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comparison pyGenomeTracks.xml @ 15:c7af51147b55 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068
author iuc
date Wed, 01 Oct 2025 19:34:28 +0000
parents d640aa8a24ab
children
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14:d640aa8a24ab 15:c7af51147b55
2 <description>plot genomic data tracks</description> 2 <description>plot genomic data tracks</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">pyGenomeTracks</token> 4 <token name="@BINARY@">pyGenomeTracks</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="xrefs" />
7 <expand macro="requirements" /> 8 <expand macro="requirements" />
8 <command detect_errors="exit_code"> 9 <command detect_errors="exit_code">
9 <![CDATA[ 10 <![CDATA[
10 ## First symlink data 11 ## First symlink data
11 ## of hic to have the good extension 12 ## of hic to have the good extension
216 #end for 217 #end for
217 #end if 218 #end if
218 219
219 ## Gene/gtf track 220 ## Gene/gtf track
220 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": 221 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
221 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): 222 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.bed_gtf.track_input_bed):
222 [genes_${counter}_${counter_bed}] 223 [genes_${counter}_${counter_bed}]
223 #set ext = $data_bed.extension
224 file = $data_bed 224 file = $data_bed
225 #if $ext == 'gtf': 225 #if $track.track_file_style_conditional.bed_gtf.input_bed_or_gtf == "bed":
226 prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name 226 file_type = bed
227 #if $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts.merge_transcripts_select == 'true': 227 #else:
228 file_type = gtf
229 prefered_name = $track.track_file_style_conditional.bed_gtf.prefered_name
230 #if $track.track_file_style_conditional.bed_gtf.merge_transcripts.merge_transcripts_select == 'true':
228 merge_transcripts = true 231 merge_transcripts = true
229 merge_overlapping_exons = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts.merge_overlapping_exons 232 merge_overlapping_exons = $track.track_file_style_conditional.bed_gtf.merge_transcripts.merge_overlapping_exons
230 #end if 233 #end if
231 #end if 234 #end if
232 #if $track.track_file_style_conditional.title: 235 #if $track.track_file_style_conditional.title:
233 title = $track.track_file_style_conditional.title 236 title = $track.track_file_style_conditional.title
234 #elif $track.track_file_style_conditional.overlay_select == 'no': 237 #elif $track.track_file_style_conditional.overlay_select == 'no':
245 #if str($track.track_file_style_conditional.color_bed.max_value) != '': 248 #if str($track.track_file_style_conditional.color_bed.max_value) != '':
246 max_value = $track.track_file_style_conditional.color_bed.max_value 249 max_value = $track.track_file_style_conditional.color_bed.max_value
247 #end if 250 #end if
248 #end if 251 #end if
249 #end if 252 #end if
250 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': 253 display = $track.track_file_style_conditional.display_cond.display
251 border_color = $track.track_file_style_conditional.border_color_bed.color 254 #if $track.track_file_style_conditional.display_cond.display in ['stacked', 'interleaved', 'collapsed']:
252 #else 255 style = $track.track_file_style_conditional.display_cond.bed_style.bed_style_select
253 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select 256 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['UCSC', 'exonarrows', 'flybase']:
254 #end if 257 #if $track.track_file_style_conditional.display_cond.bed_style.border_color_bed.border_color_bed_select == 'manually':
255 style = $track.track_file_style_conditional.bed_style.bed_style_select 258 border_color = $track.track_file_style_conditional.display_cond.bed_style.border_color_bed.color
256 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'UCSC': 259 #else
257 arrow_interval = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_interval 260 border_color = $track.track_file_style_conditional.display_cond.bed_style.border_color_bed.border_color_bed_select
258 #if $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': 261 #end if
259 color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.color
260 #else
261 color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select
262 #end if 262 #end if
263 #else: 263 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['UCSC', 'exonarrows']:
264 height_utr = $track.track_file_style_conditional.bed_style.bed_advanced.height_utr 264 arrow_interval = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrow_interval
265 #if $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'manually': 265 #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_arrow.color_arrow_select == "manually":
266 color_utr = $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color 266 color_arrow = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_arrow.color
267 #elif $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb': 267 #else
268 color_utr = bed_rgb 268 color_arrow = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_arrow.color_arrow_select
269 #end if
270 #end if
271 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'UCSC':
272 #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually':
273 color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.color
274 #else
275 color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select
276 #end if
269 #else: 277 #else:
270 ## This is 'like' 278 #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_utr.color_utr_select == 'manually':
271 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": 279 color_utr = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_utr.color
280 #elif $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb':
272 color_utr = bed_rgb 281 color_utr = bed_rgb
273 #else: 282 #else:
283 ## This is 'like'
284 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
285 color_utr = bed_rgb
286 #else:
274 color_utr = $track.track_file_style_conditional.color_bed.color 287 color_utr = $track.track_file_style_conditional.color_bed.color
288 #end if
289 #end if
290 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['flybase', 'tssarrow']:
291 height_utr = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.height_utr
292 #end if
293 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'exonarrows':
294 height_intron = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.height_intron
295 #end if
296 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrow_length != '':
297 arrow_length = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrow_length
298 #end if
299 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'flybase':
300 arrowhead_included = $track.track_file_style_conditional.display_cond.bed_style.arrowhead_included
301 arrowhead_fraction = $track.track_file_style_conditional.display_cond.bed_style.arrowhead_fraction
302 #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually':
303 color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.color
304 #else
305 color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select
306 #end if
275 #end if 307 #end if
276 #end if 308 #end if
277 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length != '': 309 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['UCSC', 'exonarrows', 'tssarrow']:
278 arrow_length = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length 310 arrowhead_fraction = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrowhead_fraction
279 #end if 311 #end if
280 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'flybase': 312 #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.gene_rows:
281 arrowhead_included = $track.track_file_style_conditional.bed_style.arrowhead_included 313 gene_rows = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.gene_rows
282 arrowhead_fraction = $track.track_file_style_conditional.bed_style.arrowhead_fraction 314 #end if
283 #if $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': 315 global_max_row = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.global_max_row
284 color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.color 316 max_labels = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.max_labels
285 #else 317 line_width = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.line_width
286 color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select 318 labels = $track.track_file_style_conditional.display_cond.labels.plot_labels
319 #if $track.track_file_style_conditional.display_cond.labels.plot_labels == 'true':
320 all_labels_inside = $track.track_file_style_conditional.display_cond.labels.all_labels_inside
321 labels_in_margin = $track.track_file_style_conditional.display_cond.labels.labels_in_margin
322 fontstyle = $track.track_file_style_conditional.display_cond.labels.fontstyle
323 #if $track.track_file_style_conditional.display_cond.labels.fontsize:
324 fontsize = $track.track_file_style_conditional.display_cond.labels.fontsize
287 #end if 325 #end if
288 #end if 326 #end if
289 #end if 327 #end if
290 display = $track.track_file_style_conditional.display 328 #if $track.track_file_style_conditional.display_cond.display in ['triangle', 'squares']:
329 #if $track.track_file_style_conditional.display_cond.border_color_bed.border_color_bed_select == 'manually':
330 border_color = $track.track_file_style_conditional.display_cond.border_color_bed.color
331 #else
332 border_color = $track.track_file_style_conditional.display_cond.border_color_bed.border_color_bed_select
333 #end if
334 #end if
335 #if $track.track_file_style_conditional.display_cond.display in ['inversions', 'deletions', 'triangles', 'squares']:
336 line_width = $track.track_file_style_conditional.display_cond.line_width
337 #end if
338 #if $track.track_file_style_conditional.display_cond.display in ['inversions', 'deletions']:
339 labels = $track.track_file_style_conditional.display_cond.labels.plot_labels
340 #if $track.track_file_style_conditional.display_cond.labels.plot_labels == 'true':
341 fontstyle = $track.track_file_style_conditional.display_cond.labels.fontstyle
342 #if $track.track_file_style_conditional.display_cond.labels.fontsize:
343 fontsize = $track.track_file_style_conditional.display_cond.labels.fontsize
344 #end if
345 #end if
346 #end if
347 #if $track.track_file_style_conditional.display_cond.display == 'deletions':
348 backbone_color = $track.track_file_style_conditional.display_cond.backbone_color
349 #end if
350 #if $track.track_file_style_conditional.display_cond.display == 'inversions':
351 arrowhead_fraction = $track.track_file_style_conditional.display_cond.arrowhead_fraction
352 #end if
291 #if $track.track_file_style_conditional.height_bed: 353 #if $track.track_file_style_conditional.height_bed:
292 height = $track.track_file_style_conditional.height_bed 354 height = $track.track_file_style_conditional.height_bed
293 #end if 355 #end if
294 labels = $track.track_file_style_conditional.labels.plot_labels
295 #if $track.track_file_style_conditional.labels.plot_labels == 'true':
296 all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside
297 labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin
298 fontstyle = $track.track_file_style_conditional.labels.fontstyle
299 #if $track.track_file_style_conditional.labels.fontsize:
300 fontsize = $track.track_file_style_conditional.labels.fontsize
301 #end if
302 #end if
303 file_type = $ext
304 #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows:
305 gene_rows = $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows
306 #end if
307 global_max_row = $track.track_file_style_conditional.bed_style.bed_advanced.global_max_row
308 max_labels = $track.track_file_style_conditional.bed_style.bed_advanced.max_labels
309 line_width = $track.track_file_style_conditional.bed_style.bed_advanced.line_width
310 #if $track.track_file_style_conditional.invert_orientation: 356 #if $track.track_file_style_conditional.invert_orientation:
311 orientation = inverted 357 orientation = inverted
312 #end if 358 #end if
