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comparison macrosbroken.xml @ 57:94264fe60478 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
author fubar
date Thu, 21 Mar 2024 08:01:42 +0000
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56:c0097a584a8a 57:94264fe60478
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">2.10.1</token>
4 <xml name = "edamInc">
5 <edam_topics>
6 <edam_topic>topic_3307</edam_topic>
7 <edam_topic>topic_0092</edam_topic>
8 </edam_topics>
9 <edam_operations>
10 <edam_operation>operation_0573</edam_operation>
11 <edam_operation>operation_0564</edam_operation>
12 </edam_operations>
13 </xml>
14 <xml name="requirements">
15 <requirements>
16 <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement>
17 <requirement type="package" version="1.81">biopython</requirement>
18 <requirement type="package" version="0.7.1">bcbio-gff</requirement>
19 <requirement type="package" version="1.19">samtools</requirement>
20 <requirement type="package" version="6.0.1">pyyaml</requirement>
21 <requirement type="package" version="1.11">tabix</requirement>
22 <requirement type="package" version="4.6.0">findutils</requirement>
23 <requirement type="package" version="0.0.8">hictk</requirement>
24 <yield/>
25 </requirements>
26 </xml>
27 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
28 <token name="@WRAPPER_VERSION@">galaxy2</token>
29 <token name="@ATTRIBUTION@"><![CDATA[
30 **Attribution**
31 This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is maintained by Ross Lazarus
32 until the IUC complete their own.
33 ]]>
34 </token>
35 <xml name="genome_selector"
36 token_help=""
37 token_label="Fasta sequences"
38 token_optional="False" >
39 <conditional name="reference_genome">
40 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
41 <option selected="True" value="indexed">Use a built-in genome</option>
42 <option value="history">Use a genome from history</option>
43 </param>
44 <when value="indexed">
45 <param
46 help="@HELP@"
47 label="@LABEL@"
48 name="genomes"
49 type="select"
50 optional="@OPTIONAL@"
51 >
52 <options from_data_table="all_fasta">
53 <filter column="2" type="sort_by" />
54 <validator message="No genomes are available for the selected input dataset" type="no_options" />
55 </options>
56 </param>
57 </when>
58 <when value="history">
59 <param
60 format="fasta"
61 label="@LABEL@"
62 help="@HELP@"
63 name="genomes"
64 type="data"
65 optional="@OPTIONAL@"
66 multiple="True" />
67 </when>
68 </conditional>
69 </xml>
70
71 <xml name="auto_manual_tk"
72 token_cond_label="Color"
73 token_cond_name="color"
74 token_select_label="Color Specification"
75 token_select_name="color_select"
76 token_automatic_label="Automatically selected"
77 token_manual_label="Manual Color Selection">
78 <conditional name="@COND_NAME@" label="@COND_LABEL@">
79 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">
80 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
81 <option value="manual">@MANUAL_LABEL@</option>
82 </param>
83 <when value="automatic">
84 </when>
85 <when value="manual">
86 <yield />
87 </when>
88 </conditional>
89 </xml>
90
91 <xml name="jb_color"
92 token_label="JBrowse style.color"
93 token_name="style_color"
94 token_value="goldenrod"
95 token_help="Basic color of features. Most glyphs interpret this as the fill color of the rectangle they draw. Color syntax is the same as that used for CSS"
96 >
97 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
98 <sanitizer>
99 <valid initial="string.letters,string.digits">
100 <add value="#" />
101 </valid>
102 </sanitizer>
103 </param>
104 </xml>
105
106 <xml name="auto_color"
107 token_cond_label="Color"
108 token_cond_name="color"
109 token_select_label="Color Selection"
110 token_select_name="color_select"
111 token_automatic_label="Automatically selected"
112 token_manual_label="Manual Color Selection">
113 <expand macro="auto_manual_tk"
114 cond_label="@COND_LABEL@"
115 cond_name="@COND_NAME@"
116 select_label="@SELECT_LABEL@"
117 select_name="@SELECT_NAME@"
118 automatic_label="@AUTOMATIC_LABEL@"
119 manual_label="@MANUAL_LABEL@">
120 <expand macro="jb_color" />
121 <yield />
122 </expand>
123 </xml>
124
125
126
127 <xml name="brewer_scheme">
128 <param type="select" label="Brewer color Scheme" name="brewer_scheme">
129 <option value="BrBg">BrBg: Brown - Blue Green</option>
