Mercurial > repos > iuc > jbrowse

comparison jbrowse.xml @ 26:08776ba76cf5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
author iuc
date Tue, 19 Feb 2019 15:43:37 -0500
parents 1cfc579079a6
children 61ce21e36cb5
comparison
equal deleted inserted replaced
25:1cfc579079a6 26:08776ba76cf5
273 #if str($track.data_format.track_config.canvas_options.subParts) != "": 273 #if str($track.data_format.track_config.canvas_options.subParts) != "":
274 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts> 274 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
275 #end if 275 #end if
276 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false": 276 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
277 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs> 277 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
278 #end if
279 #else if $track.data_format.track_config.track_class == 'JBrowse/View/Track/HTMLFeatures':
280 #if str($track.data_format.track_config.html_options.transcriptType) != "":
281 <transcriptType>${track.data_format.track_config.html_options.transcriptType}</transcriptType>
282 #end if 278 #end if
283 #end if 279 #end if
284 #if $track.data_format.match_part.match_part_select: 280 #if $track.data_format.match_part.match_part_select:
285 <match>${track.data_format.match_part.name}</match> 281 <match>${track.data_format.match_part.name}</match>
286 #end if 282 #end if
459 455
460 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> 456 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
461 457
462 <conditional name="track_config"> 458 <conditional name="track_config">
463 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class"> 459 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
460 <option value="NeatHTMLFeatures/View/Track/NeatFeatures" selected="true">Neat HTML Features</option>
461 <option value="NeatCanvasFeatures/View/Track/NeatFeatures">Neat Canvas Features</option>
464 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option> 462 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
465 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option> 463 <option value="JBrowse/View/Track/CanvasFeatures">Canvas Features</option>
466 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option><!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed --> 464 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option><!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
467 </param> 465 </param>
468 <when value="JBrowse/View/Track/CanvasFeatures"> 466 <when value="JBrowse/View/Track/CanvasFeatures">
469 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false"> 467 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
470 <param label="Transcript type" 468 <param label="Transcript type"
484 type="boolean" 482 type="boolean"
485 checked="false" 483 checked="false"
486 truevalue="true" 484 truevalue="true"
487 falsevalue="false" 485 falsevalue="false"
488 help="Check this your input files does not contain UTR features, but the UTR can be 'implied' from the difference between the exon and CDS boundaries"/> 486 help="Check this your input files does not contain UTR features, but the UTR can be 'implied' from the difference between the exon and CDS boundaries"/>
489 </section> 487 </section>
490 </when> 488 </when>
491 <when value="JBrowse/View/Track/HTMLFeatures"> 489 <when value="JBrowse/View/Track/HTMLFeatures" />
492 <section name="html_options" title="HTMLFeatures Options [Advanced]" expanded="false"> 490 <when value="BlastView/View/Track/CanvasFeatures" />
493 <param label="Transcript type" 491 <when value="NeatHTMLFeatures/View/Track/NeatFeatures" />
494 name="transcriptType" 492 <when value="NeatCanvasFeatures/View/Track/NeatFeatures" />
495 type="text"
496 value=""
497 help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')"
498 optional="True"/>
499 </section>
500 </when>
501 <!--when value="BlastView/View/Track/CanvasFeatures" /-->
502 </conditional> 493 </conditional>
503 <expand macro="track_styling" /> 494 <expand macro="track_styling" />
504 <expand macro="color_selection" /> 495 <expand macro="color_selection" />
505 <expand macro="track_menu" /> 496 <expand macro="track_menu" />
506 <expand macro="track_display" /> 497 <expand macro="track_display" />