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comparison macros_conffiles.xml @ 2:890ef899a3d7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
author iuc
date Tue, 17 Sep 2019 16:54:24 -0400
parents 8464186c8503
children 6d45ebe16927
comparison
equal deleted inserted replaced
1:95664f8de269 2:890ef899a3d7
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="configfile_circos_conf"> 3 <xml name="configfile_circos_conf">
4 <configfile name="circos_conf"><![CDATA[ 4 <configfile name="circos_conf"><![CDATA[
5 @UTILS@
6
5 <<include colors_fonts_patterns.conf>> 7 <<include colors_fonts_patterns.conf>>
6 <<include housekeeping.conf>> 8 <<include housekeeping.conf>>
9
10 <colors>
11 <<include karyotype-colors.conf>>
12
13 #for $hi, $data in enumerate($sec_tdd.data):
14 #set plot_type = str($data.plot_format.plot_format_select)
15 #if str($plot_type) == 'tile':
16 color-tile-$hi = $circosColor($data.plot_format.format_specific.fill_color)
17 #end if
18 #end for
19 </colors>
20
7 karyotype = karyotype.txt 21 karyotype = karyotype.txt
22 #if str($ideogram.units) == 'bases':
23 chromosomes_units = 1
24 #else if str($ideogram.units) == 'kb':
25 chromosomes_units = 1000
26 #else if str($ideogram.units) == 'mb':
27 chromosomes_units = 1000000
28 #else:
29 chromosomes_units = 1000000000
30 #end if
31
32 #if $ideogram.limit_chromosomes:
33 chromosomes = $ideogram.limit_chromosomes
34 chromosomes_order = $chromosomesToOrder($ideogram.limit_chromosomes)
35 chromosomes_display_default = no
36 #end if
37
38 #if $ideogram.chromosomes_reverse:
39 chromosomes_reverse = $ideogram.chromosomes_reverse
40 #end if
8 41
9 <image> 42 <image>
10 <<include etc/image.conf>> 43 # Transcluded from etc/image.generic.conf
44 dir = .
45 file = circos.png
46 #if $outputs.png:
47 png = yes
48 #end if
49 #if $outputs.svg:
50 svg = yes
51 #end if
52 # by default angle = 0 is at 3 o'clock position
53 angle_offset = -90
54 auto_alpha_colors = yes
55 auto_alpha_steps = 5
56 #if str($plot_options.background.background_select) == 'transparent':
57 background = transparent
58 #else
59 background = $circosColor($plot_options.background.background_color)
60 #end if
61 radius* = ${plot_options.radius}p
11 </image> 62 </image>
12 63
13 <<include ticks.conf>> 64 <<include ticks.conf>>
14 <<include ideogram.conf>> 65 <<include ideogram.conf>>
15 <plots> 66 <<include data.conf>>
16 <<include 2d.conf>> 67 <<include highlight.conf>>
17 </plots> 68 <<include links.conf>>
18 <links>
19 <<include links.conf>>
20 </links>
21 69
22 ]]></configfile> 70 ]]></configfile>
23 </xml> 71 </xml>
24 <xml name="configfile_ticks_conf"> 72 <xml name="configfile_ticks_conf">
25 <configfile name="ticks_conf"><![CDATA[ 73 <configfile name="ticks_conf"><![CDATA[
74 @UTILS@
75
26 show_ticks = ${ticks.show_ticks} 76 show_ticks = ${ticks.show_ticks}
27 show_tick_labels = yes 77 show_tick_labels = yes
28 78
29 #def circosColor($value)
30 #set $value = str($value)
31 #set $r = int($value[1:3], 16)
32 #set $g = int($value[3:5], 16)
33 #set $b = int($value[5:], 16)
34 $r, $g, $b
35 #end def
36
37 79
38 <ticks> 80 <ticks>
39 radius = ${ticks.radius}r 81 radius = ${ticks.radius}r
40 color = $circosColor($ticks.color) 82 color = black
83 skip_first_label = ${ticks.skip_first_label}
84 skip_last_label = ${ticks.skip_last_label}
41 thickness = 2p 85 thickness = 2p
42 multiplier = ${ticks.multiplier} 86
87 # Multiplier controls how 'u' behaves when used in numbers.
