Mercurial > repos > iuc > jbrowse
comparison jbrowse.xml @ 26:08776ba76cf5 draft
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 |
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| 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" /> |