130 <option value="PiYg">PiYg: Pink - Yellow Green</option>
131 <option value="PRGn">PRGn: Purple Red - Green</option>
132 <option value="PuOr">PuOr: Purple - Orange</option>
133 <option value="RdBu" selected="true">RdBu: Red - Blue</option>
134 <option value="RdGy">RdGy: Red - Gray</option>
135 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
136 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
137 <option value="Spectral">Spectral</option>
138 </param>
139 </xml>
140
141 <xml name="general_options">
142 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false">
143 <conditional name="ucol">
144 <param name="formcoll" type="select" label="Convert a collection of track files rather than filling in the tool form"
145 help="A collection of bam/vcf and other track types will be converted into a JBrowse2 automatically">
146 <option value="form" selected="true">Fill in the tool form to specify tracks for the output JBrowse2</option>
147 <option value="collect">Convert a collection of suitable track files</option>
148 </param>
149 <when value="collect">
150 <param label="Collection of bed, bam and other track files" name="autoCollection" type="data_collection" />
151 </when>
152 <when value="form">
153 </when>
154 </conditional>
155
156 <param label="Create a zip archive for downloading rather than viewing " name="zipOut" help="Default is to make an interactive browser appear when the 'eye' icon is activated"
157 type="boolean" checked="false" truevalue="true" falsevalue="false" />
158 <param label="Subset to display to new users" type="text" name="defaultLocation" value="" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678'"/>
159 <param label="Session name" type="text" name="session_name" value="New session" help="Displayed at the top of the window"/>
160 <param label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166" name="enableAnalytics" type="boolean" checked="false" truevalue="true" falsevalue="false" />
161
162 <param name="primary_color" type="color" label="Primary color" value="#0D233F">
163 <sanitizer>
164 <valid initial="string.ascii_letters,string.digits">
165 <add value="#" />
166 </valid>
167 </sanitizer>
168 </param>
169 <param name="secondary_color" type="color" label="Secondary color" value="#721E63">
170 <sanitizer>
171 <valid initial="string.ascii_letters,string.digits">
172 <add value="#" />
173 </valid>
174 </sanitizer>
175 </param>
176 <param name="tertiary_color" type="color" label="Tertiary color" value="#135560">
177 <sanitizer>
178 <valid initial="string.ascii_letters,string.digits">
179 <add value="#" />
180 </valid>
181 </sanitizer>
182 </param>
183 <param name="quaternary_color" type="color" label="Quaternary color" value="#FFB11D">
184 <sanitizer>
185 <valid initial="string.ascii_letters,string.digits">
186 <add value="#" />
187 </valid>
188 </sanitizer>
189 </param>
190
191 <param label="Font size" name="font_size" type="integer" value="10" />
192 </section>
193 </xml>
194
195 <xml name="color_selection_minmax">
196 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
197 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
198 auto case as well, but may be safe to just say "brewer colors? Pff,
199 red/blue" -->
200 <expand macro="auto_manual_tk"
201 token_cond_label="Color"
202 token_cond_name="color"
203 token_select_label="Color Selection"
204 token_select_name="color_select"
205 token_automatic_label="Automatically selected"
206 token_manual_label="Manual Color Selection">
207 <expand macro="jb_color"
208 label="JBrowse style.pos_color"
209 name="style_pos_color"
210 value="blue"
211 help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point." />
212 <expand macro="jb_color"
213 label="JBrowse style.neg_color"
214 name="style_neg_color"
215 value="red"
216 help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point." />
217 </expand>
218
219 <conditional name="bicolor_pivot" label="Bicolor Pivot">
220 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
221 <option value="zero" selected="true">Zero</option>
222 <option value="mean">Mean</option>
223 <option value="custom">Custom Value</option>
224 </param>
225 <when value="zero" />
226 <when value="mean" />
227 <when value="custom">
228 <param label="JBrowse style.bicolor_pivot" type="float" name="pivot_point" value="0.0" help="Where to change from pos_color to neg_color when drawing bicolor plots." />
