name="prefered_name" value="gene_name"/>
1593 <param name="merge_transcripts" value="true"/>
1594 </section>
1276 </section> 1595 </section>
1277 <section name ="gtf"> 1596 </conditional>
1278 <param name="prefered_name" value="gene_name"/> 1597 </conditional>
1279 <param name="merge_transcripts" value="true"/> 1598 </repeat>
1599 <repeat name="tracks">
1600 <conditional name="track_file_style_conditional">
1601 <param name="track_file_style_selector" value="gene_track_option" />
1602 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
1603 <param name="title" value="genes with scores" />
1604 <param name="height_bed" value="10" />
1605 <conditional name="color_bed">
1606 <param name="color_bed_select" value="colormap" />
1607 <param name="color" value="cool_r" />
1608 </conditional>
1609 </conditional>
1610 </repeat>
1611 <repeat name="tracks">
1612 <conditional name="track_file_style_conditional">
1613 <param name="track_file_style_selector" value="gene_track_option" />
1614 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
1615 <param name="title" value="genes with utr as bed_rgb" />
1616 <param name="height_bed" value="10" />
1617 <conditional name="bed_style">
1618 <section name="bed_advanced">
1619 <conditional name="color_utr">
1620 <param name="color_utr_select" value="bed_rgb"/>
1621 </conditional>
1280 </section> 1622 </section>
1281 </section> 1623 </conditional>
1624 </conditional>
1625 </repeat>
1626 <repeat name="tracks">
1627 <conditional name="track_file_style_conditional">
1628 <param name="track_file_style_selector" value="gene_track_option" />
1629 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
1630 <param name="title" value="genes with coding as bed_rgb - labels_in_margin" />
1631 <param name="height_bed" value="10" />
1632 <conditional name="color_bed">
1633 <param name="color_bed_select" value="bed_rgb" />
1634 </conditional>
1635 <conditional name="labels">
1636 <param name="plot_labels" value="true" />
1637 <param name="labels_in_margin" value="true" />
1638 </conditional>
1639 </conditional>
1640 </repeat>
1641 <repeat name="tracks">
1642 <conditional name="track_file_style_conditional">
1643 <param name="track_file_style_selector" value="gene_track_option" />
1644 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
1645 <param name="title" value="genes bed_rgb like - all_labels_inside" />
1646 <param name="height_bed" value="10" />
1647 <conditional name="color_bed">
1648 <param name="color_bed_select" value="bed_rgb" />
1649 </conditional>
1650 <conditional name="bed_style">
1651 <section name="bed_advanced">
1652 <conditional name="color_utr">
1653 <param name="color_utr_select" value="like"/>
1654 </conditional>
1655 </section>
1656 </conditional>
1657 <conditional name="labels">
1658 <param name="plot_labels" value="true" />
1659 <param name="all_labels_inside" value="true" />
1660 </conditional>
1282 </conditional> 1661 </conditional>
1283 </repeat> 1662 </repeat>
1284 <param name="image_file_format" value="png" /> 1663 <param name="image_file_format" value="png" />
1285 <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="35000" /> 1664 <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="35000" />
1286 </test> 1665 </test>
1666 <!--test 8-->
1287 <test> 1667 <test>
1288 <param name="region" value="chrX:3300000-3500000"/> 1668 <param name="region" value="chrX:3300000-3500000"/>
1289 <conditional name="x_axis"> 1669 <repeat name="tracks">
1290 <param name="x_axis_select" value="true" /> 1670 <conditional name="track_file_style_conditional">
1291 </conditional> 1671 <param name="track_file_style_selector" value="xaxis_option" />
1672 <param name="xaxis_where" value="top" />
1673 </conditional>
1674 </repeat>
1292 <repeat name="tracks"> 1675 <repeat name="tracks">
1293 <conditional name="track_file_style_conditional"> 1676 <conditional name="track_file_style_conditional">
1294 <param name="track_file_style_selector" value="gene_track_option" /> 1677 <param name="track_file_style_selector" value="gene_track_option" />
1295 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 1678 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
1296 <param name="title" value="dm3_genes.bed" /> 1679 <param name="title" value="dm3_genes.bed" />
1297 <param name="height_bed" value="10" /> 1680 <param name="height_bed" value="10" />
1298 <param name="flybase" value="false" /> 1681 <conditional name="bed_style">
1299 <section name="bed_advanced"> 1682 <param name="bed_style_select" value="UCSC"/>
1300 <param name="global_max_row" value="true" /> 1683 <section name="bed_advanced">
