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comparison jbrowse.xml @ 27:61ce21e36cb5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
author iuc
date Wed, 20 Feb 2019 11:50:21 -0500
parents 08776ba76cf5
children 112eb40ba6cf
comparison
equal deleted inserted replaced
26:08776ba76cf5 27:61ce21e36cb5
264 <index>${track.data_format.index}</index> 264 <index>${track.data_format.index}</index>
265 </blast> 265 </blast>
266 #else if str($track.data_format.data_format_select) == "gene_calls": 266 #else if str($track.data_format.data_format_select) == "gene_calls":
267 <gff> 267 <gff>
268 <trackType>${track.data_format.track_config.track_class}</trackType> 268 <trackType>${track.data_format.track_config.track_class}</trackType>
269 #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures': 269 #if $track.data_format.track_config.track_class in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
270 #if str($track.data_format.track_config.canvas_options.transcriptType) != "": 270 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
271 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType> 271 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
272 #end if 272 #end if
273 #if str($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 $track.data_format.track_config.track_class in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
280 #if str($track.data_format.track_config.html_options.topLevelFeatures) != "":
281 <topLevelFeatures>${track.data_format.track_config.html_options.topLevelFeatures}</topLevelFeatures>
278 #end if 282 #end if
279 #end if 283 #end if
280 #if $track.data_format.match_part.match_part_select: 284 #if $track.data_format.match_part.match_part_select:
281 <match>${track.data_format.match_part.name}</match> 285 <match>${track.data_format.match_part.name}</match>
282 #end if 286 #end if
462 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option> 466 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
463 <option value="JBrowse/View/Track/CanvasFeatures">Canvas Features</option> 467 <option value="JBrowse/View/Track/CanvasFeatures">Canvas Features</option>
464 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option><!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed --> 468 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option><!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
465 </param> 469 </param>
466 <when value="JBrowse/View/Track/CanvasFeatures"> 470 <when value="JBrowse/View/Track/CanvasFeatures">
467 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false"> 471 <expand macro="canvas_options" />
468 <param label="Transcript type"
469 name="transcriptType"
470 type="text"
471 value=""
472 help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')"
473 optional="True"/>
474 <param label="Subfeatures type"
475 name="subParts"
476 type="text"
477 value=""
478 help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')"
479 optional="True"/>
480 <param label="Implied UTRs"
481 name="impliedUTRs"
482 type="boolean"
483 checked="false"
484 truevalue="true"
485 falsevalue="false"
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"/>
487 </section>
488 </when> 472 </when>
489 <when value="JBrowse/View/Track/HTMLFeatures" /> 473 <when value="JBrowse/View/Track/HTMLFeatures">
474 <expand macro="html_options" />
475 </when>
490 <when value="BlastView/View/Track/CanvasFeatures" /> 476 <when value="BlastView/View/Track/CanvasFeatures" />
491 <when value="NeatHTMLFeatures/View/Track/NeatFeatures" /> 477 <when value="NeatHTMLFeatures/View/Track/NeatFeatures">
492 <when value="NeatCanvasFeatures/View/Track/NeatFeatures" /> 478 <expand macro="html_options" />
493 </conditional> 479 </when>
494 <expand macro="track_styling" /> 480 <when value="NeatCanvasFeatures/View/Track/NeatFeatures">
481 <expand macro="canvas_options" />
482 </when>
483 </conditional>
484 <expand macro="track_styling"
485 classname="feature2"
486 label="product,name,id"
487 description="note,description"
488 height="10px"/>
495 <expand macro="color_selection" /> 489 <expand macro="color_selection" />
496 <expand macro="track_menu" /> 490 <expand macro="track_menu" />
497 <expand macro="track_display" /> 491 <expand macro="track_display" />
498 </when> 492 </when>
499 <when value="pileup"> 493 <when value="pileup">