229 </when>
230 </conditional>
231 </section>
232 </xml>
233
234 <xml name="color_selection"
235 token_scaling_lin_select="true"
236 token_scaling_log_select="false"
237 >
238 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling &amp; Coloring Options [Advanced]" expanded="false">
239 <conditional name="color_score" label="JBrowse style.color &amp; Score relationship">
240 <param type="select" label="Color Score Algorithm" name="color_score_select" help="How to color the features. If it is based on score, then features with a score attribute anywhere in their hierachy will have their color affected by the score. If you choose to ignore the score, then you'll be able to select a single solid color for every feature in the track">
241 <option value="score">Based on score</option>
242 <option value="none" selected="true">Ignore score</option>
243 </param>
244 <when value="none">
245 <!-- When no scaling is done, no scores available, then just let the
246 user choose a base color for the track -->
247 <expand macro="auto_color" />
248 </when>
249 <when value="score">
250 <!-- Scaling -->
251 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
252 help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution.">
253 <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option>
254 <option value="logarithmic" selected="false">Logarithmic scaling</option>
255 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option>
256 </param>
257
258 <!-- Scaling Bounds -->
259 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
260 <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select">
261 <option value="automatic" selected="true">Automatically determined</option>
262 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option>
263 </param>
264 <when value="automatic" />
265 <when value="manual">
266 <param label="Minimum expected score" name="minimum" type="integer" value="0" />
267 <param label="Maximum expected score" name="maximum" type="integer" value="100" />
268 </when>
269 </conditional>
270
271 <!-- Scale color -->
272 <conditional name="color_scheme" label="Color Scheme for scored features">
273 <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme">
274 <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
275 <!--<option value="brewer">Brewer Color Schemes</option>-->
276 </param>
277 <when value="opacity">
278 <!-- Single color selection mode -->
279 <expand macro="auto_color" />
280 </when>
281 <!--<when value="brewer">-->
282 <!--[> Brewer continuum selection <]-->
283 <!--<expand macro="brewer_scheme" />-->
284 <!--</when>-->
285 </conditional>
286 </when>
287 </conditional>
288 </section>
289 </xml>
290
291 <xml name="track_visibility">
292 <param type="select" label="Track Visibility" name="track_visibility">
293 <option value="default_off">Off when browser opens</option>
294 <option value="default_on" selected="true">On when browser opens</option>
295 </param>
296 </xml>
297
298 <xml name="track_styling_linear">
299 <param label="Show labels" name="show_labels" type="boolean" checked="false" truevalue="true" falsevalue="false" />
300 <param label="Show descriptions" name="show_descriptions" type="boolean" checked="false" truevalue="true" falsevalue="false" />
301 <param name="display_mode" type="select" label="Display mode">
302 <option value="normal" selected="true">normal</option>
303 <option value="compact">compact</option>
304 <option value="reducedRepresentation">reducedRepresentation</option>
305 <option value="collapse">collapse</option>
306 </param>
307 <param label="Max height" name="max_height" type="integer" value="600" help="Maximum height that the track is permitted to reach in pixels."/>
308 </xml>
309
310 <xml name="track_styling_feature">
311 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
312 <conditional name="track_style">
313 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
314 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option>
315 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option>
316 <option value="LinearArcDisplay">LinearArcDisplay</option>
317 </param>
318 <when value="LinearPileupDisplay">
319 <expand macro="track_styling_linear"/>
320 </when>
321 <when value="LinearBasicDisplay">
322 <expand macro="track_styling_linear"/>