88 #if str($ideogram.units) == 'bases':
89 multiplier = 1
90 #else if str($ideogram.units) == 'kb':
91 multiplier = 1e-3
92 #else if str($ideogram.units) == 'mb':
93 multiplier = 1e-6
94 #else if str($ideogram.units) == 'gb':
95 multiplier = 1e-9
96 #end if
43 97
44 #for $tick_group in $ticks.tick_group: 98 #for $tick_group in $ticks.tick_group:
45 <tick> 99 <tick>
46 spacing = ${tick_group.spacing} 100 spacing = ${tick_group.spacing}
47 size = ${tick_group.size}p 101 size = ${tick_group.size}p
48 show_label = ${tick_group.show_tick_labels} 102 show_label = ${tick_group.ticks.show_tick_labels}
49 label_size = ${tick_group.label_size}p 103 color = $circosColor($tick_group.color)
50 label_offset = ${tick_group.label_offset}p 104
51 format = ${tick_group.format} kb 105 #if str($tick_group.ticks.show_tick_labels) == 'yes':
52 ## TODO: figure out automated tick labels 106 label_size = ${tick_group.ticks.label_size}p
53 ##if ${ticks.multiplier} * ${tick_group.spacing} 107 label_offset = ${tick_group.ticks.label_offset}p
108 #if $tick_group.ticks.format_ext:
109 #if str($ideogram.units) == 'bases':
110 format = ${tick_group.ticks.format}
111 #else if str($ideogram.units) == 'kb':
112 format = ${tick_group.ticks.format} Kb
113 #else if str($ideogram.units) == 'mb':
114 format = ${tick_group.ticks.format} Mb
115 #else if str($ideogram.units) == 'gb':
116 format = ${tick_group.ticks.format} Gb
117 #end if
118 #else
119 format = ${tick_group.ticks.format}
120 #end if
121 #end if
54 </tick> 122 </tick>
55 #end for 123 #end for
56 </ticks> 124 </ticks>
57 ]]> 125 ]]>
58 </configfile> 126 </configfile>
59 </xml> 127 </xml>
60 <xml name="configfile_ideogram_conf"> 128 <xml name="configfile_ideogram_conf">
61 <configfile name="ideogram_conf"><![CDATA[ 129 <configfile name="ideogram_conf"><![CDATA[
62 130 @UTILS@
63 <ideogram> 131 <ideogram>
64
65 <spacing> 132 <spacing>
66 ## spacing between ideograms 133 ## spacing between ideograms
67 default = ${ideogram.spacing}r 134 default = ${ideogram.spacing}r
68 </spacing> 135 </spacing>
69 136
70 # ideogram position, thickness and fill 137 # ideogram position, thickness and fill
71 radius = ${ideogram.radius}r 138 radius = ${ideogram.radius}r
72 thickness = ${ideogram.thickness}p 139 thickness = ${ideogram.thickness}p
73 fill = yes 140 fill = yes
74
75 show_label = ${ideogram.ideogram_labels.show_label} 141 show_label = ${ideogram.ideogram_labels.show_label}
76 label_radius = dims(ideogram,radius) + 0.075r 142 label_radius = dims(ideogram,radius) + ${ideogram.ideogram_labels.radius_offset}r
77 label_size = 24 143 label_size = ${ideogram.ideogram_labels.size}
78 label_parallel = ${ideogram.ideogram_labels.parallel} 144 label_parallel = ${ideogram.ideogram_labels.parallel}
79 145
146 #if $ideogram.bands.bands:
80 show_bands = yes 147 show_bands = yes
81 fill_bands = yes 148 #else
82 band_transparency = 4 149 show_bands = no
83 150 #end if
151 fill_bands = ${ideogram.bands.fill_bands}
152 #if int($ideogram.bands.band_transparency) > 0:
153 band_transparency = ${ideogram.bands.band_transparency}
154 #end if
155 band_stroke_color = $circosColor($ideogram.bands.band_stroke_color)
156 band_stroke_thickness = ${ideogram.bands.band_stroke_thickness}
84 </ideogram> 157 </ideogram>
85 ]]></configfile> 158 ]]></configfile>
86 </xml> 159 </xml>
87 <xml name="configfile_data_conf"> 160 <xml name="configfile_highlight_conf">
88 <configfile name="data_conf"><![CDATA[ 161 <configfile name="highlight_conf"><![CDATA[
89 #for $hi, $data in enumerate($sec_tdd.data): 162 @UTILS@
90 <plot> 163 <highlights>
91 #set plot_type = str($data.plot_format.plot_format_select) 164 #for $hi, $data in enumerate($sec_highlight.data):
92 #def circosColor($value) 165 <highlight>
93 #set $value = str($value) 166 file = data/highlight-${hi}.txt # ${data.data_source.element_identifier}