313 overlay_previous = $track.track_file_style_conditional.overlay_select 359 overlay_previous = $track.track_file_style_conditional.overlay_select
314 ## If spacer is asked a new section is created: 360 ## If spacer is asked a new section is created:
767 species_labels = $track.track_file_style_conditional.species_labels 813 species_labels = $track.track_file_style_conditional.species_labels
768 #end if 814 #end if
769 species_order_only = $track.track_file_style_conditional.species_order_only 815 species_order_only = $track.track_file_style_conditional.species_order_only
770 #end if 816 #end if
771 display_ref_seq = $track.track_file_style_conditional.display_ref_seq 817 display_ref_seq = $track.track_file_style_conditional.display_ref_seq
818 rasterize = $track.track_file_style_conditional.rasterize
772 file_type = maf 819 file_type = maf
773 ## If spacer is asked a new section is created: 820 ## If spacer is asked a new section is created:
774 #if $track.track_file_style_conditional.spacer_height != "": 821 #if $track.track_file_style_conditional.spacer_height != "":
775 [spacer] 822 [spacer]
776 height = $track.track_file_style_conditional.spacer_height 823 height = $track.track_file_style_conditional.spacer_height
918 <expand macro="spacer_macro" /> 965 <expand macro="spacer_macro" />
919 966
920 </when> 967 </when>
921 <when value="gene_track_option"> 968 <when value="gene_track_option">
922 <expand macro="plot_title" /> 969 <expand macro="plot_title" />
923 970 <conditional name="bed_gtf">
924 <expand macro="track_input_bed_gtf_macro" /> 971 <param name="input_bed_or_gtf" type="select" label="Use bed or gtf input:">
972 <option value="bed" selected="True">bed</option>
973 <option value="gtf">gtf</option>
974 </param>
975 <when value="bed">
976 <expand macro="track_input_bed_macro" />
977 </when>
978 <when value="gtf">
979 <!-- I call it track_input_bed to make it the same name as the bed input -->
980 <param name="track_input_bed" type="data" format="gtf" label="Track file(s) gtf format" multiple="True"/>
981 <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label"
982 help="Usually transcript_name or gene_name"/>
983 <conditional name="merge_transcripts">
984 <param name="merge_transcripts_select" type="select" label="Merge all transcripts of each gene in a single entry">
985 <option value="false" selected="True">No</option>
986 <option value="true">Yes</option>
987 </param>
988 <when value="true">
989 <param name="merge_overlapping_exons" type="boolean" truevalue="true" falsevalue="false" checked="true"
990 label="Merge overlapping exons" help="Usually it makes prettier plots" />
991 </when>
992 <when value="false" />
993 </conditional>
994 </when>
995 </conditional>
925 <conditional name="color_bed"> 996 <conditional name="color_bed">
926 <param name="color_bed_select" type="select" label="Define color:"> 997 <param name="color_bed_select" type="select" label="Define color:">
927 <option value="manually" selected="True">manually</option> 998 <option value="manually" selected="True">manually</option>
928 <option value="bed_rgb">From the 9th field</option> 999 <option value="bed_rgb">From the 9th field</option>
929 <option value="colormap">From the 5th field (score)</option> 1000 <option value="colormap">From the 5th field (score)</option>
939 <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> 1010 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
940 </param> 1011 </param>
941 <expand macro="minmax_macro" /> 1012 <expand macro="minmax_macro" />
942 </when> 1013 </when>
943 </conditional> 1014 </conditional>
944 <expand macro="border_color_bed_macro" />
945 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> 1015 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/>
946 <conditional name="labels"> 1016 <conditional name="display_cond">
947 <param name="plot_labels" type="select" label="Plot labels"> 1017 <param name="display" type="select" label="display to use">
948 <option value="true" selected="True">yes</option> 1018 <option value="stacked" selected="True">stacked (no overlap even with the label)</option>
949 <option value="false">no</option> 1019 <option value="interleaved">interleaved (everything on 2 lines)</option>
1020 <option value="collapsed">collapsed (everything on 1 line)</option>
1021 <option value="triangles">triangles (plot triangles between start and end)</option>
1022 <option value="squares">squares (plot squares on the diagonal)</option>
1023 <option value="deletions">deletions (plot a horizontal line with V for each region of your bed)</option>
1024 <option value="inversions">inversions (plot arrows around each region of your bed)</option>
950 </param> 1025 </param>
951 <when value="true"> 1026 <when value="stacked">
952 <param name="all_labels_inside" type="boolean" truevalue="true" falsevalue="false" checked="false" 1027 <expand macro="bed_style_macro" />
953 label="Put all labels inside the plotted region"
954 help="Put labels on the left of the region if the region ends after the plotted region."/>
955 <param name="labels_in_margin" type="boolean" truevalue="true" falsevalue="false" checked="false"
956 label="Allow to put labels in the right margin"
957 help="Put labels in the margin if the region ends after the plotted region."/>
958 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
959 <param name="fontstyle" type="select" label="Fontstyle">
960 <option value="normal" selected="True">normal</option>
961 <option value="italic">italic</option>
962 <option value="oblique">oblique</option>
963 </param>
964 </when> 1028 </when>
965 <when value="false"/> 1029 <when value="interleaved">
966 </conditional> 1030 <expand macro="bed_style_macro" />
967 <param name="display" type="select" label="display to use"> 1031 </when>
968 <option value="stacked" selected="True">stacked (no overlap even with the label)</option> 1032 <when value="collapsed">
969 <option value="interleaved">interleaved (everything on 2 lines)</option> 1033 <expand macro="bed_style_macro" />
970 <option value="collapsed">collapsed (everything on 1 line)</option> 1034 </when>
971 <option value="triangles">triangles (plot triangles between start and end)</option> 1035 <when value="triangles">
972 <option value="squares">squares (plot squares on the diagonal)</option> 1036 <expand macro="border_color_bed_macro" />
973 </param> 1037 <param name="line_width" type="float" value="0.5" label="width of lines" />
974 <conditional name="bed_style"> 1038 </when>
975 <param name="bed_style_select" type="select" label="Bed style"> 1039 <when value="squares">
976 <option value="flybase" selected="True">flybase (blocks with arrow at extremities)</option> 1040 <expand macro="border_color_bed_macro" />
977 <option value="UCSC">UCSC (blocks with arrows in introns)</option> 1041 <param name="line_width" type="float" value="0.5" label="width of lines" />
978 <option value="tssarrow">tssarrow (blocks with arrow above at beginning)</option> 1042 </when>
979 </param> 1043 <when value="deletions">
980 <when value="flybase"> 1044 <param name="line_width" type="float" value="0.5" label="width of lines" />
981 <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false" 1045 <param name="backbone_color" type="color" value="#000000" label="Color of the horizontal line"/>
982 label="Include the arrowhead in the bed interval:" 1046 <expand macro="delinv_labels"/>
983 help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/> 1047 </when>
1048 <when value="inversions">
984 <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1" 1049 <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1"
985 label="Size of arrowhead relative to the plotted region" 1050 label="Parameter to control the size of the arrows"/>
986 help="This size is also used to put space between the bed regions and their labels."/> 1051 <param name="line_width" type="float" value="0.5" label="width of lines" />
987 <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> 1052 <expand macro="delinv_labels"/>
988 <expand macro="utr_macro" />
989 <expand macro="bed_advanced_macro" />
990 <expand macro="backbone_color_bed_macro" />
991 </section>
992 </when>
993 <when value="UCSC">
994 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
995 <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/>
996 <expand macro="bed_advanced_macro" />
997 <expand macro="backbone_color_bed_macro" />
998 </section>
999 </when>
1000 <when value="tssarrow">
1001 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
1002 <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)"/>
1003 <expand macro="utr_macro" />
1004 <expand macro="bed_advanced_macro" />
1005 </section>
1006 </when> 1053 </when>
1007 </conditional> 1054 </conditional>
1008 <expand macro="overlay_macro" /> 1055 <expand macro="overlay_macro" />
1009 <expand macro="inverted_macro" /> 1056 <expand macro="inverted_macro" />
1010 <expand macro="spacer_macro" /> 1057 <expand macro="spacer_macro" />
1011
1012 </when> 1058 </when>
1013 <when value="link_track_option"> 1059 <when value="link_track_option">
1014 <expand macro="plot_title" /> 1060 <expand macro="plot_title" />
1015 <expand macro="track_input_link_macro" /> 1061 <expand macro="track_input_link_macro" />
1016 <conditional name="color_link"> 1062 <conditional name="color_link">
1311 <param name="species_labels" type="text" value="" label="[Optional] The label you want for the above species (space separated)"/> 1357 <param name="species_labels" type="text" value="" label="[Optional] The label you want for the above species (space separated)"/>
1312 <param name="species_order_only" type="boolean" truevalue="true" falsevalue="false" checked="false" 1358 <param name="species_order_only" type="boolean" truevalue="true" falsevalue="false" checked="false"
1313 label="Display only the species specified above"/> 1359 label="Display only the species specified above"/>
1314 <param name="display_ref_seq" type="boolean" truevalue="true" falsevalue="false" checked="false" 1360 <param name="display_ref_seq" type="boolean" truevalue="true" falsevalue="false" checked="false"
1315 label="Display the sequence of the reference"/> 1361 label="Display the sequence of the reference"/>
1362 <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="false"
1363 label="Rasterize the line and blocks of the maf track"/>
1316 <expand macro="inverted_macro" /> 1364 <expand macro="inverted_macro" />
1317 <expand macro="overlay_macro" /> 1365 <expand macro="overlay_macro" />
1318 <expand macro="spacer_macro" /> 1366 <expand macro="spacer_macro" />
1319 </when> 1367 </when>
1320 </conditional> 1368 </conditional>
1458 </conditional> 1506 </conditional>
1459 </repeat> 1507 </repeat>
1460 <repeat name="tracks"> 1508 <repeat name="tracks">
1461 <conditional name="track_file_style_conditional"> 1509 <conditional name="track_file_style_conditional">
1462 <param name="track_file_style_selector" value="gene_track_option" /> 1510 <param name="track_file_style_selector" value="gene_track_option" />
1463 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 1511 <conditional name="bed_gtf">
1512 <param name="input_bed_or_gtf" value="bed"/>
1513 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
1514 </conditional>
1464 <param name="title" value="genes" /> 1515 <param name="title" value="genes" />
1465 <param name="height_bed" value="5" /> 1516 <param name="height_bed" value="5" />
1466 <conditional name="labels"> 1517 <conditional name="display_cond">
1467 <param name="fontsize" value="10" /> 1518 <conditional name="labels">
1519 <param name="fontsize" value="10" />
1520 </conditional>
1468 </conditional> 1521 </conditional>
1469 </conditional> 1522 </conditional>
1470 </repeat> 1523 </repeat>
1471 <repeat name="tracks"> 1524 <repeat name="tracks">
1472 <conditional name="track_file_style_conditional"> 1525 <conditional name="track_file_style_conditional">
1475 </conditional> 1528 </conditional>
1476 </repeat> 1529 </repeat>
1477 <repeat name="tracks"> 1530 <repeat name="tracks">
1478 <conditional name="track_file_style_conditional"> 1531 <conditional name="track_file_style_conditional">
1479 <param name="track_file_style_selector" value="gene_track_option" /> 1532 <param name="track_file_style_selector" value="gene_track_option" />
