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comparison macros.xml @ 6:740057a5126d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
author iuc
date Fri, 01 May 2020 07:28:50 -0400
parents a64dc31ab7f2
children 4b519282a05b
comparison
equal deleted inserted replaced
5:a64dc31ab7f2 6:740057a5126d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@CIRCOS_VERSION@">0.69.8</token> 3 <token name="@CIRCOS_VERSION@">0.69.8</token>
4 4
5 <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy4</token> 5 <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy5</token>
6 6
7 <xml name="requirements"> 7 <xml name="requirements">
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@CIRCOS_VERSION@">circos</requirement> 9 <requirement type="package" version="@CIRCOS_VERSION@">circos</requirement>
10 <requirement type="package" version="2.7">python</requirement> 10 <requirement type="package" version="2.7">python</requirement>
11 <requirement type="package" version="0.6.4">bcbiogff</requirement> 11 <requirement type="package" version="0.6.4">bcbiogff</requirement>
12 <requirement type="package" version="1.70">biopython</requirement> 12 <requirement type="package" version="1.70">biopython</requirement>
13 <requirement type="package" version="0.3.13">pybigwig</requirement> 13 <requirement type="package" version="0.3.13">pybigwig</requirement>
14 <requirement type="package" version="0.23">circos-tools</requirement> 14 <requirement type="package" version="0.23">circos-tools</requirement>
15 <requirement type="package" version="3.4">grep</requirement>
16 <requirement type="package" version="5.1.0">gawk</requirement>
15 <requirement type="package" version="1.29">tar</requirement> 17 <requirement type="package" version="1.29">tar</requirement>
16 <yield /> 18 <yield />
17 </requirements> 19 </requirements>
18 </xml> 20 </xml>
19 21
78 </valid> 80 </valid>
79 </sanitizer> 81 </sanitizer>
80 </param> 82 </param>
81 </xml> 83 </xml>
82 84
85 <xml name="chrom_units"
86 token_label="Position"
87 token_help="In bases (e.g. 1000) or chromosome units (e.g. 1u)"
88 token_value="5u"
89 token_name="position"
90 >
91 <param name="@NAME@" type="text" value="@VALUE@" label="@LABEL@" help="@HELP@">
92 <sanitizer>
93 <valid initial="string.digits">
94 <add value="u"/>
95 <add value="b"/>
96 <add value="."/>
97 </valid>
98 </sanitizer>
99 </param>
100 </xml>
101
83 <xml name="circos_color_alpha" 102 <xml name="circos_color_alpha"
84 token_label="Color" 103 token_label="Color"
85 token_name="color" 104 token_name="color"
86 token_value="#000000" 105 token_value="#000000"
87 token_help="" 106 token_help=""
91 <valid initial="string.letters,string.digits"> 110 <valid initial="string.letters,string.digits">
92 <add value="#" /> 111 <add value="#" />
93 </valid> 112 </valid>
94 </sanitizer> 113 </sanitizer>
95 </param> 114 </param>
96 <param name="@NAME@_alpha" type="float" label="Transparency" value="1" min="0" max="1" help="1 = fully opaque, 0 = fully transparent"/> 115 <param name="@NAME@_alpha" type="float" label="@LABEL@ Transparency" value="1" min="0" max="1" help="1 = fully opaque, 0 = fully transparent"/>
97 </xml> 116 </xml>
98 117
99 <xml name="brewer_scale" 118 <xml name="brewer_scale"
100 token_name="color" 119 token_name="color"
101 token_label="Color"> 120 token_label="Color"
102 <param name="@NAME@" type="select" label="@LABEL@"> 121 token_help="">
122 <param name="@NAME@" type="select" label="@LABEL@" help="@HELP@">
103 <option value="purples-13-seq">Sequential: Purples</option> 123 <option value="purples-13-seq">Sequential: Purples</option>
104 <option value="reds-13-seq">Sequential: Reds</option> 124 <option value="reds-13-seq">Sequential: Reds</option>
105 <option value="oranges-13-seq">Sequential: Oranges</option> 125 <option value="oranges-13-seq">Sequential: Oranges</option>
106 <option value="greens-13-seq">Sequential: Greens</option> 126 <option value="greens-13-seq">Sequential: Greens</option>
107 <option value="blues-13-seq">Sequential: Blues</option> 127 <option value="blues-13-seq">Sequential: Blues</option>
139 <option value="set2-8-qual">Qualitative: Set2</option> 159 <option value="set2-8-qual">Qualitative: Set2</option>
140 <option value="set3-12-qual">Qualitative: Set3</option> 160 <option value="set3-12-qual">Qualitative: Set3</option>
141 </param> 161 </param>
142 </xml> 162 </xml>
143 163
144 <xml name="zdepth"> 164 <xml name="zdepth"
145 <param name="zdepth" type="float" value="" optional="true" label="Z-depth" 165 token_name="zdepth"