323
324 <!-- examples: https://github.com/GMOD/jbrowse-components/discussions/2729
325 and https://github.com/GMOD/jbrowse-components/blob/main/plugins/svg/src/SvgFeatureRenderer/configSchema.ts#L41 -->
326 <param label="Features label"
327 type="text"
328 name="label"
329 value="jexl:get(feature,'name') || get(feature,'id')"
330 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax">
331 <sanitizer>
332 <valid initial="default">
333 <add value="|" />
334 <add value="{"/>
335 <add value="}"/>
336 <add value="!"/>
337 <add value="?"/>
338 <add value="+"/>
339 <add value="="/>
340 <add value="'"/>
341 </valid>
342 </sanitizer>
343 </param>
344 <param label="Features description"
345 type="text"
346 name="description"
347 value="jexl:get(feature,'note') || get(feature,'description')"
348 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax">
349 <sanitizer>
350 <valid initial="default">
351 <add value="|" />
352 <add value="{"/>
353 <add value="}"/>
354 <add value="!"/>
355 <add value="?"/>
356 <add value="+"/>
357 <add value="="/>
358 <add value="'"/>
359 </valid>
360 </sanitizer>
361 </param>
362 </when>
363 <when value="LinearArcDisplay"/>
364 </conditional>
365 </section>
366 </xml>
367
368 <xml name="track_styling_xam">
369 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
370 <conditional name="track_style">
371 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
372 <option value="LinearAlignmentsDisplay" selected="true">LinearAlignmentsDisplay</option>
373 <option value="LinearPileupDisplay">LinearPileupDisplay</option>
374 <option value="LinearSNPCoverageDisplay">LinearSNPCoverageDisplay</option>
375 </param>
376 <when value="LinearAlignmentsDisplay"/>
377 <when value="LinearPileupDisplay"/>
378 <when value="LinearSNPCoverageDisplay">
379 <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" />
380 <param name="minScore" label="Min score" type="integer" value="" optional="true"/>
381 <param name="maxScore" label="Max score" type="integer" value="" optional="true"/>
382 </when>
383 </conditional>
384 </section>
385 </xml>
386
387 <xml name="track_styling_vcf">
388 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
389 <conditional name="track_style">
390 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
391 <option value="LinearVariantDisplay" selected="true">LinearVariantDisplay</option>
392 </param>
393 <when value="LinearVariantDisplay">
394 <expand macro="track_styling_linear"/>
395 </when>
396 </conditional>
397 </section>
398 </xml>
399
400 <xml name="track_styling_bigwig">
401 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
402 <conditional name="track_style">
403 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
404 <option value="LinearWiggleDisplay" selected="true">LinearWiggleDisplay</option>
405 </param>
406 <when value="LinearWiggleDisplay">
407 <param name="autoscale" type="select" label="Autoscale type">
408 <option value="local" selected="true">Local</option>
409 <option value="global">Global</option>
410 <option value="globalsd">Global ± 3σ</option>
411 <option value="localsd">Local ± 3σ</option>
412 </param>
413 <param name="resolution" label="Resolution" type="integer" value="1"/>
414 <param name="summaryScoreMode" type="select" label="Autoscale type">
415 <option value="max">Max</option>
416 <option value="min">Min</option>
417 <option value="avg">Avg</option>
418 <option value="whiskers" selected="true">Whiskers (combines all three)</option>
419 </param>
420 <param name="filled" label="Fill in histogram" type="boolean" checked="true" truevalue="true" falsevalue="false" />
421 <param name="scaleType" type="select" label="Autoscale type">
422 <option value="linear" selected="true">Linear</option>
423 <option value="log">Log</option>
424 </param>
425 <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" />
426 <param name="minScore" label="Min score" type="integer" value="" optional="true"/>
427 <param name="maxScore" label="Max score" type="integer" value="" optional="true"/>
428 </when>
429 </conditional>
430 </section>
431 </xml>
432
433 <xml name="track_menu">
434 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">
435 <repeat name="track_menu" title="Track Menu">
436 <param label="Menu action"
437 type="select"
438 name="menu_action"
439 help="Action performed when user clicks on the menu">