1301 <param name="max_labels" value="15" /> 1684 <param name="global_max_row" value="true" />
1302 </section> 1685 <param name="max_labels" value="15" />
1686 </section>
1687 </conditional>
1303 </conditional> 1688 </conditional>
1304 </repeat> 1689 </repeat>
1305 <repeat name="tracks"> 1690 <repeat name="tracks">
1306 <conditional name="track_file_style_conditional"> 1691 <conditional name="track_file_style_conditional">
1307 <param name="track_file_style_selector" value="gene_track_option" /> 1692 <param name="track_file_style_selector" value="gene_track_option" />
1308 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 1693 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
1309 <param name="title" value="genes.bed.gz" /> 1694 <param name="title" value="genes.bed.gz" />
1310 <param name="height_bed" value="10" /> 1695 <param name="height_bed" value="10" />
1311 <param name="flybase" value="false" /> 1696 <conditional name="bed_style">
1312 <section name="bed_advanced"> 1697 <param name="bed_style_select" value="UCSC"/>
1313 <param name="line_width" value="2"/> 1698 <section name="bed_advanced">
1314 <section name ="ucsc">
1315 <param name="arrow_interval" value="10"/> 1699 <param name="arrow_interval" value="10"/>
1700 <param name="line_width" value="2"/>
1316 </section> 1701 </section>
1317 </section> 1702 </conditional>
1318 </conditional> 1703 </conditional>
1319 </repeat> 1704 </repeat>
1320 <param name="image_file_format" value="png" /> 1705 <param name="image_file_format" value="png" />
1321 <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="35000" /> 1706 <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="35000" />
1322 </test> 1707 </test>
1708 <!--test 9-->
1323 <test> 1709 <test>
1324 <param name="region" value="X:3133000-3138000"/> 1710 <param name="region" value="X:3133000-3138000"/>
1325 <conditional name="x_axis"> 1711 <repeat name="tracks">
1326 <param name="x_axis_select" value="true" /> 1712 <conditional name="track_file_style_conditional">
1327 </conditional> 1713 <param name="track_file_style_selector" value="xaxis_option" />
1714 <param name="xaxis_where" value="top" />
1715 </conditional>
1716 </repeat>
1328 <repeat name="tracks"> 1717 <repeat name="tracks">
1329 <conditional name="track_file_style_conditional"> 1718 <conditional name="track_file_style_conditional">
1330 <param name="track_file_style_selector" value="gene_track_option" /> 1719 <param name="track_file_style_selector" value="gene_track_option" />
1331 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> 1720 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
1332 <param name="title" value="test" /> 1721 <param name="title" value="test" />
1333 <param name="height_bed" value="10" /> 1722 <param name="height_bed" value="10" />
1334 <param name="flybase" value="true" />
1335 <param name="spacer_height" value="1"/> 1723 <param name="spacer_height" value="1"/>
1336 </conditional> 1724 </conditional>
1337 </repeat> 1725 </repeat>
1338 <repeat name="tracks"> 1726 <repeat name="tracks">
1339 <conditional name="track_file_style_conditional"> 1727 <conditional name="track_file_style_conditional">
1343 <param name="height_bed" value="10" /> 1731 <param name="height_bed" value="10" />
1344 <conditional name="color_bed"> 1732 <conditional name="color_bed">
1345 <param name="color_bed_select" value="manually" /> 1733 <param name="color_bed_select" value="manually" />
1346 <param name="color" value="red" /> 1734 <param name="color" value="red" />
1347 </conditional> 1735 </conditional>
1348 <param name="flybase" value="false" /> 1736 <conditional name="bed_style">
1737 <param name="bed_style_select" value="UCSC"/>
1738 </conditional>
1349 <param name="spacer_height" value="1"/> 1739 <param name="spacer_height" value="1"/>
1350 </conditional> 1740 </conditional>
1351 </repeat> 1741 </repeat>
1352 <repeat name="tracks"> 1742 <repeat name="tracks">
1353 <conditional name="track_file_style_conditional"> 1743 <conditional name="track_file_style_conditional">
1357 <param name="height_bed" value="10" /> 1747 <param name="height_bed" value="10" />
1358 <conditional name="color_bed"> 1748 <conditional name="color_bed">
1359 <param name="color_bed_select" value="manually" /> 1749 <param name="color_bed_select" value="manually" />
1360 <param name="color" value="red" /> 1750 <param name="color" value="red" />
1361 </conditional> 1751 </conditional>
1362 <param name="flybase" value="true" />
1363 <param name="spacer_height" value="1"/> 1752 <param name="spacer_height" value="1"/>
1364 <param name="arrowhead_included" value="true"/> 1753 <conditional name="bed_style">
1754 <param name="arrowhead_included" value="true"/>