94 #set $r = int($value[1:3], 16) 167 r1 = ${data.r1}r
95 #set $g = int($value[3:5], 16) 168 r0 = ${data.r0}r
96 #set $b = int($value[5:], 16) 169 fill_color = $circosColor($data.fill_color)
97 $r, $g, $b
98 #end def
99
100 type = ${plot_type}
101 file = data/data-${hi}.txt
102
103 r1 = ${data.r1}r
104 r0 = ${data.r0}r
105 orientation = ${data.orientation}
106
107 #if str($plot_type) == 'histogram':
108 extend_bin = ${data.plot_format.format_specific.extend_bins}
109 fill_color = ${data.plot_format.format_specific.fill_color}
110 #else if str($plot_type) == 'heatmap':
111 color = $circosColor($data.plot_format.format_specific.fill_color)
112 scale_log_base = ${data.plot_format.format_specific.scale_log_base}
113 #else if str($plot_type) == 'line':
114 color = $circosColor($data.plot_format.format_specific.color)
115 thickness = ${data.plot_format.format_specific.thickness}
116 #else if str($plot_type) == 'scatter':
117 glyph = ${data.plot_format.format_specific.glyph}
118 glyph_size = ${data.plot_format.format_specific.glyph_size}
119 color = $circosColor($data.plot_format.format_specific.color)
120 stroke_color = $circosColor($data.plot_format.format_specific.stroke_color)
121 stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
122 #else if str($plot_type) == 'tile':
123 color = ${data.plot_format.format_specific.color}
124 stroke_color = $circosColor($data.plot_format.format_specific.color)
125 stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
126 layers = ${data.plot_format.format_specific.layers}
127 thickness = ${data.plot_format.format_specific.thickness}
128 padding = ${data.plot_format.format_specific.padding}
129
130 layers_overflow = ${data.plot_format.format_specific.overflow.overflow_behavior}
131 #if str($data.plot_format.format_specific.overflow.overflow_behavior) != "hide":
132 layers_overflow_color = $circosColor($data.plot_format.format_specific.overflow.layer_overflow_color)
133 #end if
134 #end if
135 170
136 <rules> 171 <rules>
137 #for $rule in $data.sec_rule.rules: 172 #for $rule in $data.sec_rule.rules:
138 <rule> 173 <rule>
139 #for $condition in $rule.conditions 174 #for $condition in $rule.conditions
141 condition = 1 176 condition = 1
142 #elif str($condition.application.application_select) == "on": 177 #elif str($condition.application.application_select) == "on":
143 #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ]) 178 #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ])
144 condition = $on_str 179 condition = $on_str
145 #elif str($condition.application.application_select) == "pos": 180 #elif str($condition.application.application_select) == "pos":
146 #if float($condition.application.pos_gt) != 0: 181 #if $condition.application.pos_gt:
147 condition = var(start) > $condition.application.pos_gt 182 condition = var(start) > $condition.application.pos_gt
148 #end if 183 #end if
149 184
150 #if float($condition.application.pos_lt) != 0: 185 #if $condition.application.pos_lt:
151 condition = var(start) < $condition.application.pos_lt 186 #if $condition.application.pos_lt_sub == 'yes':
187 condition = var(end) < chrlen(var(chr)) - $condition.application.pos_lt
188 #else
189 condition = var(end) < $condition.application.pos_lt
190 #end if
152 #end if 191 #end if
153 #elif str($condition.application.application_select) == "value": 192 #elif str($condition.application.application_select) == "value":
154 #if float($condition.application.pos_gt) != 0: 193 #if $condition.application.pos_gt:
155 condition = var(value) > $condition.application.pos_gt 194 condition = var(value) > $condition.application.pos_gt
156 #end if 195 #end if
157 196
158 #if float($condition.application.pos_lt) != 0: 197 #if $condition.application.pos_lt:
159 condition = var(value) < $condition.application.pos_lt 198 condition = var(value) < $condition.application.pos_lt