146 help="Optional. Datasets with a higher z-depth value are drawn on top of data sets with a lower value. Only useful if plotting multiple tracks"/> 166 >
167 <param name="@NAME@" type="integer" value="0" optional="true" label="Z-index"
168 help="Datasets with a higher z-index value are drawn on top of data sets with a lower value. 0 is the default and plots added lower in the configuration file will be plotted above."/>
147 </xml> 169 </xml>
148 170
149 <xml name="font_select" 171 <xml name="font_select"
150 token_normal="true" 172 token_normal="true"
151 token_bold="false"> 173 token_bold="false">
159 <option value="bolditalic">bolditalic</option> 181 <option value="bolditalic">bolditalic</option>
160 <option value="italicbold">italicbold</option> 182 <option value="italicbold">italicbold</option>
161 </param> 183 </param>
162 </xml> 184 </xml>
163 185
186 <xml name="radial_position">
187 <conditional name="radial_position">
188 <param name="select" type="select" label="Radial Position">
189 <option value="plot">Relative position</option>
190 <option value="data" selected="True">Absolute position (values match data values)</option>
191 </param>
192 <when value="plot">
193 <param name="y0" type="float" value="0" label="y0" help="Values are relative (0=inside of track, 1=outside of track)"/>
194 <param name="y1" type="float" value="1" label="y1" help="Values are relative (0=inside of track, 1=outside of track)"/>
195 </when>
196 <when value="data">
197 <param name="y0" type="float" value="0" label="y0" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y0 should be -10."/>
198 <param name="y1" type="float" value="1" label="y1" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y1 should be 10."/>
199 </when>
200 </conditional>
201 </xml>
202
203 <xml name="radial_position_axes">
204 <conditional name="radial_position">
205 <param name="select" type="select" label="Radial Position">
206 <option value="plot">Relative position</option>
207 <option value="data" selected="True">Absolute position (values match data values)</option>
208 </param>
209 <when value="plot">
210 <param name="spacing" type="float" value="0.1" min="0" max="1" label="Spacing" help="This many % of the distance between axis lines, set between the data minimum/maximum. If data goes from -1 to 1, and this is set to 0.33, and y0/y1 radius are 0/1, this produces two bands [0.33, 1]. If the y0/y1 radius are set to -1/1, this produces 4 bands: [-1, -0.33, 0.33, 1]. The y0/y1 radius act as clipping."/>
211 </when>
212 <when value="data">
213 <param name="spacing" type="float" value="0.1" label="Spacing" help="Equal to data value difference. E.g. 0.25 here when data goes from -1 to 1 and y0/y1 are 0/1 produces 5 bands at [0, 0.25, 0.5, 0.75, 1]. If y0/y1 and radius are -1/1 produces 9 bands at [-1, -0.75, -0.5, -0.25, 0, 0.25, 0.5, 0.75, 1]. The y0/y1 radius act as clipping."/>
214 </when>
215 </conditional>
216 <param name="y0" type="float" value="0" label="y0" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y0 should be -10. These clip the axes, any axes which would be drawn on the data outside of these bounds will not be drawn."/>
217 <param name="y1" type="float" value="1" label="y1" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y1 should be 10. These clip the axes, any axes which would be drawn on the data outside of these bounds will not be drawn."/>
218 </xml>
219
220 <xml name="minsize">
221 <param name="minsize" type="float" value="0" label="Minimum size (in chromosome units)" min="0"/>
222 </xml>
223
224 <xml name="only_if_data">
225 <param name="only_if_data" type="select" label="When to show">
226 <option value="always" selected="True">Always</option>
227 <option value="data">Only when data is present on the ideogram</option>
228 </param>
229 </xml>
230
164 <xml name="axes"> 231 <xml name="axes">
165 <section name="sec_axes" title="Axes"> 232 <section name="sec_axes" title="Axes">
166 <repeat name="axes" title="Axis"> 233 <repeat name="axes" title="Axis">
167 <param name="y0" type="float" value="0" label="Inside Radius" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y0 should be -10"/> 234 <expand macro="radial_position_axes" />
168 <param name="y1" type="float" value="1" label="Outside Radius" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y1 should be 10"/> 235 <expand macro="circos_color_alpha"/>
169
170 <expand macro="circos_color"/>
171 <param name="thickness" type="integer" value="1" label="Thickness"/> 236 <param name="thickness" type="integer" value="1" label="Thickness"/>