1755 </conditional>
1365 </conditional> 1756 </conditional>
1366 </repeat> 1757 </repeat>
1367 <repeat name="tracks"> 1758 <repeat name="tracks">
1368 <conditional name="track_file_style_conditional"> 1759 <conditional name="track_file_style_conditional">
1369 <param name="track_file_style_selector" value="vlines_track_option" /> 1760 <param name="track_file_style_selector" value="vlines_track_option" />
1371 </conditional> 1762 </conditional>
1372 </repeat> 1763 </repeat>
1373 <param name="image_file_format" value="png" /> 1764 <param name="image_file_format" value="png" />
1374 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="35000" /> 1765 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="35000" />
1375 </test> 1766 </test>
1767 <!--test 10-->
1376 <test> 1768 <test>
1377 <param name="region" value="X:3340000-3380000"/> 1769 <param name="region" value="X:3340000-3380000"/>
1378 <conditional name="x_axis"> 1770 <repeat name="tracks">
1379 <param name="x_axis_select" value="true" /> 1771 <conditional name="track_file_style_conditional">
1380 </conditional> 1772 <param name="track_file_style_selector" value="xaxis_option" />
1773 <param name="xaxis_where" value="top" />
1774 </conditional>
1775 </repeat>
1381 <repeat name="tracks"> 1776 <repeat name="tracks">
1382 <conditional name="track_file_style_conditional"> 1777 <conditional name="track_file_style_conditional">
1383 <param name="track_file_style_selector" value="gene_track_option" /> 1778 <param name="track_file_style_selector" value="gene_track_option" />
1384 <param name="track_input_bed" value="domains.bed" ftype="bed" /> 1779 <param name="track_input_bed" value="domains.bed" ftype="bed" />
1385 <param name="height_bed" value="6" /> 1780 <param name="height_bed" value="6" />
1417 </conditional> 1812 </conditional>
1418 </repeat> 1813 </repeat>
1419 <param name="image_file_format" value="png" /> 1814 <param name="image_file_format" value="png" />
1420 <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="35000" /> 1815 <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="35000" />
1421 </test> 1816 </test>
1817 <!--test 11-->
1422 <test> 1818 <test>
1423 <param name="region" value="chrX:3250000-3400000"/> 1819 <param name="region" value="chrX:3250000-3400000"/>
1424 <conditional name="x_axis"> 1820 <repeat name="tracks">
1425 <param name="x_axis_select" value="true" /> 1821 <conditional name="track_file_style_conditional">
1426 </conditional> 1822 <param name="track_file_style_selector" value="xaxis_option" />
1823 <param name="xaxis_where" value="top" />
1824 </conditional>
1825 </repeat>
1427 <repeat name="tracks"> 1826 <repeat name="tracks">
1428 <conditional name="track_file_style_conditional"> 1827 <conditional name="track_file_style_conditional">
1429 <param name="track_file_style_selector" value="hic_matrix_option" /> 1828 <param name="track_file_style_selector" value="hic_matrix_option" />
1430 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> 1829 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
1431 <param name="title" value="Kc DpnII (Li et al. 2015)" /> 1830 <param name="title" value="Kc DpnII (Li et al. 2015)" />
1432 <param name="colormap" value="RdYlBu_r" /> 1831 <!--<param name="colormap" value="RdYlBu_r" />-->
1433 <param name="depth" value="100000" /> 1832 <param name="depth" value="100000" />
1434 <param name="transform" value="log1p" /> 1833 <param name="transform" value="log1p" />
1435 <param name="show_masked_bins" value="true" /> 1834 <param name="show_masked_bins" value="true" />
1436 <param name="scale_factor" value="2.0" /> 1835 <param name="scale_factor" value="2.0" />
1437 </conditional> 1836 </conditional>
1446 <conditional name="track_file_style_conditional"> 1845 <conditional name="track_file_style_conditional">
1447 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> 1846 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
1448 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> 1847 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
1449 <param name="title" value="TAD separation score (Ramirez et al.)" /> 1848 <param name="title" value="TAD separation score (Ramirez et al.)" />
1450 <param name="height_bedgraph" value="10" /> 1849 <param name="height_bedgraph" value="10" />
1451 <param name="type_lines" value="lines" /> 1850 <conditional name="type">
1452 <param name="pos_score_in_bin" value="block" /> 1851 <param name="type_selector" value="lines" />
1453 <param name="plot_horizontal_lines" value="true" /> 1852 <param name="pos_score_in_bin" value="block" />
1454 <param name="show_data" value="true" /> 1853 <param name="plot_horizontal_lines" value="true" />