160 #end if 199 #end if
161 #elif str($condition.application.application_select) == "var": 200 #elif str($condition.application.application_select) == "var":
162 condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}" 201 condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}"
202 #elif str($condition.application.application_select) == "random":
203 condition = rand() < ${condition.application.value}
163 #end if 204 #end if
164 #end for 205 #end for
165 206
166 #for $action in $rule.actions: 207 #for $action in $rule.actions:
167 #if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" : 208 #if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" :
168 #set x_fill_color = $action.action.action_value 209 #set x_fill_color = $action.action.action_value
169 #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) 210 #set x_fill_color_count = int(str($x_fill_color).split('-')[1])
170 #set x_min = $x_fill_color_count if $action.action.invert else 1 211 #set x_min = $x_fill_color_count if $action.action.invert else 1
171 #set x_max = 1 if $action.action.invert else $x_fill_color_count 212 #set x_max = 1 if $action.action.invert else $x_fill_color_count
172 #set color_action = "fill_color" if str($plot_type) == 'histogram' else "color" 213 #set color_action = "fill_color" if str($plot_type) in ('histogram', 'histogram-stacked') else "color"
173 214
174 $color_action = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max}))) 215 $color_action = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max})))
216 #else
217 $action.action.action_select = $circosColor($action.action.action_value)
218 #end if
219 #end for
220 $rule.continue_flow
221 </rule>
222 #end for
223 </rules>
224 </highlight>
225 #end for
226 </highlights>
227 ]]></configfile>
228 </xml>
229
230
231 <xml name="configfile_data_conf">
232 <configfile name="data_conf"><![CDATA[
233 <plots>
234 @UTILS@
235
236 #for $hi, $data in enumerate($sec_tdd.data):
237 <plot>
238 #set plot_type = str($data.plot_format.plot_format_select)
239 file = data/data-${hi}.txt # ${data.plot_format.data_source.element_identifier}
240 r1 = ${data.r1}r
241 r0 = ${data.r0}r
242 orientation = ${data.orientation}
243 #if str($data.minmax.minmax_select) == 'yes':
244 min = ${$data.minmax.min_value}
245 max = ${$data.minmax.max_value}
246 #end if
247
248 #if str($plot_type) in ('histogram', 'histogram-stacked'):
249 type = histogram
250 extend_bin = ${data.plot_format.format_specific.extend_bins}
251 #if str($plot_type) == 'histogram':
252 fill_color = $circosColorAlpha($data.plot_format.format_specific.fill_color, $data.plot_format.format_specific.fill_color_alpha)
253 #else:
254 fill_color = $data.plot_format.format_specific.fill_color
255 #end if
256 fill_under = ${data.plot_format.format_specific.fill_under}
257 color = $circosColorAlpha($data.plot_format.format_specific.stroke_color, $data.plot_format.format_specific.stroke_color_alpha)
258 thickness = ${data.plot_format.format_specific.stroke_thickness}
259 #else if str($plot_type) == 'heatmap':
260 type = ${plot_type}
261 color = ${data.plot_format.format_specific.fill_color}
262 scale_log_base = ${data.plot_format.format_specific.scale_log_base}
263 #else if str($plot_type) == 'line':
264 type = ${plot_type}
265 color = $circosColor($data.plot_format.format_specific.stroke_color)
266 thickness = ${data.plot_format.format_specific.stroke_thickness}
267 #else if str($plot_type) == 'scatter':
268 type = ${plot_type}
269 glyph = ${data.plot_format.format_specific.glyph}
270 glyph_size = ${data.plot_format.format_specific.glyph_size}
271 # So this option is ignored, and we have added an always-on rule in the
272 # first place to override the colour. This is because this color option will
273 # only accept named colours, while you can override the colour in a rule
274 # block with an RGB colour.