1480 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 1533 <conditional name="bed_gtf">
1534 <param name="input_bed_or_gtf" value="bed"/>
1535 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
1536 </conditional>
1481 <param name="title" value="max num rows 3" /> 1537 <param name="title" value="max num rows 3" />
1482 <param name="height_bed" value="3" /> 1538 <param name="height_bed" value="3" />
1483 <conditional name="labels"> 1539 <conditional name="display_cond">
1484 <param name="fontsize" value="8" /> 1540 <conditional name="labels">
1485 </conditional> 1541 <param name="fontsize" value="8" />
1486 <conditional name="bed_style"> 1542 </conditional>
1487 <section name="bed_advanced"> 1543 <conditional name="bed_style">
1488 <param name="gene_rows" value="3" /> 1544 <section name="bed_advanced">
1489 </section> 1545 <param name="gene_rows" value="3" />
1546 </section>
1547 </conditional>
1490 </conditional> 1548 </conditional>
1491 </conditional> 1549 </conditional>
1492 </repeat> 1550 </repeat>
1493 <repeat name="tracks"> 1551 <repeat name="tracks">
1494 <conditional name="track_file_style_conditional"> 1552 <conditional name="track_file_style_conditional">
1497 </conditional> 1555 </conditional>
1498 </repeat> 1556 </repeat>
1499 <repeat name="tracks"> 1557 <repeat name="tracks">
1500 <conditional name="track_file_style_conditional"> 1558 <conditional name="track_file_style_conditional">
1501 <param name="track_file_style_selector" value="gene_track_option" /> 1559 <param name="track_file_style_selector" value="gene_track_option" />
1502 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> 1560 <conditional name="bed_gtf">
1561 <param name="input_bed_or_gtf" value="bed"/>
1562 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
1563 </conditional>
1503 <param name="title" value="bed6 global max row" /> 1564 <param name="title" value="bed6 global max row" />
1504 <param name="height_bed" value="20" /> 1565 <param name="height_bed" value="20" />
1505 <conditional name="labels"> 1566 <conditional name="display_cond">
1506 <param name="fontsize" value="10" /> 1567 <conditional name="labels">
1507 </conditional> 1568 <param name="fontsize" value="10" />
1508 <conditional name="bed_style"> 1569 </conditional>
1509 <section name="bed_advanced"> 1570 <conditional name="bed_style">
1510 <param name="global_max_row" value="true" /> 1571 <section name="bed_advanced">
1511 </section> 1572 <param name="global_max_row" value="true" />
1573 </section>
1574 </conditional>
1512 </conditional> 1575 </conditional>
1513 </conditional> 1576 </conditional>
1514 </repeat> 1577 </repeat>
1515 <repeat name="tracks"> 1578 <repeat name="tracks">
1516 <conditional name="track_file_style_conditional"> 1579 <conditional name="track_file_style_conditional">
1517 <param name="track_file_style_selector" value="vlines_track_option" /> 1580 <param name="track_file_style_selector" value="vlines_track_option" />
1518 <param name="track_input_bed_single" value="domains.bed" ftype="bed" /> 1581 <param name="track_input_bed_single" value="domains.bed" ftype="bed" />
1519 </conditional> 1582 </conditional>
1520 </repeat> 1583 </repeat>
1521 <param name="image_file_format" value="png" /> 1584 <param name="image_file_format" value="png" />
1522 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="100" /> 1585 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="image_diff" />
1523 </test> 1586 </test>
1524 <!--test 2--> 1587 <!--test 2-->
1525 <test> 1588 <test>
1526 <param name="region" value="chrX:3000000-3500000"/> 1589 <param name="region" value="chrX:3000000-3500000"/>
1527 <repeat name="tracks"> 1590 <repeat name="tracks">
1593 <param name="show_data" value="true" /> 1656 <param name="show_data" value="true" />
1594 <param name="invert_orientation" value="true" /> 1657 <param name="invert_orientation" value="true" />
1595 </conditional> 1658 </conditional>
1596 </repeat> 1659 </repeat>
1597 <param name="image_file_format" value="png" /> 1660 <param name="image_file_format" value="png" />
1598 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="100" /> 1661 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="image_diff" />
1599 </test> 1662 </test>
1600 <!--test 3--> 1663 <!--test 3-->
1601 <test> 1664 <test>
1602 <param name="region" value="chrX:3000000-3500000"/> 1665 <param name="region" value="chrX:3000000-3500000"/>
1603 <repeat name="tracks"> 1666 <repeat name="tracks">
1738 </conditional> 1801 </conditional>
1739 </repeat> 1802 </repeat>
1740 <repeat name="tracks"> 1803 <repeat name="tracks">
1741 <conditional name="track_file_style_conditional"> 1804 <conditional name="track_file_style_conditional">
1742 <param name="track_file_style_selector" value="gene_track_option" /> 1805 <param name="track_file_style_selector" value="gene_track_option" />
1743 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 1806 <conditional name="bed_gtf">
1807 <param name="input_bed_or_gtf" value="bed"/>
1808 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
1809 </conditional>
1744 <param name="title" value="genes in ucsc" /> 1810 <param name="title" value="genes in ucsc" />
1745 <param name="height_bed" value="5" /> 1811 <param name="height_bed" value="5" />
1746 <conditional name="labels"> 1812 <conditional name="display_cond">
1747 <param name="fontsize" value="10" /> 1813 <conditional name="labels">
1748 </conditional> 1814 <param name="fontsize" value="10" />
1749 <conditional name="bed_style"> 1815 </conditional>
1750 <param name="bed_style_select" value="UCSC"/> 1816 <conditional name="bed_style">
1817 <param name="bed_style_select" value="UCSC"/>
1818 </conditional>
1751 </conditional> 1819 </conditional>
1752 </conditional> 1820 </conditional>
1753 </repeat> 1821 </repeat>
1754 <repeat name="tracks"> 1822 <repeat name="tracks">
1755 <conditional name="track_file_style_conditional"> 1823 <conditional name="track_file_style_conditional">
1756 <param name="track_file_style_selector" value="gene_track_option" /> 1824 <param name="track_file_style_selector" value="gene_track_option" />
1757 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> 1825 <conditional name="bed_gtf">
1826 <param name="input_bed_or_gtf" value="bed"/>
1827 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
1828 </conditional>
1758 <param name="title" value="bed6 global max row color from score" /> 1829 <param name="title" value="bed6 global max row color from score" />
1759 <param name="height_bed" value="20" /> 1830 <param name="height_bed" value="20" />
1760 <conditional name="labels"> 1831 <conditional name="display_cond">
1761 <param name="fontsize" value="10" /> 1832 <conditional name="labels">
1762 </conditional> 1833 <param name="fontsize" value="10" />
1763 <conditional name="bed_style"> 1834 </conditional>
1764 <section name="bed_advanced"> 1835 <conditional name="bed_style">
1765 <param name="global_max_row" value="true" /> 1836 <section name="bed_advanced">
1766 </section> 1837 <param name="global_max_row" value="true" />
1838 </section>
1839 </conditional>
1767 </conditional> 1840 </conditional>
1768 <conditional name="color_bed"> 1841 <conditional name="color_bed">
1769 <param name="color_bed_select" value="colormap" /> 1842 <param name="color_bed_select" value="colormap" />
1770 <param name="color" value="RdYlBu_r" /> 1843 <param name="color" value="RdYlBu_r" />
1771 <param name="min_value" value="0" /> 1844 <param name="min_value" value="0" />
1774 </conditional> 1847 </conditional>
1775 </repeat> 1848 </repeat>
1776 <repeat name="tracks"> 1849 <repeat name="tracks">
1777 <conditional name="track_file_style_conditional"> 1850 <conditional name="track_file_style_conditional">
1778 <param name="track_file_style_selector" value="gene_track_option" /> 1851 <param name="track_file_style_selector" value="gene_track_option" />
1779 <param name="track_input_bed" value="domains.bed" ftype="bed" /> 1852 <conditional name="bed_gtf">
1853 <param name="input_bed_or_gtf" value="bed"/>
1854 <param name="track_input_bed" value="domains.bed" ftype="bed" />
1855 </conditional>
1780 <param name="title" value="domains.bed using the 9th field for colors interleaved border=red" /> 1856 <param name="title" value="domains.bed using the 9th field for colors interleaved border=red" />
1781 <param name="height_bed" value="2" /> 1857 <param name="height_bed" value="2" />
1782 <conditional name="color_bed"> 1858 <conditional name="color_bed">
1783 <param name="color_bed_select" value="bed_rgb" /> 1859 <param name="color_bed_select" value="bed_rgb" />
1784 </conditional> 1860 </conditional>
1785 <conditional name="border_color_bed"> 1861 <conditional name="display_cond">
1786 <param name="border_color_bed_select" value="manually" /> 1862 <conditional name="bed_style">
1787 <param name="color" value="red" /> 1863 <conditional name="border_color_bed">
1788 </conditional> 1864 <param name="border_color_bed_select" value="manually" />
1789 <conditional name="labels"> 1865 <param name="color" value="red" />
1790 <param name="plot_labels" value="false" /> 1866 </conditional>
1791 </conditional> 1867 </conditional>
1792 <param name="display" value="interleaved" /> 1868 <conditional name="labels">
1869 <param name="plot_labels" value="false" />
1870 </conditional>
1871 <param name="display" value="interleaved" />
1872 </conditional>
1793 </conditional> 1873 </conditional>
1794 </repeat> 1874 </repeat>
1795 <repeat name="tracks"> 1875 <repeat name="tracks">
1796 <conditional name="track_file_style_conditional"> 1876 <conditional name="track_file_style_conditional">
1797 <param name="track_file_style_selector" value="gene_track_option" /> 1877 <param name="track_file_style_selector" value="gene_track_option" />
1798 <param name="track_input_bed" value="domains.bed" ftype="bed" /> 1878 <conditional name="bed_gtf">
1879 <param name="input_bed_or_gtf" value="bed"/>
1880 <param name="track_input_bed" value="domains.bed" ftype="bed" />
1881 </conditional>
1799 <param name="title" value="domains.bed using the 9th field for colors interleaved border=bed_rgb" /> 1882 <param name="title" value="domains.bed using the 9th field for colors interleaved border=bed_rgb" />
1800 <param name="height_bed" value="2" /> 1883 <param name="height_bed" value="2" />
1801 <conditional name="color_bed"> 1884 <conditional name="color_bed">
1802 <param name="color_bed_select" value="bed_rgb" /> 1885 <param name="color_bed_select" value="bed_rgb" />
1803 </conditional> 1886 </conditional>
1804 <conditional name="border_color_bed"> 1887 <conditional name="display_cond">
1805 <param name="border_color_bed_select" value="bed_rgb" /> 1888 <conditional name="bed_style">
1806 </conditional> 1889 <conditional name="border_color_bed">
1807 <conditional name="labels"> 1890 <param name="border_color_bed_select" value="bed_rgb" />
1808 <param name="plot_labels" value="false" /> 1891 </conditional>
1809 </conditional> 1892 </conditional>
1810 <param name="display" value="interleaved" /> 1893 <conditional name="labels">
1894 <param name="plot_labels" value="false" />
1895 </conditional>
1896 <param name="display" value="interleaved" />
1897 </conditional>
1811 </conditional> 1898 </conditional>
1812 </repeat> 1899 </repeat>
1813 <repeat name="tracks"> 1900 <repeat name="tracks">
1814 <conditional name="track_file_style_conditional"> 1901 <conditional name="track_file_style_conditional">
1815 <param name="track_file_style_selector" value="gene_track_option" /> 1902 <param name="track_file_style_selector" value="gene_track_option" />
1816 <param name="track_input_bed" value="domains.bed" ftype="bed" /> 1903 <conditional name="bed_gtf">
1904 <param name="input_bed_or_gtf" value="bed"/>
1905 <param name="track_input_bed" value="domains.bed" ftype="bed" />
1906 </conditional>
1817 <param name="title" value="domains.bed using the 9th field for colors interleaved border=none" /> 1907 <param name="title" value="domains.bed using the 9th field for colors interleaved border=none" />
1818 <param name="height_bed" value="2" /> 1908 <param name="height_bed" value="2" />