1854 <param name="show_data" value="true" />
1855 </conditional>
1455 </conditional> 1856 </conditional>
1456 </repeat> 1857 </repeat>
1457 <repeat name="tracks"> 1858 <repeat name="tracks">
1458 <conditional name="track_file_style_conditional"> 1859 <conditional name="track_file_style_conditional">
1459 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> 1860 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
1460 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> 1861 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
1461 <param name="title" value="TAD separation score (Ramirez et al.)" /> 1862 <param name="title" value="TAD separation score (Ramirez et al.)" />
1462 <param name="height_bedgraph" value="10" /> 1863 <param name="height_bedgraph" value="10" />
1463 <param name="type_lines" value="lines" /> 1864 <conditional name="type">
1464 <param name="pos_score_in_bin" value="center" /> 1865 <param name="type_selector" value="lines" />
1465 <param name="plot_horizontal_lines" value="false" /> 1866 <param name="pos_score_in_bin" value="center" />
1867 <param name="plot_horizontal_lines" value="false" />
1868 </conditional>
1466 </conditional> 1869 </conditional>
1467 </repeat> 1870 </repeat>
1468 <param name="image_file_format" value="png" /> 1871 <param name="image_file_format" value="png" />
1469 <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="35000" /> 1872 <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="35000" />
1470 </test> 1873 </test>
1874 <!--test 12-->
1471 <test> 1875 <test>
1472 <param name="region" value="chrX:3000000-3300000"/> 1876 <param name="region" value="chrX:3000000-3300000"/>
1473 <conditional name="x_axis"> 1877 <repeat name="tracks">
1474 <param name="x_axis_select" value="true" /> 1878 <conditional name="track_file_style_conditional">
1475 </conditional> 1879 <param name="track_file_style_selector" value="xaxis_option" />
1880 <param name="xaxis_where" value="top" />
1881 </conditional>
1882 </repeat>
1476 <repeat name="tracks"> 1883 <repeat name="tracks">
1477 <conditional name="track_file_style_conditional"> 1884 <conditional name="track_file_style_conditional">
1478 <param name="track_file_style_selector" value="hic_matrix_option" /> 1885 <param name="track_file_style_selector" value="hic_matrix_option" />
1479 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> 1886 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
1480 <param name="title" value="Kc DpnII (Li et al. 2015)" /> 1887 <param name="title" value="Kc DpnII (Li et al. 2015)" />
1511 <param name="invert_orientation" value="true" /> 1918 <param name="invert_orientation" value="true" />
1512 </conditional> 1919 </conditional>
1513 </repeat> 1920 </repeat>
1514 <param name="image_file_format" value="png" /> 1921 <param name="image_file_format" value="png" />
1515 <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" /> 1922 <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" />
1923 </test>
1924 <!--test 13-->
1925 <test>
1926 <param name="region" value="chrX:3000000-3300000"/>
1927 <repeat name="tracks">
1928 <conditional name="track_file_style_conditional">
1929 <param name="track_file_style_selector" value="link_track_option" />
1930 <param name="track_input_link" value="test.arcs" ftype="bed" />
1931 <param name="title" value="default" />
1932 <conditional name="color_link">
1933 <param name="color_link_select" value="manually" />
1934 <param name="color" value="#000000" />
1935 </conditional>
1936 </conditional>
1937 </repeat>
1938 <repeat name="tracks">
1939 <conditional name="track_file_style_conditional">
1940 <param name="track_file_style_selector" value="link_track_option" />
1941 <param name="track_input_link" value="test.arcs" ftype="bed" />
1942 <param name="title" value="ylim 20kb" />
1943 <conditional name="color_link">
1944 <param name="color_link_select" value="manually" />
1945 <param name="color" value="#000000" />
1946 </conditional>
1947 <param name="ylim" value="20000" />
1948 </conditional>
1949 </repeat>
1950 <repeat name="tracks">
1951 <conditional name="track_file_style_conditional">
1952 <param name="track_file_style_selector" value="link_track_option" />
1953 <param name="track_input_link" value="test.arcs" ftype="bed" />
1954 <param name="title" value="compacted" />
1955 <conditional name="color_link">
1956 <param name="color_link_select" value="manually" />
1957 <param name="color" value="#000000" />
1958 </conditional>
1959 <param name="compact_arcs_level" value="1" />
1960 </conditional>
1961 </repeat>
1962 <repeat name="tracks">
