Mercurial > repos > fubar > jbrowse2

comparison macros.xml @ 62:ab0d6782a95f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
author fubar
date Thu, 28 Mar 2024 04:51:06 +0000
parents 81d535970196
children c4eb6a85db70
comparison
equal deleted inserted replaced
61:e7a6f7a7148d 62:ab0d6782a95f
135 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option> 135 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
136 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option> 136 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
137 <option value="Spectral">Spectral</option> 137 <option value="Spectral">Spectral</option>
138 </param> 138 </param>
139 </xml> 139 </xml>
140
140 141
141 <xml name="general_options"> 142 <xml name="general_options">
142 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false"> 143 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false">
143 <conditional name="ucol"> 144 <conditional name="ucol">
144 <param name="formcoll" type="select" label="Convert a collection of track files rather than filling in the tool form" 145 <param name="formcoll" type="select" label="Convert a collection of track files rather than filling in the tool form"
370 <conditional name="track_style"> 371 <conditional name="track_style">
371 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> 372 <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="LinearAlignmentsDisplay" selected="true">LinearAlignmentsDisplay</option>
373 <option value="LinearPileupDisplay">LinearPileupDisplay</option> 374 <option value="LinearPileupDisplay">LinearPileupDisplay</option>
374 <option value="LinearSNPCoverageDisplay">LinearSNPCoverageDisplay</option> 375 <option value="LinearSNPCoverageDisplay">LinearSNPCoverageDisplay</option>
375 </param> 376 <option value="LinearReadArcsDisplay">LinearReadArcsDisplay</option>
377 <option value="LinearReadCloudDisplay">LinearReadCloudDisplay</option>
378 </param>
379 <!-- TODO check if possible to handle more options than just the display style-->
376 <when value="LinearAlignmentsDisplay"/> 380 <when value="LinearAlignmentsDisplay"/>
377 <when value="LinearPileupDisplay"/> 381 <when value="LinearPileupDisplay"/>
378 <when value="LinearSNPCoverageDisplay"> 382 <when value="LinearSNPCoverageDisplay">
379 <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" /> 383 <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"/> 384 <param name="minScore" label="Min score" type="integer" value="" optional="true"/>
381 <param name="maxScore" label="Max score" type="integer" value="" optional="true"/> 385 <param name="maxScore" label="Max score" type="integer" value="" optional="true"/>
382 </when> 386 </when>
387 <when value="LinearReadArcsDisplay"/>
388 <when value="LinearReadCloudDisplay"/>
383 </conditional> 389 </conditional>
384 </section> 390 </section>
385 </xml> 391 </xml>
386 392
387 <xml name="track_styling_vcf"> 393 <xml name="track_styling_vcf">
388 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> 394 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
389 <conditional name="track_style"> 395 <conditional name="track_style">
390 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> 396 <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> 397 <option value="LinearVariantDisplay" selected="true">LinearVariantDisplay</option>
398 <option value="LinearPairedArcDisplay">LinearPairedArcDisplay</option>
392 </param> 399 </param>
393 <when value="LinearVariantDisplay"> 400 <when value="LinearVariantDisplay">
394 <expand macro="track_styling_linear"/> 401 <expand macro="track_styling_linear"/>
395 </when> 402 </when>
403 <when value="LinearPairedArcDisplay"/>
396 </conditional> 404 </conditional>
397 </section> 405 </section>
398 </xml> 406 </xml>
399 407
400 <xml name="track_styling_bigwig"> 408 <xml name="track_styling_bigwig">
428 </when> 436 </when>
429 </conditional> 437 </conditional>
430 </section> 438 </section>
431 </xml> 439 </xml>
432 440
441 <!-- TODO use this -->
433 <xml name="track_menu"> 442 <xml name="track_menu">
434 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false"> 443 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">
435 <repeat name="track_menu" title="Track Menu"> 444 <repeat name="track_menu" title="Track Menu">
436 <param label="Menu action" 445 <param label="Menu action"
437 type="select" 446 type="select"