1819 <conditional name="color_bed"> 1909 <conditional name="color_bed">
1820 <param name="color_bed_select" value="bed_rgb" /> 1910 <param name="color_bed_select" value="bed_rgb" />
1821 </conditional> 1911 </conditional>
1822 <conditional name="border_color_bed"> 1912 <conditional name="display_cond">
1823 <param name="border_color_bed_select" value="none" /> 1913 <conditional name="bed_style">
1824 </conditional> 1914 <conditional name="border_color_bed">
1825 <conditional name="labels"> 1915 <param name="border_color_bed_select" value="none" />
1826 <param name="plot_labels" value="false" /> 1916 </conditional>
1827 </conditional> 1917 </conditional>
1828 <param name="display" value="interleaved" /> 1918 <conditional name="labels">
1919 <param name="plot_labels" value="false" />
1920 </conditional>
1921 <param name="display" value="interleaved" />
1922 </conditional>
1829 </conditional> 1923 </conditional>
1830 </repeat> 1924 </repeat>
1831 <param name="image_file_format" value="png" /> 1925 <param name="image_file_format" value="png" />
1832 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="100" /> 1926 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="image_diff" />
1833 </test> 1927 </test>
1834 <!--test 4--> 1928 <!--test 4-->
1835 <test> 1929 <test>
1836 <param name="region" value="X:2700000-3100000"/> 1930 <param name="region" value="X:2700000-3100000"/>
1837 <repeat name="tracks"> 1931 <repeat name="tracks">
1838 <conditional name="track_file_style_conditional"> 1932 <conditional name="track_file_style_conditional">
1839 <param name="track_file_style_selector" value="bigwig_track_option" /> 1933 <param name="track_file_style_selector" value="bigwig_track_option" />
1840 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 1934 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
1841 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" /> 1935 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig color=red alpha = 0.5 max over 300 bins)" />
1842 <param name="height_bigwig" value="7" /> 1936 <param name="height_bigwig" value="7" />
1843 <param name="color" value="#00b0f0" /> 1937 <param name="color" value="#00b0f0" />
1844 <section name="reading_bw_conditional"> 1938 <section name="reading_bw_conditional">
1845 <param name="number_of_bins" value="2000"/> 1939 <param name="number_of_bins" value="2000"/>
1846 </section> 1940 </section>
1851 <param name="track_file_style_selector" value="bigwig_track_option" /> 1945 <param name="track_file_style_selector" value="bigwig_track_option" />
1852 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 1946 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
1853 <param name="title" value="" /> 1947 <param name="title" value="" />
1854 <param name="color" value="#ff0000" /> 1948 <param name="color" value="#ff0000" />
1855 <param name="alpha" value="0.5" /> 1949 <param name="alpha" value="0.5" />
1856 <param name="summary_method" value="max" />
1857 <section name="reading_bw_conditional"> 1950 <section name="reading_bw_conditional">
1951 <param name="summary_method" value="max" />
1858 <param name="number_of_bins" value="300"/> 1952 <param name="number_of_bins" value="300"/>
1859 </section> 1953 </section>
1860 <param name="overlay_select" value="share-y"/> 1954 <param name="overlay_select" value="share-y"/>
1861 </conditional> 1955 </conditional>
1862 </repeat> 1956 </repeat>
1865 <param name="track_file_style_selector" value="xaxis_option" /> 1959 <param name="track_file_style_selector" value="xaxis_option" />
1866 <param name="xaxis_where" value="bottom" /> 1960 <param name="xaxis_where" value="bottom" />
1867 </conditional> 1961 </conditional>
1868 </repeat> 1962 </repeat>
1869 <param name="image_file_format" value="png" /> 1963 <param name="image_file_format" value="png" />
1870 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="100" /> 1964 <output name="outFileName" file="test_alpha.png" ftype="png" compare="image_diff" />
1871 </test> 1965 </test>
1872 <!--test 5--> 1966 <!--test 5-->
1873 <test> 1967 <test>
1874 <param name="region" value="X:3000000-3300000"/> 1968 <param name="region" value="X:3000000-3300000"/>
1875 <repeat name="tracks"> 1969 <repeat name="tracks">
1879 </conditional> 1973 </conditional>
1880 </repeat> 1974 </repeat>
1881 <repeat name="tracks"> 1975 <repeat name="tracks">
1882 <conditional name="track_file_style_conditional"> 1976 <conditional name="track_file_style_conditional">
1883 <param name="track_file_style_selector" value="gene_track_option" /> 1977 <param name="track_file_style_selector" value="gene_track_option" />
1884 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> 1978 <conditional name="bed_gtf">
1979 <param name="input_bed_or_gtf" value="gtf"/>
1980 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
1981 </conditional>
1885 <param name="title" value="test" /> 1982 <param name="title" value="test" />
1886 <param name="height_bed" value="10" /> 1983 <param name="height_bed" value="10" />
1887 <param name="color" value="#000000" /> 1984 <conditional name="color_bed">
1888 <conditional name="bed_style"> 1985 <param name="color" value="#000000" />
1889 <param name="bed_style_select" value="UCSC"/> 1986 </conditional>
1987 <conditional name="display_cond">
1988 <conditional name="bed_style">
1989 <param name="bed_style_select" value="UCSC"/>
1990 </conditional>
1890 </conditional> 1991 </conditional>
1891 <param name="spacer_height" value="1"/> 1992 <param name="spacer_height" value="1"/>
1892 </conditional> 1993 </conditional>
1893 </repeat> 1994 </repeat>
1894 <repeat name="tracks"> 1995 <repeat name="tracks">
1895 <conditional name="track_file_style_conditional"> 1996 <conditional name="track_file_style_conditional">
1896 <param name="track_file_style_selector" value="gene_track_option" /> 1997 <param name="track_file_style_selector" value="gene_track_option" />
1897 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> 1998 <conditional name="bed_gtf">
1999 <param name="input_bed_or_gtf" value="bed"/>
2000 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
2001 </conditional>
1898 <param name="title" value="test" /> 2002 <param name="title" value="test" />
1899 <param name="height_bed" value="10" /> 2003 <param name="height_bed" value="10" />
1900 <param name="color" value="#000000" /> 2004 <conditional name="color_bed">
1901 <conditional name="bed_style"> 2005 <param name="color" value="#000000" />
1902 <param name="bed_style_select" value="UCSC"/> 2006 </conditional>
2007 <conditional name="display_cond">
2008 <conditional name="bed_style">
2009 <param name="bed_style_select" value="UCSC"/>
2010 </conditional>
1903 </conditional> 2011 </conditional>
1904 <param name="spacer_height" value="1"/> 2012 <param name="spacer_height" value="1"/>
1905 </conditional> 2013 </conditional>
1906 </repeat> 2014 </repeat>
1907 <param name="image_file_format" value="png" /> 2015 <param name="image_file_format" value="png" />
1908 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="100" /> 2016 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="image_diff" />
1909 </test> 2017 </test>
1910 <!--test 6--> 2018 <!--test 6-->
1911 <test> 2019 <test>
1912 <param name="region" value="X:2760000-2802000"/> 2020 <param name="region" value="X:2760000-2802000"/>
1913 <repeat name="tracks"> 2021 <repeat name="tracks">
1976 <param name="track_file_style_selector" value="xaxis_option" /> 2084 <param name="track_file_style_selector" value="xaxis_option" />
1977 <param name="xaxis_where" value="bottom" /> 2085 <param name="xaxis_where" value="bottom" />
1978 </conditional> 2086 </conditional>
1979 </repeat> 2087 </repeat>
1980 <param name="image_file_format" value="png" /> 2088 <param name="image_file_format" value="png" />
1981 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="100" /> 2089 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="image_diff" />
1982 </test> 2090 </test>
1983 <!--test 7--> 2091 <!--test 7-->
1984 <test> 2092 <test>
1985 <param name="region" value="chrX:3300000-3500000"/> 2093 <param name="region" value="chrX:3300000-3500000"/>
1986 <repeat name="tracks"> 2094 <repeat name="tracks">
1990 </conditional> 2098 </conditional>
1991 </repeat> 2099 </repeat>
1992 <repeat name="tracks"> 2100 <repeat name="tracks">
1993 <conditional name="track_file_style_conditional"> 2101 <conditional name="track_file_style_conditional">
1994 <param name="track_file_style_selector" value="gene_track_option" /> 2102 <param name="track_file_style_selector" value="gene_track_option" />
1995 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> 2103 <conditional name="bed_gtf">
2104 <param name="input_bed_or_gtf" value="gtf"/>
2105 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
2106 </conditional>
1996 <param name="title" value="gtf default" /> 2107 <param name="title" value="gtf default" />
1997 <param name="height_bed" value="10" /> 2108 <param name="height_bed" value="10" />
1998 </conditional> 2109 </conditional>
1999 </repeat> 2110 </repeat>
2000 <repeat name="tracks"> 2111 <repeat name="tracks">
2001 <conditional name="track_file_style_conditional"> 2112 <conditional name="track_file_style_conditional">
2002 <param name="track_file_style_selector" value="gene_track_option" /> 2113 <param name="track_file_style_selector" value="gene_track_option" />
2003 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> 2114 <conditional name="bed_gtf">
2115 <param name="input_bed_or_gtf" value="gtf"/>
2116 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
2117 <param name="prefered_name" value="gene_name"/>
2118 <conditional name="merge_transcripts">
2119 <param name="merge_transcripts_select" value="true"/>
2120 <param name="merge_overlapping_exons" value="false"/>
2121 </conditional>
2122 </conditional>
2004 <param name="title" value="gtf merge transcripts, use gene_name, red 0.75 UTR" /> 2123 <param name="title" value="gtf merge transcripts, use gene_name, red 0.75 UTR" />
2005 <param name="height_bed" value="10" /> 2124 <param name="height_bed" value="10" />
2006 <conditional name="bed_style"> 2125 <conditional name="display_cond">
2007 <section name="bed_advanced"> 2126 <conditional name="bed_style">
2008 <param name="height_utr" value="0.75"/> 2127 <section name="bed_advanced">
2009 <conditional name="color_utr"> 2128 <param name="height_utr" value="0.75"/>
2010 <param name="color_utr_select" value="manually"/> 2129 <conditional name="color_utr">
2011 <param name="color" value="#ff0000"/> 2130 <param name="color_utr_select" value="manually"/>
2012 </conditional> 2131 <param name="color" value="#ff0000"/>
2013 <section name ="gtf">
2014 <param name="prefered_name" value="gene_name"/>
2015 <conditional name="merge_transcripts">
2016 <param name="merge_transcripts_select" value="true"/>
2017 <param name="merge_overlapping_exons" value="false"/>
2018 </conditional> 2132 </conditional>
2019 </section> 2133 </section>
2020 </section> 2134 </conditional>
2021 </conditional> 2135 </conditional>
2022 </conditional> 2136 </conditional>
2023 </repeat> 2137 </repeat>
2024 <repeat name="tracks"> 2138 <repeat name="tracks">
2025 <conditional name="track_file_style_conditional"> 2139 <conditional name="track_file_style_conditional">
2026 <param name="track_file_style_selector" value="gene_track_option" /> 2140 <param name="track_file_style_selector" value="gene_track_option" />
2027 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> 2141 <conditional name="bed_gtf">
2142 <param name="input_bed_or_gtf" value="gtf"/>
2143 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
2144 <param name="prefered_name" value="gene_name"/>
2145 <conditional name="merge_transcripts">
2146 <param name="merge_transcripts_select" value="true"/>
2147 <param name="merge_overlapping_exons" value="true"/>
2148 </conditional>
2149 </conditional>
2028 <param name="title" value="same but merge overlapping exons" /> 2150 <param name="title" value="same but merge overlapping exons" />
2029 <param name="height_bed" value="10" /> 2151 <param name="height_bed" value="10" />
2030 <conditional name="bed_style"> 2152 <conditional name="display_cond">