172 <param name="spacing" type="float" value="0.1" label="Spacing" help="Relative spacing between each concentric arc"/>
173 </repeat> 237 </repeat>
238 <expand macro="only_if_data" />
174 </section> 239 </section>
175 </xml> 240 </xml>
176 241
177 <xml name="backgrounds"> 242 <xml name="backgrounds">
178 <section name="sec_bkgs" title="Backgrounds"> 243 <section name="sec_bkgs" title="Backgrounds">
179 <repeat name="backgrounds" title="Background"> 244 <repeat name="backgrounds" title="Background">
180 <param name="y0" type="float" value="0" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/> 245 <expand macro="radial_position" />
181 <param name="y1" type="float" value="1" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/> 246 <expand macro="circos_color_alpha"/>
182 <expand macro="circos_color"/>
183 </repeat> 247 </repeat>
248 <expand macro="only_if_data" />
184 </section> 249 </section>
185 </xml> 250 </xml>
186 251
187 <xml name="rules"> 252 <xml name="rules">
188 <section name="sec_rule" title="Rules"> 253 <section name="sec_rule" title="Rules">
189 <repeat name="rules" title="Rule"> 254 <repeat name="rules" title="Rule">
190 <repeat name="conditions" title="Conditions to Apply"> 255 <repeat name="conditions" title="Conditions to Apply">
191 <conditional name="application"> 256 <conditional name="application">
192 <param name="application_select" type="select" label="Condition"> 257 <param name="application_select" type="select" label="Condition">
193 <option value="1">Apply to Every Point</option> 258 <option value="always">Apply to Every Point</option>
259 <option value="random">Randomly</option>
194 <option value="on">Check for presence/absence per chromosome</option> 260 <option value="on">Check for presence/absence per chromosome</option>
195 <option value="pos">Based on numerical position</option> 261 <option value="pos">Based on position on chromosome</option>
196 <option value="random">Randomly</option> 262 <option value="value">Based on position value (ONLY for scatter/histogram/heatmap/line)</option>
197 <option value="value">Apply based on point value</option> 263 <option value="var">Based on qualifier value (when available)</option>
198 <option value="var">Apply based on qualifier value (when available)</option>
199 </param> 264 </param>
200 <when value="1"> 265 <when value="always">
201 </when> 266 </when>
202 <when value="on"> 267 <when value="on">
203 <param name="on_genomes" type="text" label="Contig IDs" help="Pipe | separated list of contig IDs"> 268 <param name="on_genomes" type="text" label="Chromosome IDs" help="Pipe | separated list of chromosome IDs">
204 <sanitizer> 269 <sanitizer>
205 <valid initial="string.letters,string.digits"> 270 <valid initial="string.letters,string.digits">
206 <add value="|" /> 271 <add value="|" />
272 <add value="-" />
273 <add value="." />
207 </valid> 274 </valid>
208 </sanitizer> 275 </sanitizer>
209 </param> 276 </param>
210 </when> 277 </when>
211 <when value="pos"> 278 <when value="pos">
254 </repeat> 321 </repeat>
255 <repeat name="actions" title="Actions to Apply"> 322 <repeat name="actions" title="Actions to Apply">
256 <conditional name="action"> 323 <conditional name="action">
257 <param name="action_select" type="select" label="Action"> 324 <param name="action_select" type="select" label="Action">
258 <option value="show">Change Visibility</option> 325 <option value="show">Change Visibility</option>
326 <option value="z">Change Z-index</option>
259 <option value="fill_color">Change Fill Color for all points</option> 327 <option value="fill_color">Change Fill Color for all points</option>
260 <option value="fill_color_value">Change Fill Color based on Value</option> 328 <option value="fill_color_value">Change Fill Color based on Value</option>
261 <option value="stroke_color">Change Stroke Color</option> 329 <option value="stroke_color">Change Stroke Color</option>
262 <option value="color_value">Change Stroke Color based on Value</option> 330 <option value="color_value">Change Stroke Color based on Value</option>
331 <option value="value_from_attr">Change value of point based on attribute</option>
263 </param> 332 </param>
264 <when value="show"> 333 <when value="show">
265 <param name="action_value" type="boolean" truevalue="yes" falsevalue="no" label="Show"/> 334 <param name="action_value" type="boolean" truevalue="yes" falsevalue="no" label="Show"/>
266 </when> 335 </when>
336 <when value="value_from_attr">
337 <param name="action_value" type="text" label="Attribute to pull value from" help="From the optional x1=y1;x2=y2... formatted attributes in the last column">