440 <option value="iframeDialog" selected="true">iframeDialog: causes the given url to be opened in a popup dialog box within JBrowse, in an iframe element.</option>
441 <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option>
442 <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option>
443 </param>
444 <param label="Menu label"
445 type="text"
446 name="menu_label"
447 help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
448 <expand macro="menu_sanitize" />
449 </param>
450 <param label="Menu title"
451 type="text"
452 name="menu_title"
453 help="Will be displayed in the popup title bar if displayed ({id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
454 <expand macro="menu_sanitize" />
455 </param>
456 <param label="Menu url"
457 type="text"
458 name="menu_url"
459 help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
460 <expand macro="menu_sanitize" />
461 </param>
462 <param label="Menu icon"
463 type="select"
464 name="menu_icon"
465 help="Icon to display next to menu label">
466 <option value="dijitIconBookmark" selected="true">Bookmark</option>
467 <option value="dijitIconSave">Save</option>
468 <option value="dijitIconPrint">Print</option>
469 <option value="dijitIconCut">Cut</option>
470 <option value="dijitIconCopy">Copy</option>
471 <option value="dijitIconClear">Clear</option>
472 <option value="dijitIconDelete">Delete</option>
473 <option value="dijitIconUndo">Undo</option>
474 <option value="dijitIconEdit">Edit</option>
475 <option value="dijitIconNewTask">New Task</option>
476 <option value="dijitIconEditTask">Edit Task</option>
477 <option value="dijitIconEditProperty">Edit Property</option>
478 <option value="dijitIconTask">Task</option>
479 <option value="dijitIconFilter">Filter</option>
480 <option value="dijitIconConfigure">Configure</option>
481 <option value="dijitIconSearch">Search</option>
482 <option value="dijitIconApplication">Application</option>
483 <option value="dijitIconChart">Chart</option>
484 <option value="dijitIconConnector">Connector</option>
485 <option value="dijitIconDatabase">Database</option>
486 <option value="dijitIconDocuments">Documents</option>
487 <option value="dijitIconMail">Mail</option>
488 <option value="dijitLeaf">Leaf</option>
489 <option value="dijitIconFile">File</option>
490 <option value="dijitIconFunction">Function</option>
491 <option value="dijitIconKey">Key</option>
492 <option value="dijitIconPackage">Package</option>
493 <option value="dijitIconSample">Sample</option>
494 <option value="dijitIconTable">Table</option>
495 <option value="dijitIconUsers">Users</option>
496 <option value="dijitIconFolderClosed">Folder Closed</option>
497 <option value="dijitIconFolderOpen">Folder Open</option>
498 <option value="dijitIconError">Error</option>
499 </param>
500 </repeat>
501 </section>
502 </xml>
503
504 <xml name="menu_sanitize">
505 <sanitizer>
506 <valid>
507 <add value="{"/>
508 <add value="}"/>
509 <add value="!"/>
510 <add value="?"/>
511 <add value="&amp;"/>
512 <add value="+"/>
513 <add value="="/>
514 <add value="'"/>
515 <add value='"'/>
516 </valid>
517 </sanitizer>
518 </xml>
519
520 <xml name="input_conditional" token_label="Track Data" token_format="data">
521 <conditional name="useuri">
522 <param name="insource" type="select" label="Define track data as a history file or an internet URI"
523 help="A public URI implies that all the associated tabix files are also in place. They are created for history files">
524 <option value="history" selected="true">Track data from a history file</option>
525 <option value="uri" selected="true">Tabix data URI - index files must be available at corresponding URI</option>
526 </param>
527 <when value="history">
528 <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />
529 </when>
530 <when value="uri">
531 <param label="@LABEL@" name="annouri" type="text" />
532 <param label="Short name for track display" name="annoname" type="text" >
533 <sanitizer invalid_char="_">
534 <valid initial="string.printable" >
535 <remove value="'" />
536 </valid>
537 </sanitizer>
538 </param>
539 </when>
540 </conditional>
541 </xml>
542 <xml name="citations">
543 <citations>
544 <citation type="doi">10.1186/s13059-016-0924-1</citation>
545 <citation type="doi">10.1101/gr.094607.109</citation>
546 </citations>
547 </xml>
548 </macros>