2031 <section name="bed_advanced"> 2153 <conditional name="bed_style">
2032 <param name="height_utr" value="0.75"/> 2154 <section name="bed_advanced">
2033 <conditional name="color_utr"> 2155 <param name="height_utr" value="0.75"/>
2034 <param name="color_utr_select" value="manually"/> 2156 <conditional name="color_utr">
2035 <param name="color" value="#ff0000"/> 2157 <param name="color_utr_select" value="manually"/>
2036 </conditional> 2158 <param name="color" value="#ff0000"/>
2037 <section name ="gtf">
2038 <param name="prefered_name" value="gene_name"/>
2039 <conditional name="merge_transcripts">
2040 <param name="merge_transcripts_select" value="true"/>
2041 <param name="merge_overlapping_exons" value="true"/>
2042 </conditional> 2159 </conditional>
2043 </section> 2160 </section>
2044 </section> 2161 </conditional>
2045 </conditional> 2162 </conditional>
2046 </conditional> 2163 </conditional>
2047 </repeat> 2164 </repeat>
2048 <repeat name="tracks"> 2165 <repeat name="tracks">
2049 <conditional name="track_file_style_conditional"> 2166 <conditional name="track_file_style_conditional">
2050 <param name="track_file_style_selector" value="gene_track_option" /> 2167 <param name="track_file_style_selector" value="gene_track_option" />
2051 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> 2168 <conditional name="bed_gtf">
2169 <param name="input_bed_or_gtf" value="bed"/>
2170 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
2171 </conditional>
2052 <param name="title" value="genes with scores" /> 2172 <param name="title" value="genes with scores" />
2053 <param name="height_bed" value="10" /> 2173 <param name="height_bed" value="10" />
2054 <conditional name="color_bed"> 2174 <conditional name="color_bed">
2055 <param name="color_bed_select" value="colormap" /> 2175 <param name="color_bed_select" value="colormap" />
2056 <param name="color" value="cool_r" /> 2176 <param name="color" value="cool_r" />
2058 </conditional> 2178 </conditional>
2059 </repeat> 2179 </repeat>
2060 <repeat name="tracks"> 2180 <repeat name="tracks">
2061 <conditional name="track_file_style_conditional"> 2181 <conditional name="track_file_style_conditional">
2062 <param name="track_file_style_selector" value="gene_track_option" /> 2182 <param name="track_file_style_selector" value="gene_track_option" />
2063 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> 2183 <conditional name="bed_gtf">
2184 <param name="input_bed_or_gtf" value="bed"/>
2185 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
2186 </conditional>
2064 <param name="title" value="genes with utr as bed_rgb" /> 2187 <param name="title" value="genes with utr as bed_rgb" />
2065 <param name="height_bed" value="10" /> 2188 <param name="height_bed" value="10" />
2066 <conditional name="bed_style"> 2189 <conditional name="display_cond">
2067 <section name="bed_advanced"> 2190 <conditional name="bed_style">
2068 <conditional name="color_utr"> 2191 <section name="bed_advanced">
2069 <param name="color_utr_select" value="bed_rgb"/> 2192 <conditional name="color_utr">
2070 </conditional> 2193 <param name="color_utr_select" value="bed_rgb"/>
2071 </section> 2194 </conditional>
2195 </section>
2196 </conditional>
2072 </conditional> 2197 </conditional>
2073 </conditional> 2198 </conditional>
2074 </repeat> 2199 </repeat>
2075 <repeat name="tracks"> 2200 <repeat name="tracks">
2076 <conditional name="track_file_style_conditional"> 2201 <conditional name="track_file_style_conditional">
2077 <param name="track_file_style_selector" value="gene_track_option" /> 2202 <param name="track_file_style_selector" value="gene_track_option" />
2078 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> 2203 <conditional name="bed_gtf">
2204 <param name="input_bed_or_gtf" value="bed"/>
2205 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
2206 </conditional>
2079 <param name="title" value="genes with coding as bed_rgb - labels_in_margin" /> 2207 <param name="title" value="genes with coding as bed_rgb - labels_in_margin" />
2080 <param name="height_bed" value="10" /> 2208 <param name="height_bed" value="10" />
2081 <conditional name="color_bed"> 2209 <conditional name="color_bed">
2082 <param name="color_bed_select" value="bed_rgb" /> 2210 <param name="color_bed_select" value="bed_rgb" />
2083 </conditional> 2211 </conditional>
2084 <conditional name="labels"> 2212 <conditional name="display_cond">
2085 <param name="plot_labels" value="true" /> 2213 <conditional name="labels">
2086 <param name="labels_in_margin" value="true" /> 2214 <param name="plot_labels" value="true" />
2215 <param name="labels_in_margin" value="true" />
2216 </conditional>
2087 </conditional> 2217 </conditional>
2088 </conditional> 2218 </conditional>
2089 </repeat> 2219 </repeat>
2090 <repeat name="tracks"> 2220 <repeat name="tracks">
2091 <conditional name="track_file_style_conditional"> 2221 <conditional name="track_file_style_conditional">
2092 <param name="track_file_style_selector" value="gene_track_option" /> 2222 <param name="track_file_style_selector" value="gene_track_option" />
2093 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> 2223 <conditional name="bed_gtf">
2224 <param name="input_bed_or_gtf" value="bed"/>
2225 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
2226 </conditional>
2094 <param name="title" value="genes bed_rgb like - all_labels_inside" /> 2227 <param name="title" value="genes bed_rgb like - all_labels_inside" />
2095 <param name="height_bed" value="10" /> 2228 <param name="height_bed" value="10" />
2096 <conditional name="color_bed"> 2229 <conditional name="color_bed">
2097 <param name="color_bed_select" value="bed_rgb" /> 2230 <param name="color_bed_select" value="bed_rgb" />
2098 </conditional> 2231 </conditional>
2099 <conditional name="bed_style"> 2232 <conditional name="display_cond">
2100 <section name="bed_advanced"> 2233 <conditional name="bed_style">
2101 <conditional name="color_utr"> 2234 <section name="bed_advanced">
2102 <param name="color_utr_select" value="like"/> 2235 <conditional name="color_utr">
2103 </conditional> 2236 <param name="color_utr_select" value="like"/>
2104 </section> 2237 </conditional>
2105 </conditional> 2238 </section>
2106 <conditional name="labels"> 2239 </conditional>
2107 <param name="plot_labels" value="true" /> 2240 <conditional name="labels">
2108 <param name="all_labels_inside" value="true" /> 2241 <param name="plot_labels" value="true" />
2242 <param name="all_labels_inside" value="true" />
2243 </conditional>
2109 </conditional> 2244 </conditional>
2110 </conditional> 2245 </conditional>
2111 </repeat> 2246 </repeat>
2112 <param name="image_file_format" value="png" /> 2247 <param name="image_file_format" value="png" />
2113 <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="100" /> 2248 <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="image_diff" />
2114 </test> 2249 </test>
2115 <!--test 8--> 2250 <!--test 8-->
2116 <test> 2251 <test>
2117 <param name="region" value="chrX:3300000-3500000"/> 2252 <param name="region" value="chrX:3300000-3500000"/>
2118 <repeat name="tracks"> 2253 <repeat name="tracks">
2122 </conditional> 2257 </conditional>
2123 </repeat> 2258 </repeat>
2124 <repeat name="tracks"> 2259 <repeat name="tracks">
2125 <conditional name="track_file_style_conditional"> 2260 <conditional name="track_file_style_conditional">
2126 <param name="track_file_style_selector" value="gene_track_option" /> 2261 <param name="track_file_style_selector" value="gene_track_option" />
2127 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 2262 <conditional name="bed_gtf">
2128 <param name="title" value="dm3_genes.bed" /> 2263 <param name="input_bed_or_gtf" value="bed"/>
2264 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2265 </conditional>
2266 <param name="title" value="global max row max 15 labels" />
2129 <param name="height_bed" value="10" /> 2267 <param name="height_bed" value="10" />
2130 <conditional name="bed_style"> 2268 <conditional name="display_cond">
2131 <param name="bed_style_select" value="UCSC"/> 2269 <conditional name="bed_style">
2132 <section name="bed_advanced"> 2270 <param name="bed_style_select" value="UCSC"/>
2133 <param name="global_max_row" value="true" /> 2271 <section name="bed_advanced">
2134 <param name="max_labels" value="15" /> 2272 <param name="global_max_row" value="true" />
2135 </section> 2273 <param name="max_labels" value="15" />
2274 </section>
2275 </conditional>
2136 </conditional> 2276 </conditional>
2137 </conditional> 2277 </conditional>
2138 </repeat> 2278 </repeat>
2139 <repeat name="tracks"> 2279 <repeat name="tracks">
2140 <conditional name="track_file_style_conditional"> 2280 <conditional name="track_file_style_conditional">
2141 <param name="track_file_style_selector" value="gene_track_option" /> 2281 <param name="track_file_style_selector" value="gene_track_option" />
2142 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 2282 <conditional name="bed_gtf">
2143 <param name="title" value="genes.bed.gz" /> 2283 <param name="input_bed_or_gtf" value="bed"/>
2284 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2285 </conditional>
2286 <param name="title" value="arrow_interval 10 line_width 2 change color_arrow" />
2144 <param name="height_bed" value="10" /> 2287 <param name="height_bed" value="10" />
2145 <conditional name="bed_style"> 2288 <conditional name="display_cond">
2146 <param name="bed_style_select" value="UCSC"/> 2289 <conditional name="bed_style">
2147 <section name="bed_advanced"> 2290 <param name="bed_style_select" value="UCSC"/>
2148 <param name="arrow_interval" value="10"/> 2291 <section name="bed_advanced">
2149 <param name="line_width" value="2"/> 2292 <param name="arrow_interval" value="10"/>
2150 </section> 2293 <param name="line_width" value="2"/>
2294 <conditional name="color_arrow">
2295 <param name="color" value="#00ffff"/>
2296 </conditional>
2297 </section>
2298 </conditional>
2299 </conditional>
2300 </conditional>
2301 </repeat>
2302 <repeat name="tracks">
2303 <conditional name="track_file_style_conditional">
2304 <param name="track_file_style_selector" value="gene_track_option" />
2305 <conditional name="bed_gtf">
2306 <param name="input_bed_or_gtf" value="bed"/>
2307 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2308 </conditional>
2309 <param name="title" value="same as above but arrowhead_fraction = 0.02" />
2310 <param name="height_bed" value="10" />
2311 <conditional name="display_cond">
2312 <conditional name="bed_style">
2313 <param name="bed_style_select" value="UCSC"/>
2314 <section name="bed_advanced">
2315 <param name="arrow_interval" value="10"/>
2316 <param name="line_width" value="2"/>
2317 <conditional name="color_arrow">
2318 <param name="color" value="#00ffff"/>
2319 </conditional>
2320 <param name="arrowhead_fraction" value="0.02"/>
2321 </section>
2322 </conditional>
2151 </conditional> 2323 </conditional>
2152 </conditional> 2324 </conditional>
2153 </repeat> 2325 </repeat>
2154 <param name="image_file_format" value="png" /> 2326 <param name="image_file_format" value="png" />
2155 <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="100" /> 2327 <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="image_diff" />
2156 </test> 2328 </test>
2157 <!--test 9--> 2329 <!--test 9-->
2158 <test> 2330 <test>
2159 <param name="region" value="X:3133000-3138000"/> 2331 <param name="region" value="X:3133000-3138000"/>
2160 <repeat name="tracks"> 2332 <repeat name="tracks">
2164 </conditional> 2336 </conditional>
2165 </repeat> 2337 </repeat>
2166 <repeat name="tracks"> 2338 <repeat name="tracks">
2167 <conditional name="track_file_style_conditional"> 2339 <conditional name="track_file_style_conditional">
2168 <param name="track_file_style_selector" value="gene_track_option" /> 2340 <param name="track_file_style_selector" value="gene_track_option" />
2169 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> 2341 <conditional name="bed_gtf">
2342 <param name="input_bed_or_gtf" value="gtf"/>
2343 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
2344 </conditional>
2170 <param name="title" value="defaut arrowhead fontstyle italic" /> 2345 <param name="title" value="defaut arrowhead fontstyle italic" />