275 #
276 # Additionally it is named "color" in a scatter track whilst in the rule
277 # you must override it with "fill_color"
278 color = $circosColor($data.plot_format.format_specific.fill_color)
279 stroke_color = $circosColor($data.plot_format.format_specific.stroke_color)
280 stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
281 #else if str($plot_type) == 'tile':
282 type = ${plot_type}
283 color = color-tile-$hi
284 stroke_color = $circosColor($data.plot_format.format_specific.stroke_color)
285 stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
286 layers = ${data.plot_format.format_specific.layers}
287 thickness = ${data.plot_format.format_specific.thickness}
288 padding = ${data.plot_format.format_specific.padding}
289 margin = ${data.plot_format.format_specific.margin}u
290 layers_overflow = ${data.plot_format.format_specific.overflow.overflow_behavior}
291 #if str($data.plot_format.format_specific.overflow.overflow_behavior) != "hide":
292 layers_overflow_color = $circosColor($data.plot_format.format_specific.overflow.layer_overflow_color)
293 #end if
294 #else if str($plot_type) == 'text':
295 type = ${plot_type}
296 #if $data.plot_format.format_specific.link.show_link == "yes":
297 show_links = yes
298 link_dims = ${data.plot_format.format_specific.link.link_dims}
299 link_thickness = ${data.plot_format.format_specific.link.link_thickness}p
300 link_color = ${data.plot_format.format_specific.link.link_color}
301 #else
302 show_links = no
303 #end if
304
305 #if $data.plot_format.format_specific.snuggle.label_snuggle == "yes":
306 label_snuggle = ${data.plot_format.format_specific.snuggle.label_snuggle}
307 max_snuggle_distance = ${data.plot_format.format_specific.snuggle.max_snuggle_distance}r
308 snuggle_sampling = ${data.plot_format.format_specific.snuggle.snuggle_sampling}
309 snuggle_tolerance = ${data.plot_format.format_specific.snuggle.snuggle_tolerance}r
310 snuggle_link_overlap_test = ${data.plot_format.format_specific.snuggle.snuggle_link_overlap_test}
311 snuggle_link_overlap_tolerance = ${data.plot_format.format_specific.snuggle.snuggle_link_overlap_tolerance}p
312 snuggle_refine = ${data.plot_format.format_specific.snuggle.snuggle_refine}
313 #end if
314
315 label_size = ${data.plot_format.format_specific.label_size}p
316 label_font = condensed
317 padding = 0p
318 rpadding = 0p
319 #end if
320
321 <rules>
322 #if str($plot_type) == 'scatter':
323 <rule>
324 # Workaround for above commented colour bug.
325 condition = 1
326 fill_color = $circosColor($data.plot_format.format_specific.fill_color)
327 flow = continue
328 </rule>
329 #end if
330 #for $rule in $data.sec_rule.rules:
331 <rule>
332 #for $condition in $rule.conditions
333 #if str($condition.application.application_select) == "1":
334 condition = 1
335 #elif str($condition.application.application_select) == "on":
336 #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ])
337 condition = $on_str
338 #elif str($condition.application.application_select) == "pos":
339 #if $condition.application.pos_gt:
340 condition = var(start) > $condition.application.pos_gt
341 #end if
342
343 #if $condition.application.pos_lt:
344 condition = var(start) < $condition.application.pos_lt
345 #end if
346 #elif str($condition.application.application_select) == "value":
347 #if $condition.application.pos_gt:
348 condition = var(value) > $condition.application.pos_gt
349 #end if
350
351 #if $condition.application.pos_lt:
352 condition = var(value) < $condition.application.pos_lt
353 #end if
354 #elif str($condition.application.application_select) == "var":
355 condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}"
356 #end if
357 #end for
358
359 #for $action in $rule.actions:
360 #if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" :
361 #set x_fill_color = $action.action.action_value
362 #set x_fill_color_count = int(str($x_fill_color).split('-')[1])
363 #set x_min = $x_fill_color_count if $action.action.invert else 1
364 #set x_max = 1 if $action.action.invert else $x_fill_color_count
365 #set color_action = "fill_color" if str($plot_type) in ('histogram', 'histogram-stacked') else "color"
366
367 $color_action = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max})))
368 #elif str($action.action.action_select) in ('fill_color', 'stroke_color'):
369 #if str($plot_type) in ('tile', ):
370 color = $circosColor($action.action.action_value)
371 #else:
372 #if str($action.action.action_select) == "stroke_color" and str($plot_type) == "histogram":
373 color = $circosColor($action.action.action_value)
374 #else
375 $action.action.action_select = $circosColor($action.action.action_value)
376 #end if
377 #end if
175 #else 378 #else
176 $action.action.action_select = ${action.action.action_value} 379 $action.action.action_select = ${action.action.action_value}
177 #end if 380 #end if
178 #end for 381 #end for
179 $rule.continue_flow 382 $rule.continue_flow
201 </background> 404 </background>
202 #end for 405 #end for
203 </backgrounds> 406 </backgrounds>
204 </plot> 407 </plot>
205 #end for 408 #end for
409 </plots>
206 ]]></configfile> 410 ]]></configfile>
207 </xml> 411 </xml>
208 412
209 <xml name="configfile_links_conf"> 413 <xml name="configfile_links_conf">
210 <configfile name="links_conf"><![CDATA[ 414 <configfile name="links_conf"><![CDATA[
415 @UTILS@
416 <links>
211 #for $hi, $data in enumerate($sec_links.data): 417 #for $hi, $data in enumerate($sec_links.data):
212 <link> 418 <link>
213 #def circosColor($value) 419 file = data/links-${hi}.txt
214 #set $value = str($value) 420 radius = ${data.radius}r
215 #set $r = int($value[1:3], 16) 421 ribbon = ${data.linktype.ribbon}
216 #set $g = int($value[3:5], 16) 422 #if $data.linktype.ribbon == 'yes'
217 #set $b = int($value[5:], 16) 423 ${data.linktype.twist}
218 $r, $g, $b 424 #if $data.linktype.pattern != 'solid':
219 #end def 425 pattern = ${data.linktype.pattern}
220 426 #end if
221 file = data/links-${hi}.txt 427 #end if
222 428 color = $circosColorAlpha($data.color, $data.color_alpha)
223 radius = ${data.radius}r
224 ribbon = ${data.linktype.ribbon}
225 #if $data.linktype.ribbon == 'yes'
226 ${data.linktype.twist}
227 #end if
228 color = $circosColor($data.color)
229 bezier_radius = ${data.bezier_radius}r 429 bezier_radius = ${data.bezier_radius}r
230 thickness = ${data.thickness} 430 thickness = ${data.thickness}
231 crest = ${data.advanced.crest} 431 crest = ${data.advanced.crest}
232 bezier_radius_purity = ${data.advanced.bezier_radius_purity} 432 bezier_radius_purity = ${data.advanced.bezier_radius_purity}
233 433 #if $data.advanced.perturbation.perturb == 'yes'
234 #if $data.advanced.perturbation.perturb == 'yes' 434 perturb = yes
235 perturb = yes 435 perturb_crest = ${data.advanced.perturbation.perturb_crest_min},${data.advanced.perturbation.perturb_crest_max}
236 perturb_crest = ${data.advanced.perturbation.perturb_crest_min},${data.advanced.perturbation.perturb_crest_max} 436 perturb_bezier_radius = ${data.advanced.perturbation.perturb_bezier_radius_min},${data.advanced.perturbation.perturb_bezier_radius_max}
237 perturb_bezier_radius = ${data.advanced.perturbation.perturb_bezier_radius_min},${data.advanced.perturbation.perturb_bezier_radius_max} 437 perturb_bezier_radius_purity = ${data.advanced.perturbation.perturb_bezier_radius_purity_min},${data.advanced.perturbation.perturb_bezier_radius_purity_max}
238 perturb_bezier_radius_purity = ${data.advanced.perturbation.perturb_bezier_radius_purity_min},${data.advanced.perturbation.perturb_bezier_radius_purity_max} 438 #end if
239 #end if 439 #if $data.advanced.zdepth
240 440 z = ${data.advanced.zdepth}
241 #if $data.advanced.zdepth 441 #end if
242 z = ${data.advanced.zdepth}
243 #end if
244 442
245 <rules> 443 <rules>
246 #for $rule in $data.sec_link_rule.rules: 444 #for $rule in $data.sec_link_rule.rules:
247 <rule> 445 <rule>
248 #for $condition in $rule.conditions 446 #for $condition in $rule.conditions
249 #set cond = $condition.application.application_select 447 #set cond = $condition.application.application_select
250 #if $cond == 'interchr' or $cond == 'intrachr' or $cond == 'inv' or $cond == 'rev' 448 #if $cond == 'interchr' or $cond == 'intrachr' or $cond == 'inv' or $cond == 'rev'
251 condition = var($cond) 449 condition = var($cond)
252 #elif $cond == 'always' 450 #elif $cond == 'always'
253 condition = 1 451 condition = 1
452 #elif $cond == 'random'
453 condition = rand() < ${condition.application.value}
254 #else 454 #else
255 #set op = $condition.application.comparison.compare 455 #set op = $condition.application.comparison.compare
256 #set val = $condition.application.comparison.compval 456 #set val = $condition.application.comparison.compval
257 #if $cond == 'chr' 457 #if $cond == 'chr'
258 #if $op == 'between' or $op == 'fromto' 458 #if $op == 'between' or $op == 'fromto'