338 <sanitizer>
339 <valid initial="string.letters,string.digits">
340 </valid>
341 </sanitizer>
342 </param>
343 </when>
267 <when value="fill_color"> 344 <when value="fill_color">
268 <expand macro="circos_color" name="action_value" label="Fill Color"/> 345 <expand macro="circos_color" name="action_value" label="Fill Color"/>
269 </when> 346 </when>
270 <when value="stroke_color"> 347 <when value="stroke_color">
271 <expand macro="circos_color" name="action_value" label="Stroke Color"/> 348 <expand macro="circos_color" name="action_value" label="Stroke Color"/>
272 </when> 349 </when>
273 <when value="fill_color_value"> 350 <when value="fill_color_value">
274 <expand macro="brewer_scale" name="action_value" label="Fill Color"/> 351 <expand macro="brewer_scale" name="action_value" label="Fill Color" help="Fill will be changed based on a mapping of dataset values to colours, but to do this the mapping needs to be defined. Minimum and maximum values are defined below, and will map to the minimum and maximum values of this brewer scale."/>
275 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/> 352 <param name="min_value" type="float" value="-1" label="Minimum value of dataset"/>
276 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/> 353 <param name="max_value" type="float" value="1" label="Maximum value of dataset"/>
277 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" /> 354 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />
278 </when> 355 </when>
279 <when value="color_value"> 356 <when value="color_value">
280 <expand macro="brewer_scale" name="action_value" label="Stroke Color"/> 357 <expand macro="brewer_scale" name="action_value" label="Stroke Color" help="Stroke will be changed based on a mapping of dataset values to colours, but to do this the mapping needs to be defined. Minimum and maximum values are defined below, and will map to the minimum and maximum values of this brewer scale."/>
281 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/> 358 <param name="min_value" type="float" value="-1" label="Minimum value of dataset"/>
282 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/> 359 <param name="max_value" type="float" value="1" label="Maximum value of dataset"/>
283 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" /> 360 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />
361 </when>
362 <when value="z">
363 <conditional name="dynamic">
364 <param name="dynamic_select" type="select" label="Static or Dynamic Z-Index">
365 <option value="static">Static</option>
366 <option value="dynamic">Dynamic (based on value)</option>
367 </param>
368 <when value="static">
369 <expand macro="zdepth" name="action_value"/>
370 </when>
371 <when value="dynamic">
372 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
373 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
374 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Z-Index Mapping" />
375 </when>
376 </conditional>
284 </when> 377 </when>
285 </conditional> 378 </conditional>
286 </repeat> 379 </repeat>
287 <param name="continue_flow" type="boolean" truevalue="flow = continue" falsevalue="" label="Continue flow" 380 <param name="continue_flow" type="boolean" truevalue="flow = continue" falsevalue="" label="Continue flow"
288 help="Allow rules after this one to be applied in addition to this rule. E.g. if one rule modifies font size, and another font colour, with continued flow they could both be applied rather than whichever was encountered first."/> 381 help="Allow rules after this one to be applied in addition to this rule. E.g. if one rule modifies font size, and another font colour, with continued flow they could both be applied rather than whichever was encountered first."/>
289 </repeat> 382 </repeat>
290 </section> 383 </section>
384 </xml>
385
386 <xml name="link_color_action_options"
387 token_section="ERROR">
388
389 <conditional name="dynamic">
390 <param name="dynamic_select" type="select" label="Static / Dynamic Change">
391 <option value="static">Color is always applied</option>
392 <option value="dynamic">Color is applied based on value</option>
393 <option value="source">Color based on source chromosome color</option>
394 <option value="dest">Color based on destination chromosome color</option>
395 </param>
396 <when value="static">
397 <expand macro="circos_color_alpha" label="@SECTION@ Color" name="action_value"/>
398 </when>
399 <when value="dynamic">