2171 <param name="height_bed" value="10" /> 2346 <param name="height_bed" value="10" />
2172 <param name="spacer_height" value="1"/> 2347 <param name="spacer_height" value="1"/>
2173 <conditional name="labels"> 2348 <conditional name="display_cond">
2174 <param name="fontstyle" value="italic"/> 2349 <conditional name="labels">
2350 <param name="fontstyle" value="italic"/>
2351 </conditional>
2175 </conditional> 2352 </conditional>
2176 </conditional> 2353 </conditional>
2177 </repeat> 2354 </repeat>
2178 <repeat name="tracks"> 2355 <repeat name="tracks">
2179 <conditional name="track_file_style_conditional"> 2356 <conditional name="track_file_style_conditional">
2180 <param name="track_file_style_selector" value="gene_track_option" /> 2357 <param name="track_file_style_selector" value="gene_track_option" />
2181 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> 2358 <conditional name="bed_gtf">
2359 <param name="input_bed_or_gtf" value="gtf"/>
2360 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
2361 </conditional>
2182 <param name="title" value="arrowhead_fraction 0.1 fontstyle oblique" /> 2362 <param name="title" value="arrowhead_fraction 0.1 fontstyle oblique" />
2183 <param name="height_bed" value="10" /> 2363 <param name="height_bed" value="10" />
2184 <param name="spacer_height" value="1"/> 2364 <param name="spacer_height" value="1"/>
2185 <conditional name="labels"> 2365 <conditional name="display_cond">
2186 <param name="fontstyle" value="oblique"/> 2366 <conditional name="labels">
2187 </conditional> 2367 <param name="fontstyle" value="oblique"/>
2188 <conditional name="bed_style"> 2368 </conditional>
2189 <param name="arrowhead_fraction" value="0.1"/> 2369 <conditional name="bed_style">
2370 <param name="arrowhead_fraction" value="0.1"/>
2371 </conditional>
2190 </conditional> 2372 </conditional>
2191 </conditional> 2373 </conditional>
2192 </repeat> 2374 </repeat>
2193 <repeat name="tracks"> 2375 <repeat name="tracks">
2194 <conditional name="track_file_style_conditional"> 2376 <conditional name="track_file_style_conditional">
2195 <param name="track_file_style_selector" value="gene_track_option" /> 2377 <param name="track_file_style_selector" value="gene_track_option" />
2196 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> 2378 <conditional name="bed_gtf">
2379 <param name="input_bed_or_gtf" value="bed"/>
2380 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
2381 </conditional>
2197 <param name="title" value="genes without orientation" /> 2382 <param name="title" value="genes without orientation" />
2198 <param name="height_bed" value="10" /> 2383 <param name="height_bed" value="10" />
2199 <conditional name="color_bed"> 2384 <conditional name="color_bed">
2200 <param name="color_bed_select" value="manually" /> 2385 <param name="color_bed_select" value="manually" />
2201 <param name="color" value="red" /> 2386 <param name="color" value="red" />
2202 </conditional> 2387 </conditional>
2203 <conditional name="bed_style"> 2388 <conditional name="display_cond">
2204 <param name="bed_style_select" value="UCSC"/> 2389 <conditional name="bed_style">
2390 <param name="bed_style_select" value="UCSC"/>
2391 </conditional>
2205 </conditional> 2392 </conditional>
2206 <param name="spacer_height" value="1"/> 2393 <param name="spacer_height" value="1"/>
2207 </conditional> 2394 </conditional>
2208 </repeat> 2395 </repeat>
2209 <repeat name="tracks"> 2396 <repeat name="tracks">
2210 <conditional name="track_file_style_conditional"> 2397 <conditional name="track_file_style_conditional">
2211 <param name="track_file_style_selector" value="gene_track_option" /> 2398 <param name="track_file_style_selector" value="gene_track_option" />
2212 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> 2399 <conditional name="bed_gtf">
2400 <param name="input_bed_or_gtf" value="gtf"/>
2401 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
2402 </conditional>
2213 <param name="title" value="arrowhead included" /> 2403 <param name="title" value="arrowhead included" />
2214 <param name="height_bed" value="10" /> 2404 <param name="height_bed" value="10" />
2215 <conditional name="color_bed"> 2405 <conditional name="color_bed">
2216 <param name="color_bed_select" value="manually" /> 2406 <param name="color_bed_select" value="manually" />
2217 <param name="color" value="red" /> 2407 <param name="color" value="red" />
2218 </conditional> 2408 </conditional>
2219 <param name="spacer_height" value="1"/> 2409 <param name="spacer_height" value="1"/>
2220 <conditional name="bed_style"> 2410 <conditional name="display_cond">
2221 <param name="arrowhead_included" value="true"/> 2411 <conditional name="bed_style">
2412 <param name="arrowhead_included" value="true"/>
2413 </conditional>
2222 </conditional> 2414 </conditional>
2223 </conditional> 2415 </conditional>
2224 </repeat> 2416 </repeat>
2225 <repeat name="tracks"> 2417 <repeat name="tracks">
2226 <conditional name="track_file_style_conditional"> 2418 <conditional name="track_file_style_conditional">
2240 <param name="color" value="blue"/> 2432 <param name="color" value="blue"/>
2241 <param name="line_style" value="solid"/> 2433 <param name="line_style" value="solid"/>
2242 </conditional> 2434 </conditional>
2243 </repeat> 2435 </repeat>
2244 <param name="image_file_format" value="png" /> 2436 <param name="image_file_format" value="png" />
2245 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="100" /> 2437 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="image_diff" />
2246 </test> 2438 </test>
2247 <!--test 10--> 2439 <!--test 10-->
2248 <test> 2440 <test>
2249 <param name="region" value="X:3340000-3380000"/> 2441 <param name="region" value="X:3340000-3380000"/>
2250 <repeat name="tracks"> 2442 <repeat name="tracks">
2254 </conditional> 2446 </conditional>
2255 </repeat> 2447 </repeat>
2256 <repeat name="tracks"> 2448 <repeat name="tracks">
2257 <conditional name="track_file_style_conditional"> 2449 <conditional name="track_file_style_conditional">
2258 <param name="track_file_style_selector" value="gene_track_option" /> 2450 <param name="track_file_style_selector" value="gene_track_option" />
2259 <param name="track_input_bed" value="domains.bed" ftype="bed" /> 2451 <conditional name="bed_gtf">
2452 <param name="input_bed_or_gtf" value="bed"/>
2453 <param name="track_input_bed" value="domains.bed" ftype="bed" />
2454 </conditional>
2260 <param name="height_bed" value="6" /> 2455 <param name="height_bed" value="6" />
2261 <conditional name="color_bed"> 2456 <conditional name="color_bed">
2262 <param name="color_bed_select" value="manually" /> 2457 <param name="color_bed_select" value="manually" />
2263 <param name="color" value="yellow" /> 2458 <param name="color" value="yellow" />
2264 </conditional> 2459 </conditional>
2265 <param name="display" value="triangles" /> 2460 <conditional name="display_cond">
2461 <param name="display" value="triangles" />
2462 <param name="line_width" value="3"/>
2463 </conditional>
2266 <param name="spacer_height" value="1"/> 2464 <param name="spacer_height" value="1"/>
2267 </conditional> 2465 </conditional>
2268 </repeat> 2466 </repeat>
2269 <repeat name="tracks"> 2467 <repeat name="tracks">
2270 <conditional name="track_file_style_conditional"> 2468 <conditional name="track_file_style_conditional">
2290 <param name="type_selector" value="line_option" /> 2488 <param name="type_selector" value="line_option" />
2291 </conditional> 2489 </conditional>
2292 </conditional> 2490 </conditional>
2293 </repeat> 2491 </repeat>
2294 <param name="image_file_format" value="png" /> 2492 <param name="image_file_format" value="png" />
2295 <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="100" /> 2493 <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="image_diff" />
2296 </test> 2494 </test>
2297 <!--test 11--> 2495 <!--test 11-->
2298 <test> 2496 <test>
2299 <param name="region" value="chrX:3250000-3400000"/> 2497 <param name="region" value="chrX:3250000-3400000"/>
2300 <repeat name="tracks"> 2498 <repeat name="tracks">
2349 <param name="summary_color" value="red"/> 2547 <param name="summary_color" value="red"/>
2350 </conditional> 2548 </conditional>
2351 </conditional> 2549 </conditional>
2352 </repeat> 2550 </repeat>
2353 <param name="image_file_format" value="png" /> 2551 <param name="image_file_format" value="png" />
2354 <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="100" /> 2552 <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="image_diff" />
2355 </test> 2553 </test>
2356 <!--test 12--> 2554 <!--test 12-->
2357 <test> 2555 <test>
2358 <param name="region" value="chrX:3000000-3300000"/> 2556 <param name="region" value="chrX:3000000-3300000"/>
2359 <repeat name="tracks"> 2557 <repeat name="tracks">
2401 <param name="max_value" value="5"/> 2599 <param name="max_value" value="5"/>
2402 <param name="invert_orientation" value="true" /> 2600 <param name="invert_orientation" value="true" />
2403 </conditional> 2601 </conditional>
2404 </repeat> 2602 </repeat>
2405 <param name="image_file_format" value="png" /> 2603 <param name="image_file_format" value="png" />
2406 <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="100" /> 2604 <output name="outFileName" file="test_link.png" ftype="png" compare="image_diff" />
2407 </test> 2605 </test>
2408 <!--test 13--> 2606 <!--test 13-->
2409 <test> 2607 <test>
2410 <param name="region" value="chrX:3000000-3300000"/> 2608 <param name="region" value="chrX:3000000-3300000"/>
2411 <repeat name="tracks"> 2609 <repeat name="tracks">
2460 <param name="compact_arcs_level" value="2" /> 2658 <param name="compact_arcs_level" value="2" />
2461 </conditional> 2659 </conditional>
2462 </conditional> 2660 </conditional>
2463 </repeat> 2661 </repeat>
2464 <param name="image_file_format" value="png" /> 2662 <param name="image_file_format" value="png" />
2465 <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="100" /> 2663 <output name="outFileName" file="test_link2.png" ftype="png" compare="image_diff" />
2466 </test> 2664 </test>
2467 <!--test 14--> 2665 <!--test 14-->
2468 <test> 2666 <test>
2469 <param name="region" value="chrX:3000000-3300000"/> 2667 <param name="region" value="chrX:3000000-3300000"/>
2470 <section name="global_args"> 2668 <section name="global_args">
2500 <param name="fontsize" value="8"/> 2698 <param name="fontsize" value="8"/>
2501 <param name="spacer_height" value="4"/> 2699 <param name="spacer_height" value="4"/>
2502 </conditional> 2700 </conditional>
2503 </repeat> 2701 </repeat>
2504 <param name="image_file_format" value="png" /> 2702 <param name="image_file_format" value="png" />
2505 <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="100" /> 2703 <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="image_diff" />
2506 </test> 2704 </test>
2507 <!--test 15--> 2705 <!--test 15-->
2508 <test> 2706 <test>
2509 <param name="region" value="chrX:3300000-3500000"/> 2707 <param name="region" value="chrX:3300000-3500000"/>
2510 <repeat name="tracks"> 2708 <repeat name="tracks">
2514 </conditional> 2712 </conditional>
2515 </repeat> 2713 </repeat>
2516 <repeat name="tracks"> 2714 <repeat name="tracks">
2517 <conditional name="track_file_style_conditional"> 2715 <conditional name="track_file_style_conditional">
2518 <param name="track_file_style_selector" value="gene_track_option" /> 2716 <param name="track_file_style_selector" value="gene_track_option" />
2519 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 2717 <conditional name="bed_gtf">
2718 <param name="input_bed_or_gtf" value="bed"/>
2719 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2720 </conditional>
2520 <param name="title" value="flybase backbone blue" /> 2721 <param name="title" value="flybase backbone blue" />
2521 <param name="height_bed" value="10" /> 2722 <param name="height_bed" value="10" />
2522 <conditional name="bed_style"> 2723 <conditional name="display_cond">
2523 <param name="bed_style_select" value="flybase"/> 2724 <conditional name="bed_style">
2524 <section name="bed_advanced"> 2725 <param name="bed_style_select" value="flybase"/>