259 #set val2 = $condition.application.comparison.compval2 459 #set val2 = $condition.application.comparison.compval2
260 #set c=''.join([str($op),"(",str($val),",",str($val2),")"]) 460 #set c=''.join([str($op),"(",str($val),",",str($val2),")"])
461 #elif $op == 'on'
462 #set c='(var(chr1) eq "%s" or var(chr2) eq "%s")' % (str($val), str($val))
261 #else 463 #else
262 #set c=''.join([str($op),"(",str($val),")"]) 464 #set c=''.join([str($op),"(",str($val),")"])
263 #end if 465 #end if
264 condition = $c 466 condition = $c
265 #else 467 #else
278 480
279 #for $action in $rule.actions: 481 #for $action in $rule.actions:
280 #set actiontype = $action.action.action_select 482 #set actiontype = $action.action.action_select
281 #if $actiontype == 'color': 483 #if $actiontype == 'color':
282 #if $action.action.dynamic.dynamic_select == "static": 484 #if $action.action.dynamic.dynamic_select == "static":
283 #set actionval = $circosColor($action.action.dynamic.action_value) 485 #set actionval = $circosColorAlpha($action.action.dynamic.action_value, $action.action.dynamic.action_value_alpha)
284 $actiontype = $actionval 486 $actiontype = $actionval
285 #else 487 #else
286 #set x_fill_color = $action.action.dynamic.action_value 488 #set x_fill_color = $action.action.dynamic.action_value
287 #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) 489 #set x_fill_color_count = int(str($x_fill_color).split('-')[1])
288 #set x_min = $x_fill_color_count if $action.action.dynamic.invert else 1 490 #set x_min = $x_fill_color_count if $action.action.dynamic.invert else 1
310 </rule> 512 </rule>
311 #end for 513 #end for
312 </rules> 514 </rules>
313 </link> 515 </link>
314 #end for 516 #end for
517 </links>
315 ]]></configfile> 518 ]]></configfile>
316 </xml> 519 </xml>
317 520
318 <xml name="test_case"> 521 <xml name="test_case">
319 <configfile name="test_case_conf"><![CDATA[ 522 <inputs name="test_case_conf" />
320 <!--
321 mkdir -p test-data/my-test-case/ &&
322 #if $reference_genome.reference_genome_source == 'history':
323 cp '${genome_fasta}' test-data/my-test-case/input.fa &&
324 #end if
325
326 #if $reference_genome.reference_genome_source != 'karyotype':
327 #if $reference_genome.bands:
328 cp '${reference_genome.bands}' test-data/my-test-case/bands.${reference_genome.bands.ext} &&
329 #end if
330 #end if
331
332 #for $idx, $data in enumerate($sec_tdd.data):
333 #if str($data.plot_format.plot_format_select) in ('histogram', 'heatmap'):
334 #for $jdx, $file in enumerate($data.plot_format.data_source):
335 cp '${file}' test-data/my-test-case/${idx}-${jdx}.${file.ext} &&
336 #end for
337 #else
338 cp '${data.plot_format.data_source}' test-data/my-test-case/${idx}.${data.plot_format.data_source.ext} &&
339 #end if
340 #end for
341 cp "$output_png" test-data/my-test-case/output.png &&
342 cp "$output_svg" test-data/my-test-case/output.svg &&
343 -->
344 <test>
345 <param name="reference_genome|reference_genome_source" value="${reference_genome.reference_genome_source}"/>
346 <param name="reference_genome|genome_fasta" value="my-test-case/input.fa" />
347 <!-- ideograms -->
348 <param name="ideogram|spacing" value="${ideogram.spacing}" />
349 <param name="ideogram|radius" value="${ideogram.radius}" />
350 <param name="ideogram|thickness" value="${ideogram.thickness}" />
351 <param name="ideogram|ideogram_labels|show_label" value="${ideogram.ideogram_labels.show_label}" />
352 <param name="ideogram|ideogram_labels|parallel" value="${ideogram.ideogram_labels.parallel}" />
353 #if $reference_genome.reference_genome_source != 'karyotype':
354 #if $reference_genome.bands:
355 <param name="reference_genome.bands" value="my-test-case/bands.${reference_genome.bands.ext}" />
356 #end if
357 #end if
358 <!-- Ticks -->
359 <param name="ticks|show_ticks" value="${ticks.show_ticks}" />
360 <param name="ticks|radius" value="${ticks.radius}" />
361 <param name="ticks|color" value="${ticks.color}" />
362 <param name="ticks|multiplier" value="${ticks.multiplier}" />
363 #for $idx, $tick_group in enumerate($ticks.tick_group):
364 <param name="ticks|tick_group_${idx}|tickspacing" value="${tick_group.spacing}" />
365 <param name="ticks|tick_group_${idx}|size" value="${tick_group.size}" />
366 <param name="ticks|tick_group_${idx}|show_tick_labels" value="${tick_group.show_tick_labels}" />
367 <param name="ticks|tick_group_${idx}|label_size" value="${tick_group.label_size}" />