1963 <conditional name="track_file_style_conditional">
1964 <param name="track_file_style_selector" value="link_track_option" />
1965 <param name="track_input_link" value="test.arcs" ftype="bed" />
1966 <param name="title" value="highly compacted" />
1967 <conditional name="color_link">
1968 <param name="color_link_select" value="manually" />
1969 <param name="color" value="#000000" />
1970 </conditional>
1971 <param name="compact_arcs_level" value="2" />
1972 </conditional>
1973 </repeat>
1974 <param name="image_file_format" value="png" />
1975 <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="35000" />
1976 </test>
1977 <!--test 14-->
1978 <test>
1979 <param name="region" value="chrX:3000000-3300000"/>
1980 <section name="global_args">
1981 <param name="title" value="Scale bar"/>
1982 <param name="trackLabelFraction" value="0.5"/>
1983 <param name="trackLabelHAlign" value="center"/>
1984 </section>
1985 <repeat name="tracks">
1986 <conditional name="track_file_style_conditional">
1987 <param name="track_file_style_selector" value="spacer_option" />
1988 <param name="spacer_height" value="1.0" />
1989 </conditional>
1990 </repeat>
1991 <repeat name="tracks">
1992 <conditional name="track_file_style_conditional">
1993 <param name="track_file_style_selector" value="scale_bar_option" />
1994 <param name="title" value="default" />
1995 <param name="spacer_height" value="1"/>
1996 </conditional>
1997 </repeat>
1998 <repeat name="tracks">
1999 <conditional name="track_file_style_conditional">
2000 <param name="track_file_style_selector" value="scale_bar_option" />
2001 <param name="title" value="scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5" />
2002 <param name="color" value="red"/>
2003 <param name="alpha" value="0.5"/>
2004 <param name="line_width" value="2"/>
2005 <param name="x_center" value="3200000"/>
2006 <param name="size" value="100002"/>
2007 <param name="sb_where" value="right"/>
2008 <param name="fontsize" value="8"/>
2009 <param name="spacer_height" value="4"/>
2010 </conditional>
2011 </repeat>
2012 <param name="image_file_format" value="png" />
2013 <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="35000" />
2014 </test>
2015 <!--test 15-->
2016 <test>
2017 <param name="region" value="chrX:3300000-3500000"/>
2018 <repeat name="tracks">
2019 <conditional name="track_file_style_conditional">
2020 <param name="track_file_style_selector" value="xaxis_option" />
2021 <param name="xaxis_where" value="bottom" />
2022 </conditional>
2023 </repeat>
2024 <repeat name="tracks">
2025 <conditional name="track_file_style_conditional">
2026 <param name="track_file_style_selector" value="gene_track_option" />
2027 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2028 <param name="title" value="flybase" />
2029 <param name="height_bed" value="10" />
2030 </conditional>
2031 </repeat>
2032 <repeat name="tracks">
2033 <conditional name="track_file_style_conditional">
2034 <param name="track_file_style_selector" value="gene_track_option" />
2035 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2036 <param name="title" value="UCSC" />
2037 <param name="height_bed" value="10" />
2038 <conditional name="bed_style">
2039 <param name="bed_style_select" value="UCSC"/>
2040 <section name="bed_advanced">
2041 <param name="arrow_interval" value="10"/>
2042 </section>
2043 </conditional>
2044 </conditional>
2045 </repeat>
2046 <repeat name="tracks">
2047 <conditional name="track_file_style_conditional">
2048 <param name="track_file_style_selector" value="gene_track_option" />
2049 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2050 <param name="title" value="tssarrow" />
2051 <param name="height_bed" value="10" />
2052 <conditional name="bed_style">
2053 <param name="bed_style_select" value="tssarrow"/>
2054 </conditional>
2055 </conditional>
2056 </repeat>
2057 <repeat name="tracks">
2058 <conditional name="track_file_style_conditional">
2059 <param name="track_file_style_selector" value="gene_track_option" />
2060 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2061 <param name="title" value="tssarrow 5kb" />
2062 <param name="height_bed" value="10" />
2063 <conditional name="bed_style">
2064 <param name="bed_style_select" value="tssarrow"/>
2065 <section name="bed_advanced">
2066 <param name="arrow_length" value="5000"/>
2067 </section>
2068 </conditional>
2069 </conditional>
2070 </repeat>
2071 <param name="image_file_format" value="png" />
2072 <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" />
1516 </test> 2073 </test>
1517 </tests> 2074 </tests>
1518 <help><![CDATA[ 2075 <help><![CDATA[
1519 2076
1520 pyGenomeTracks 2077 pyGenomeTracks