2525 <conditional name="backbone_color_bed"> 2726 <section name="bed_advanced">
2526 <param name="backbone_color_bed_select" value="manually" /> 2727 <conditional name="backbone_color_bed">
2527 <param name="color" value="blue" /> 2728 <param name="backbone_color_bed_select" value="manually" />
2528 </conditional> 2729 <param name="color" value="blue" />
2529 </section> 2730 </conditional>
2731 </section>
2732 </conditional>
2530 </conditional> 2733 </conditional>
2531 </conditional> 2734 </conditional>
2532 </repeat> 2735 </repeat>
2533 <repeat name="tracks"> 2736 <repeat name="tracks">
2534 <conditional name="track_file_style_conditional"> 2737 <conditional name="track_file_style_conditional">
2535 <param name="track_file_style_selector" value="gene_track_option" /> 2738 <param name="track_file_style_selector" value="gene_track_option" />
2536 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 2739 <conditional name="bed_gtf">
2740 <param name="input_bed_or_gtf" value="bed"/>
2741 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2742 </conditional>
2537 <param name="title" value="UCSC backbone blue" /> 2743 <param name="title" value="UCSC backbone blue" />
2538 <param name="height_bed" value="10" /> 2744 <param name="height_bed" value="10" />
2539 <conditional name="bed_style"> 2745 <conditional name="display_cond">
2540 <param name="bed_style_select" value="UCSC"/> 2746 <conditional name="bed_style">
2541 <section name="bed_advanced"> 2747 <param name="bed_style_select" value="UCSC"/>
2542 <param name="arrow_interval" value="10"/> 2748 <section name="bed_advanced">
2543 <conditional name="backbone_color_bed"> 2749 <param name="arrow_interval" value="10"/>
2544 <param name="backbone_color_bed_select" value="manually" /> 2750 <conditional name="backbone_color_bed">
2751 <param name="backbone_color_bed_select" value="manually" />
2545 <param name="color" value="blue" /> 2752 <param name="color" value="blue" />
2546 </conditional> 2753 </conditional>
2547 </section> 2754 </section>
2755 </conditional>
2548 </conditional> 2756 </conditional>
2549 </conditional> 2757 </conditional>
2550 </repeat> 2758 </repeat>
2551 <repeat name="tracks"> 2759 <repeat name="tracks">
2552 <conditional name="track_file_style_conditional"> 2760 <conditional name="track_file_style_conditional">
2553 <param name="track_file_style_selector" value="gene_track_option" /> 2761 <param name="track_file_style_selector" value="gene_track_option" />
2554 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 2762 <conditional name="bed_gtf">
2763 <param name="input_bed_or_gtf" value="bed"/>
2764 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2765 </conditional>
2555 <param name="title" value="tssarrow" /> 2766 <param name="title" value="tssarrow" />
2556 <param name="height_bed" value="10" /> 2767 <param name="height_bed" value="10" />
2557 <conditional name="bed_style"> 2768 <conditional name="display_cond">
2558 <param name="bed_style_select" value="tssarrow"/> 2769 <conditional name="bed_style">
2770 <param name="bed_style_select" value="tssarrow"/>
2771 </conditional>
2559 </conditional> 2772 </conditional>
2560 </conditional> 2773 </conditional>
2561 </repeat> 2774 </repeat>
2562 <repeat name="tracks"> 2775 <repeat name="tracks">
2563 <conditional name="track_file_style_conditional"> 2776 <conditional name="track_file_style_conditional">
2564 <param name="track_file_style_selector" value="gene_track_option" /> 2777 <param name="track_file_style_selector" value="gene_track_option" />
2565 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 2778 <conditional name="bed_gtf">
2566 <param name="title" value="tssarrow 5kb" /> 2779 <param name="input_bed_or_gtf" value="bed"/>
2780 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2781 </conditional>
2782 <param name="title" value="tssarrow 20kb increase arrowhead" />
2567 <param name="height_bed" value="10" /> 2783 <param name="height_bed" value="10" />
2568 <conditional name="bed_style"> 2784 <conditional name="display_cond">
2569 <param name="bed_style_select" value="tssarrow"/> 2785 <conditional name="bed_style">
2570 <section name="bed_advanced"> 2786 <param name="bed_style_select" value="tssarrow"/>
2571 <param name="arrow_length" value="5000"/> 2787 <section name="bed_advanced">
2572 </section> 2788 <param name="arrow_length" value="20000"/>
2789 <param name="arrowhead_fraction" value="0.01"/>
2790 </section>
2791 </conditional>
2792 </conditional>
2793 </conditional>
2794 </repeat>
2795 <repeat name="tracks">
2796 <conditional name="track_file_style_conditional">
2797 <param name="track_file_style_selector" value="gene_track_option" />
2798 <conditional name="bed_gtf">
2799 <param name="input_bed_or_gtf" value="bed"/>
2800 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2801 </conditional>
2802 <param name="title" value="exonarrows" />
2803 <conditional name="color_bed">
2804 <param name="color_bed_select" value="manually" />
2805 <param name="color" value="red"/>
2806 </conditional>
2807 <param name="height_bed" value="10" />
2808 <conditional name="display_cond">
2809 <conditional name="bed_style">
2810 <param name="bed_style_select" value="exonarrows"/>
2811 <conditional name="border_color_bed">
2812 <param name="border_color_bed_select" value="manually"/>
2813 <param name="color" value="red"/>
2814 </conditional>
2815 <section name="bed_advanced">
2816 <param name="line_width" value="2" />
2817 <conditional name="color_utr">
2818 <param name="color_utr_select" value="manually"/>
2819 <param name="color" value="blue"/>
2820 </conditional>
2821 <conditional name="color_arrow">
2822 <param name="color" value="white"/>
2823 </conditional>
2824 </section>
2825 </conditional>
2573 </conditional> 2826 </conditional>
2574 </conditional> 2827 </conditional>
2575 </repeat> 2828 </repeat>
2576 <param name="image_file_format" value="png" /> 2829 <param name="image_file_format" value="png" />
2577 <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="100" /> 2830 <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="image_diff" />
2578 </test> 2831 </test>
2579 <!--test 16--> 2832 <!--test 16-->
2580 <test> 2833 <test>
2581 <param name="region" value="X:2700000-3100000"/> 2834 <param name="region" value="chrX:2700000-3100000"/>
2582 <section name="global_args"> 2835 <section name="global_args">
2583 <param name="decreasingXAxis" value="true"/> 2836 <param name="decreasingXAxis" value="true"/>
2584 </section> 2837 </section>
2585 <repeat name="tracks"> 2838 <repeat name="tracks">
2586 <conditional name="track_file_style_conditional"> 2839 <conditional name="track_file_style_conditional">
2587 <param name="track_file_style_selector" value="bigwig_track_option" /> 2840 <param name="track_file_style_selector" value="bigwig_track_option" />
2588 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 2841 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
2589 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" /> 2842 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig color=red alpha = 0.5 max over 300 bins)" />
2590 <param name="height_bigwig" value="7" /> 2843 <param name="height_bigwig" value="7" />
2591 <param name="color" value="#00b0f0" /> 2844 <param name="color" value="#00b0f0" />
2592 <section name="reading_bw_conditional"> 2845 <section name="reading_bw_conditional">
2593 <param name="number_of_bins" value="2000"/> 2846 <param name="number_of_bins" value="2000"/>
2594 </section> 2847 </section>
2599 <param name="track_file_style_selector" value="bigwig_track_option" /> 2852 <param name="track_file_style_selector" value="bigwig_track_option" />
2600 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 2853 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
2601 <param name="title" value="" /> 2854 <param name="title" value="" />
2602 <param name="color" value="#ff0000" /> 2855 <param name="color" value="#ff0000" />
2603 <param name="alpha" value="0.5" /> 2856 <param name="alpha" value="0.5" />
2604 <param name="summary_method" value="max" />
2605 <section name="reading_bw_conditional"> 2857 <section name="reading_bw_conditional">
2858 <param name="summary_method" value="max" />
2606 <param name="number_of_bins" value="300"/> 2859 <param name="number_of_bins" value="300"/>
2607 </section> 2860 </section>
2608 <param name="overlay_select" value="share-y"/> 2861 <param name="overlay_select" value="share-y"/>
2609 </conditional> 2862 </conditional>
2610 </repeat> 2863 </repeat>
2613 <param name="track_file_style_selector" value="xaxis_option" /> 2866 <param name="track_file_style_selector" value="xaxis_option" />
2614 <param name="xaxis_where" value="bottom" /> 2867 <param name="xaxis_where" value="bottom" />
2615 </conditional> 2868 </conditional>
2616 </repeat> 2869 </repeat>
2617 <param name="image_file_format" value="png" /> 2870 <param name="image_file_format" value="png" />
2618 <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="sim_size" delta="1000" /> 2871 <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="image_diff" />
2619 </test> 2872 </test>
2620 <!--test 17--> 2873 <!--test 17-->
2621 <test> 2874 <test>
2622 <param name="region" value="chr2:73,800,000-75,744,000"/> 2875 <param name="region" value="chr2:73,800,000-75,744,000"/>
2623 <repeat name="tracks"> 2876 <repeat name="tracks">
2736 <param name="track_file_style_selector" value="xaxis_option" /> 2989 <param name="track_file_style_selector" value="xaxis_option" />
2737 <param name="xaxis_where" value="bottom" /> 2990 <param name="xaxis_where" value="bottom" />
2738 </conditional> 2991 </conditional>
2739 </repeat> 2992 </repeat>
2740 <param name="image_file_format" value="png" /> 2993 <param name="image_file_format" value="png" />
2741 <output name="outFileName" file="test_log.png" ftype="png" compare="sim_size" delta="100" /> 2994 <output name="outFileName" file="test_log.png" ftype="png" compare="image_diff" />
2742 </test> 2995 </test>
2743 <!--test 18--> 2996 <!--test 18-->
2744 <test> 2997 <test>
2745 <param name="region" value="chrX:2700000-3100000"/> 2998 <param name="region" value="chrX:2700000-3100000"/>
2746 <repeat name="tracks"> 2999 <repeat name="tracks">
2814 <param name="min_value" value="-30" /> 3067 <param name="min_value" value="-30" />
2815 <param name="max_value" value="30" /> 3068 <param name="max_value" value="30" />
2816 </conditional> 3069 </conditional>
2817 </repeat> 3070 </repeat>
2818 <param name="image_file_format" value="png" /> 3071 <param name="image_file_format" value="png" />
2819 <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="100" /> 3072 <output name="outFileName" file="test_operation.png" ftype="png" compare="image_diff" />
2820 </test> 3073 </test>
2821 <!--test 19--> 3074 <!--test 19-->
2822 <test> 3075 <test>
2823 <param name="region" value="chr2:73,800,000-75,744,000"/> 3076 <param name="region" value="chr2:73,800,000-75,744,000"/>
2824 <repeat name="tracks"> 3077 <repeat name="tracks">
2945 <param name="track_file_style_selector" value="xaxis_option" /> 3198 <param name="track_file_style_selector" value="xaxis_option" />
2946 <param name="xaxis_where" value="bottom" /> 3199 <param name="xaxis_where" value="bottom" />
2947 </conditional> 3200 </conditional>
2948 </repeat> 3201 </repeat>
2949 <param name="image_file_format" value="png" /> 3202 <param name="image_file_format" value="png" />
2950 <output name="outFileName" file="test_log_grid.png" ftype="png" compare="sim_size" delta="100" /> 3203 <output name="outFileName" file="test_log_grid.png" ftype="png" compare="image_diff" />
2951 </test> 3204 </test>
2952 <!--test 20--> 3205 <!--test 20-->
2953 <test> 3206 <test>
2954 <param name="region" value="chrX:3000000-3300000"/> 3207 <param name="region" value="chrX:3000000-3300000"/>
2955 <repeat name="tracks"> 3208 <repeat name="tracks">
2966 </repeat> 3219 </repeat>
2967 <repeat name="tracks"> 3220 <repeat name="tracks">
2968 <conditional name="track_file_style_conditional"> 3221 <conditional name="track_file_style_conditional">
2969 <param name="track_file_style_selector" value="hic_matrix_option" /> 3222 <param name="track_file_style_selector" value="hic_matrix_option" />
