Mercurial > repos > iuc > jbrowse

comparison jbrowse.xml @ 10:1a6d882d340d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
author iuc
date Fri, 02 Dec 2016 17:58:54 -0500
parents ad4b9d7eae6a
children db5fe5a3176a
comparison
equal deleted inserted replaced
9:f422ba2e9aa5 10:1a6d882d340d
214 <min_gap>${track.data_format.min_gap}</min_gap> 214 <min_gap>${track.data_format.min_gap}</min_gap>
215 <index>${track.data_format.index}</index> 215 <index>${track.data_format.index}</index>
216 </blast> 216 </blast>
217 #else if str($track.data_format.data_format_select) == "gene_calls": 217 #else if str($track.data_format.data_format_select) == "gene_calls":
218 <gff> 218 <gff>
219 <trackType>${track.data_format.track_class}</trackType> 219 <trackType>${track.data_format.track_config.track_class}</trackType>
220 #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures':
221 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
222 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
223 #end if
224 #if str($track.data_format.track_config.canvas_options.subParts) != "":
225 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
226 #end if
227 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
228 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
229 #end if
230 #end if
220 #if $track.data_format.match_part.match_part_select: 231 #if $track.data_format.match_part.match_part_select:
221 <match>${track.data_format.match_part.name}</match> 232 <match>${track.data_format.match_part.name}</match>
222 #end if 233 #end if
223 <index>${track.data_format.index}</index> 234 <index>${track.data_format.index}</index>
224 </gff> 235 </gff>
379 <when value="false" /> 390 <when value="false" />
380 </conditional> 391 </conditional>
381 392
382 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> 393 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
383 394
384 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class"> 395 <conditional name="track_config">
385 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option> 396 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
386 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option> 397 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
387 </param> 398 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
399 </param>
400 <when value="JBrowse/View/Track/CanvasFeatures">
401 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
402 <param label="Transcript type"
403 name="transcriptType"
404 type="text"
405 value=""
406 help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')"
407 optional="True"/>
408 <param label="Subfeatures type"
409 name="subParts"
410 type="text"
411 value=""
412 help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')"
413 optional="True"/>
414 <param label="Implied UTRs"
415 name="impliedUTRs"
416 type="boolean"
417 checked="false"
418 truevalue="true"
419 falsevalue="false"
420 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"/>
421 </section>
422 </when>
423 <when value="JBrowse/View/Track/HTMLFeatures" />
424 </conditional>
388 <expand macro="track_styling" /> 425 <expand macro="track_styling" />
389 <expand macro="color_selection" /> 426 <expand macro="color_selection" />
390 <expand macro="track_menu" /> 427 <expand macro="track_menu" />
391 <expand macro="track_display" /> 428 <expand macro="track_display" />
392 </when> 429 </when>
727 </repeat> 764 </repeat>
728 765
729 <param name="uglyTestingHack" value="enabled" /> 766 <param name="uglyTestingHack" value="enabled" />
730 <output name="output" file="menus/test.xml" lines_diff="6"/> 767 <output name="output" file="menus/test.xml" lines_diff="6"/>
731 </test> 768 </test>
769 <test>
770 <param name="reference_genome|genome_type_select" value="history"/>
771 <param name="reference_genome|genomes" value="merlin.fa"/>
772 <param name="gencode" value="11" />
773 <param name="standalone" value="Data Directory" />
774
775 <repeat name="track_groups">
776 <param name="category" value="With canvas config" />
777 <repeat name="data_tracks">
778 <conditional name="data_format">
779 <param name="data_format_select" value="gene_calls"/>
780 <param name="annotation" value="gff3/1.gff"/>
781 <conditional name="match_part">
782 <param name="match_part_select" value="false"/>
783 </conditional>
784 <conditional name="track_config">
785 <section name="canvas_options">
786 <param name="transcriptType" value="transcript"/>
787 <param name="subParts" value="exon"/>
788 <param name="impliedUTRs" value="true"/>
789 </section>
790 </conditional>
791 <section name="jbcolor_scale">
792 <conditional name="color_score">
793 <param name="color_score_select" value="none"/>
794 </conditional>
795 <conditional name="color">
796 <param name="color_select" value="automatic"/>
797 </conditional>
798 </section>
799 </conditional>
800 </repeat>
801 </repeat>
802
803 <param name="uglyTestingHack" value="enabled" />
804 <output name="output" file="track_config/test.xml" lines_diff="6"/>
805 </test>
732 </tests> 806 </tests>
733 <help><![CDATA[ 807 <help><![CDATA[
734 JBrowse-in-Galaxy 808 JBrowse-in-Galaxy
735 ================= 809 =================
736 810