400 <expand macro="brewer_scale" name="action_value" label="@SECTION@ Color" help="@SECTION@ will be changed based on a mapping of dataset values to colours, but to do this the mapping needs to be defined. Minimum and maximum values are defined below, and will map to the minimum and maximum values of this brewer scale."/>
401 <param name="min_value" type="float" value="-1" label="Minimum value of dataset"/>
402 <param name="max_value" type="float" value="1" label="Maximum value of dataset"/>
403 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />
404 </when>
405 <when value="source">
406 </when>
407 <when value="dest">
408 </when>
409 </conditional>
291 </xml> 410 </xml>
292 411
293 <xml name="linkrules"> 412 <xml name="linkrules">
294 <section name="sec_link_rule" title="Rules"> 413 <section name="sec_link_rule" title="Rules">
295 <repeat name="rules" title="Rule"> 414 <repeat name="rules" title="Rule">
357 </repeat> 476 </repeat>
358 <repeat name="actions" title="Actions to Apply"> 477 <repeat name="actions" title="Actions to Apply">
359 <conditional name="action"> 478 <conditional name="action">
360 <param name="action_select" type="select" label="Action"> 479 <param name="action_select" type="select" label="Action">
361 <option value="show">Change Visibility</option> 480 <option value="show">Change Visibility</option>
362 <option value="color">Change Link Color</option> 481 <option value="z">Change Z-index</option>
482 <option value="color">Change Fill Color</option>
483 <option value="stroke_color">Change Stroke Color (Ribbons Only)</option>
363 <option value="thickness">Change Thickness</option> 484 <option value="thickness">Change Thickness</option>
364 <option value="z">Change Z-depth</option>
365 </param> 485 </param>
366 <when value="show"> 486 <when value="show">
367 <param name="action_value" type="boolean" label="Show" truevalue="yes" falsevalue="no"/> 487 <param name="action_value" type="boolean" label="Show" truevalue="yes" falsevalue="no"/>
368 </when> 488 </when>
489 <when value="stroke_color">
490 <expand macro="link_color_action_options" section="Stroke"/>
491 </when>
369 <when value="color"> 492 <when value="color">
370 <conditional name="dynamic"> 493 <expand macro="link_color_action_options" section="Fill"/>
371 <param name="dynamic_select" type="select" label="Static / Dynamic Change">
372 <option value="static">Static: Change is always applied</option>
373 <option value="dynamic">Dynamic: Change is sometimes applied</option>
374 </param>
375 <when value="static">
376 <expand macro="circos_color_alpha" label="Link Color" name="action_value"/>
377 </when>
378 <when value="dynamic">
379 <expand macro="brewer_scale" label="Fill Color" name="action_value"/>
380 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
381 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
382 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />
383 </when>
384 </conditional>
385 </when> 494 </when>
386 <when value="thickness"> 495 <when value="thickness">
387 <param name="action_value" type="integer" value="1" label="Thickness"/> 496 <param name="action_value" type="integer" value="1" label="Thickness"/>
388 </when> 497 </when>
389 <when value="z"> 498 <when value="z">
390 <conditional name="dynamic"> 499 <conditional name="dynamic">
391 <param name="dynamic_select" type="select" label="Static or Dynamic Z-Depth"> 500 <param name="dynamic_select" type="select" label="Static or Dynamic Z-Index">
392 <option value="static">Static</option> 501 <option value="static">Static</option>
393 <option value="dynamic">Dynamic (based on value)</option> 502 <option value="dynamic">Dynamic (based on value)</option>
394 </param> 503 </param>
395 <when value="static"> 504 <when value="static">
396 <param name="action_value" type="float" value="1" label="Z-depth" help="Datasets with a higher z-depth value are drawn on top of datasets with lower z value"/> 505 <expand macro="zdepth" name="action_value"/>
397 </when> 506 </when>
398 <when value="dynamic"> 507 <when value="dynamic">
399 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/> 508 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
400 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/> 509 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
401 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Z-Depth Mapping" /> 510 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Z-Index Mapping" />
402 </when> 511 </when>
403 </conditional> 512 </conditional>
404 </when> 513 </when>
405 </conditional> 514 </conditional>
406 </repeat> 515 </repeat>