2970 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> 3223 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
2971 <param name="title" value="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" /> 3224 <param name="title" value="depth = 300000 transform = log1p min_value = 5 (next track: overlay_previous = share-y links_type = loops)" />
2972 <param name="depth" value="300000" /> 3225 <param name="depth" value="300000" />
2973 <param name="transform" value="log1p" /> 3226 <param name="transform" value="log1p" />
2974 <param name="min_value" value="5" /> 3227 <param name="min_value" value="5" />
2975 <param name="show_masked_bins" value="false" /> 3228 <param name="show_masked_bins" value="false" />
2976 </conditional> 3229 </conditional>
3010 </repeat> 3263 </repeat>
3011 <repeat name="tracks"> 3264 <repeat name="tracks">
3012 <conditional name="track_file_style_conditional"> 3265 <conditional name="track_file_style_conditional">
3013 <param name="track_file_style_selector" value="hic_matrix_option" /> 3266 <param name="track_file_style_selector" value="hic_matrix_option" />
3014 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> 3267 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
3015 <param name="title" value="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" /> 3268 <param name="title" value="depth = 300000 transform = log1p min_value = 5 (next track: overlay_previous = share-y links_type = loops)" />
3016 <param name="depth" value="300000" /> 3269 <param name="depth" value="300000" />
3017 <param name="transform" value="log1p" /> 3270 <param name="transform" value="log1p" />
3018 <param name="min_value" value="5" /> 3271 <param name="min_value" value="5" />
3019 <param name="show_masked_bins" value="false" /> 3272 <param name="show_masked_bins" value="false" />
3020 </conditional> 3273 </conditional>
3055 <param name="track_input_bed_single" value="tad_classification.bed" ftype="bed" /> 3308 <param name="track_input_bed_single" value="tad_classification.bed" ftype="bed" />
3056 <param name="line_width" value="3" /> 3309 <param name="line_width" value="3" />
3057 </conditional> 3310 </conditional>
3058 </repeat> 3311 </repeat>
3059 <param name="image_file_format" value="png" /> 3312 <param name="image_file_format" value="png" />
3060 <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="1200" /> 3313 <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="image_diff" />
3061 </test> 3314 </test>
3062 <!--test 21--> 3315 <!--test 21-->
3063 <test> 3316 <test>
3064 <param name="region" value="X:3000000-3600000"/> 3317 <param name="region" value="X:3000000-3600000"/>
3065 <section name="global_args"> 3318 <section name="global_args">
3133 <param name="track_file_style_selector" value="xaxis_option" /> 3386 <param name="track_file_style_selector" value="xaxis_option" />
3134 <param name="xaxis_where" value="bottom" /> 3387 <param name="xaxis_where" value="bottom" />
3135 </conditional> 3388 </conditional>
3136 </repeat> 3389 </repeat>
3137 <param name="image_file_format" value="png" /> 3390 <param name="image_file_format" value="png" />
3138 <output name="outFileName" file="master_scale_bar_startend.png" ftype="png" compare="sim_size" delta="100" /> 3391 <output name="outFileName" file="master_scale_bar_startend.png" ftype="png" compare="image_diff" />
3139 </test> 3392 </test>
3140 <!--test 22--> 3393 <!--test 22-->
3141 <test> 3394 <test>
3142 <param name="region" value="chrM:10-30"/> 3395 <param name="region" value="chrM:10-30"/>
3143 <repeat name="tracks"> 3396 <repeat name="tracks">
3170 </conditional> 3423 </conditional>
3171 <param name="height" value="5"/> 3424 <param name="height" value="5"/>
3172 </conditional> 3425 </conditional>
3173 </repeat> 3426 </repeat>
3174 <param name="image_file_format" value="png" /> 3427 <param name="image_file_format" value="png" />
3175 <output name="outFileName" file="master_fasta.png" ftype="png" compare="sim_size" delta="100" /> 3428 <output name="outFileName" file="master_fasta.png" ftype="png" compare="image_diff" />
3176 </test> 3429 </test>
3177 <!--test 23--> 3430 <!--test 23-->
3178 <test> 3431 <test>
3179 <param name="region" value="chrX:3000000-3300000"/> 3432 <param name="region" value="chrX:3000000-3300000"/>
3180 <repeat name="tracks"> 3433 <repeat name="tracks">
3264 <param name="transform" value="no" /> 3517 <param name="transform" value="no" />
3265 <param name="boundaries_file" value="tad_classification.bed" /> 3518 <param name="boundaries_file" value="tad_classification.bed" />
3266 </conditional> 3519 </conditional>
3267 </repeat> 3520 </repeat>
3268 <param name="image_file_format" value="png" /> 3521 <param name="image_file_format" value="png" />
3269 <output name="outFileName" file="test_matrix_square.png" ftype="png" compare="sim_size" delta="1200" /> 3522 <output name="outFileName" file="test_matrix_square.png" ftype="png" compare="image_diff" />
3270 </test> 3523 </test>
3271 <!--test 24--> 3524 <!--test 24-->
3272 <test> 3525 <test>
3273 <param name="region" value="2:34704975-34705208"/> 3526 <param name="region" value="2:34704975-34705208"/>
3274 <repeat name="tracks"> 3527 <repeat name="tracks">
3311 <param name="title" value="species_order = hg19, species_labels = Human, species_order_only = true" /> 3564 <param name="title" value="species_order = hg19, species_labels = Human, species_order_only = true" />
3312 <param name="height" value="3"/> 3565 <param name="height" value="3"/>
3313 <param name="species_order" value="hg19"/> 3566 <param name="species_order" value="hg19"/>
3314 <param name="species_labels" value="Human"/> 3567 <param name="species_labels" value="Human"/>
3315 <param name="species_order_only" value="true"/> 3568 <param name="species_order_only" value="true"/>
3316 <param name="spacer_height" value="1"/>
3317 </conditional> 3569 </conditional>
3318 </repeat> 3570 </repeat>
3319 <repeat name="tracks"> 3571 <repeat name="tracks">
3320 <conditional name="track_file_style_conditional"> 3572 <conditional name="track_file_style_conditional">
3321 <param name="track_file_style_selector" value="xaxis_option" /> 3573 <param name="track_file_style_selector" value="xaxis_option" />
3322 <param name="xaxis_where" value="bottom" /> 3574 <param name="xaxis_where" value="bottom" />
3323 </conditional> 3575 </conditional>
3324 </repeat> 3576 </repeat>
3325 <param name="image_file_format" value="png" /> 3577 <param name="image_file_format" value="png" />
3326 <output name="outFileName" file="test_maf.png" ftype="png" compare="sim_size" delta="1200" /> 3578 <output name="outFileName" file="test_maf.png" ftype="png" compare="image_diff" />
3327 </test> 3579 </test>
3328 <!--test 25--> 3580 <!--test 25-->
3329 <test> 3581 <test>
3330 <param name="region" value="chr2:73,800,000-75,744,000"/> 3582 <param name="region" value="chr2:73,800,000-75,744,000"/>
3331 <repeat name="tracks"> 3583 <repeat name="tracks">
3350 <param name="track_file_style_selector" value="xaxis_option" /> 3602 <param name="track_file_style_selector" value="xaxis_option" />
3351 <param name="xaxis_where" value="bottom" /> 3603 <param name="xaxis_where" value="bottom" />
3352 </conditional> 3604 </conditional>
3353 </repeat> 3605 </repeat>
3354 <param name="image_file_format" value="png" /> 3606 <param name="image_file_format" value="png" />
3355 <output name="outFileName" file="test_vhighlight.png" ftype="png" compare="sim_size" delta="1200" /> 3607 <output name="outFileName" file="test_vhighlight.png" ftype="png" compare="image_diff" />
3608 </test>
3609 <!--test 26-->
3610 <test>
3611 <param name="region" value="chrX:3060000-3080000"/>
3612 <repeat name="tracks">
3613 <conditional name="track_file_style_conditional">
3614 <param name="track_file_style_selector" value="gene_track_option" />
3615 <conditional name="bed_gtf">
3616 <param name="input_bed_or_gtf" value="bed"/>
3617 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
3618 </conditional>
3619 <param name="title" value="default inversions overlayed with empty deletion" />
3620 <param name="height_bed" value="2" />
3621 <conditional name="display_cond">
3622 <param name="display" value = "inversions"/>
3623 </conditional>
3624 </conditional>
3625 </repeat>
3626 <repeat name="tracks">
3627 <conditional name="track_file_style_conditional">
3628 <param name="track_file_style_selector" value="gene_track_option" />
3629 <conditional name="bed_gtf">
3630 <param name="input_bed_or_gtf" value="bed"/>
3631 <param name="track_input_bed" value="empty.bed" ftype="bed" />
3632 </conditional>
3633 <param name="title" value="" />
3634 <conditional name="display_cond">
3635 <param name="display" value = "deletions"/>
3636 </conditional>
3637 <param name="overlay_select" value="share-y" />
3638 <param name="spacer_height" value="1" />
3639 </conditional>
3640 </repeat>
3641 <repeat name="tracks">
3642 <conditional name="track_file_style_conditional">
3643 <param name="track_file_style_selector" value="gene_track_option" />
3644 <conditional name="bed_gtf">
3645 <param name="input_bed_or_gtf" value="bed"/>
3646 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
3647 </conditional>
3648 <param name="title" value="inversions rgb no labels" />
3649 <param name="height_bed" value="2" />
3650 <conditional name="color_bed">
3651 <param name="color_bed_select" value="bed_rgb" />
3652 </conditional>
3653 <conditional name="display_cond">
3654 <param name="display" value = "inversions"/>
3655 <conditional name="labels">
3656 <param name="plot_labels" value = "false"/>
3657 </conditional>
3658 </conditional>
3659 </conditional>
3660 </repeat>
3661 <repeat name="tracks">
3662 <conditional name="track_file_style_conditional">
3663 <param name="track_file_style_selector" value="gene_track_option" />
3664 <conditional name="bed_gtf">
3665 <param name="input_bed_or_gtf" value="bed"/>
3666 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
3667 </conditional>
3668 <param name="title" value="deletions colormap no labels" />
3669 <param name="height_bed" value="2" />
3670 <conditional name="color_bed">
3671 <param name="color_bed_select" value="colormap" />
3672 <param name="color" value="viridis"/>
3673 </conditional>
3674 <conditional name="display_cond">
3675 <param name="display" value = "deletions"/>
3676 <conditional name="labels">
3677 <param name="plot_labels" value = "false"/>
3678 </conditional>
3679 </conditional>
3680 <param name="spacer_height" value="1" />
3681 </conditional>
3682 </repeat>
3683 <repeat name="tracks">
3684 <conditional name="track_file_style_conditional">
3685 <param name="track_file_style_selector" value="gene_track_option" />
3686 <conditional name="bed_gtf">
3687 <param name="input_bed_or_gtf" value="bed"/>
3688 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
3689 </conditional>
3690 <param name="title" value="default deletions" />
3691 <param name="height_bed" value="2" />
3692 <conditional name="display_cond">
3693 <param name="display" value = "deletions"/>
3694 </conditional>
3695 </conditional>
3696 </repeat>
3697 <repeat name="tracks">
3698 <conditional name="track_file_style_conditional">
3699 <param name="track_file_style_selector" value="gene_track_option" />
3700 <conditional name="bed_gtf">
3701 <param name="input_bed_or_gtf" value="bed"/>
3702 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
3703 </conditional>
3704 <param name="title" value="squares border_color orange line_width 3" />
3705 <param name="height_bed" value="10" />
3706 <conditional name="display_cond">
3707 <param name="display" value="squares"/>
3708 <param name="line_width" value="3"/>
3709 <conditional name="border_color_bed">
3710 <param name="border_color_bed_select" value="manually"/>
3711 <param name="color" value="orange"/>
3712 </conditional>
3713 </conditional>
3714 </conditional>
3715 </repeat>
3716 <param name="image_file_format" value="png" />
3717 <output name="outFileName" file="test_bed_invdelsquares.png" ftype="png" compare="image_diff" />
3356 </test> 3718 </test>
3357 </tests> 3719 </tests>
3358 <help><![CDATA[ 3720 <help><![CDATA[
3359 3721
3360 pyGenomeTracks 3722 pyGenomeTracks