368 <param name="ticks|tick_group_${idx}|label_offset" value="${tick_group.label_offset}" />
369 <param name="ticks|tick_group_${idx}|label_format" value="${tick_group.format}" />
370 #end for
371 <!-- Data -->
372 #for $idx, $data_group in enumerate($sec_tdd.data):
373 <param name="sec_tdd|data_${idx}|r0" value="${data_group.r0}" />
374 <param name="sec_tdd|data_${idx}|r1" value="${data_group.r1}" />
375 <param name="sec_tdd|data_${idx}|orientation" value="${data_group.orientation}" />
376 <param name="sec_tdd|data_${idx}|plot_format|plot_format_select" value="${data_group.plot_format.plot_format_select}" />
377 <!-- Note, please double check your files -->
378 #if str($data_group.plot_format.plot_format_select) == 'histogram':
379 #set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)])
380 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="${my_files}" />
381 <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
382 <param name="sec_tdd|data_${idx}|plot_format|format_specific|extend_bins" value="${data_group.plot_format.format_specific.extend_bins}" />
383 #else if str($data_group.plot_format.plot_format_select) == 'heatmap':
384 #set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)])
385 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="${my_files}" />
386 <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
387 <param name="sec_tdd|data_${idx}|plot_format|format_specific|scale_log_base" value="${data_group.plot_format.format_specific.scale_log_base}" />
388 #else if str($data_group.plot_format.plot_format_select) == 'line':
389 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
390 <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
391 <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke" value="${data_group.plot_format.format_specific.stroke}" />
392 #else if str($data_group.plot_format.plot_format_select) == 'scatter':
393 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
394 <param name="sec_tdd|data_${idx}|plot_format|format_specific|glyph" value="${data_group.plot_format.format_specific.glyph}" />
395 <param name="sec_tdd|data_${idx}|plot_format|format_specific|glyph_size" value="${data_group.plot_format.format_specific.glyph_size}" />
396 <param name="sec_tdd|data_${idx}|plot_format|format_specific|data_min" value="${data_group.plot_format.format_specific.data_min}" />
397 <param name="sec_tdd|data_${idx}|plot_format|format_specific|data_max" value="${data_group.plot_format.format_specific.data_max}" />
398 <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
399 <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_color" value="${data_group.plot_format.format_specific.stroke_color}" />
400 <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_thickness" value="${data_group.plot_format.format_specific.stroke_thickness}" />
401 #else if str($data_group.plot_format.plot_format_select) == 'tile':
402 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
403 <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
404 <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
405 <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_thickness" value="${data_group.plot_format.format_specific.stroke_thickness}" />
406 <param name="sec_tdd|data_${idx}|plot_format|format_specific|layers" value="${data_group.plot_format.format_specific.layers}" />
407 <param name="sec_tdd|data_${idx}|plot_format|format_specific|thickness" value="${data_group.plot_format.format_specific.thickness}" />
408 <param name="sec_tdd|data_${idx}|plot_format|format_specific|padding" value="${data_group.plot_format.format_specific.padding}" />
409 <param name="sec_tdd|data_${idx}|plot_format|format_specific|overflow|overflow_behavior" value="${data_group.plot_format.format_specific.overflow.overflow_behavior}" />
410 #if str($data_group.plot_format.format_specific.overflow.overflow_behavior) != 'hide':
411 <param name="sec_tdd|data_${idx}|plot_format|format_specific|overflow|layer_overflow_color" value="${data_group.plot_format.format_specific.overflow.layer_overflow_color}" />
412 #end if
413 #end if
414 ## Next line intentionally blank
415
416 #end for
417
418 <!-- Outputs -->
419 <output name="output_png" file="my-test-case/output.png" />
420 <output name="output_svg" file="my-test-case/output.svg" />
421 </test>
422 ]]></configfile>
423 </xml> 523 </xml>
424 </macros> 524 </macros>