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comparison jbrowse2.xml @ 57:94264fe60478 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
author fubar
date Thu, 21 Mar 2024 08:01:42 +0000
parents d6b0feb22584
children 0e592dcaeb7f
comparison
equal deleted inserted replaced
56:c0097a584a8a 57:94264fe60478
192 </trackFile> 192 </trackFile>
193 #end for 193 #end for
194 </files> 194 </files>
195 195
196 <options> 196 <options>
197 197 <style>
198 #if str($track.data_format.data_format_select) in ["gff", "bed", "vcf", "paf", "maf", "blastxml"]:
199 <type>${track.data_format.jbstyle.track_style.display}</type>
200 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
201 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels>
202 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions>
203 #end if
204 #end if
205 #if str($track.data_format.data_format_select) in ["bam", "cram"]:
206 <type>"LinearAlignmentsDisplay"</type>
207 #end if
208 </style>
198 #if str($track.data_format.data_format_select) == "bam": 209 #if str($track.data_format.data_format_select) == "bam":
199 <bam> 210 <bam>
200 #for $dataset in $track.data_format.useuri.annotation: 211 #for $dataset in $track.data_format.useuri.annotation:
201 <bam_index>${dataset.metadata.bam_index}</bam_index> 212 <bam_index>${dataset.metadata.bam_index}</bam_index>
202 #end for 213 #end for
347 <param label="Is this a protein blast search?" 358 <param label="Is this a protein blast search?"
348 type="boolean" 359 type="boolean"
349 name="is_protein" 360 name="is_protein"
350 truevalue="true" 361 truevalue="true"
351 falsevalue="false" /> 362 falsevalue="false" />
363 <expand macro="track_styling_feature" />
352 <expand macro="track_visibility" /> 364 <expand macro="track_visibility" />
353 </when> 365 </when>
354 <when value="vcf"> 366 <when value="vcf">
355 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" /> 367 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" />
356 <expand macro="track_styling_vcf"/> 368 <expand macro="track_styling_vcf"/>
371 help="Match_parts have options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)." 383 help="Match_parts have options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)."
372 optional="True"/> 384 optional="True"/>
373 </when> 385 </when>
374 <when value="false" /> 386 <when value="false" />
375 </conditional> 387 </conditional>
388 <expand macro="track_styling_feature" />
376 <expand macro="track_visibility" /> 389 <expand macro="track_visibility" />
377 </when> 390 </when>
378 <when value="bam"> 391 <when value="bam">
379 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> 392 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
380 <expand macro="track_visibility" /> 393 <expand macro="track_visibility" />
381 </when> 394 </when>
382 <when value="bed"> 395 <when value="bed">
383 <expand macro="input_conditional" label="BED Track Data" format="bed" /> 396 <expand macro="input_conditional" label="BED Track Data" format="bed" />
397 <expand macro="track_styling_feature" />
384 <expand macro="track_visibility" /> 398 <expand macro="track_visibility" />
385 </when> 399 </when>
386 <when value="cram"> 400 <when value="cram">
387 <expand macro="input_conditional" label="CRAM Track Data" format="cram" /> 401 <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
388 <expand macro="track_visibility" /> 402 <expand macro="track_visibility" />
389 </when> 403 </when>
390 <when value="maf"> 404 <when value="maf">
391 <expand macro="input_conditional" label="MAF Track Data" format="maf" /> 405 <expand macro="input_conditional" label="MAF Track Data" format="maf" />
406 <expand macro="track_styling_feature" />
392 <expand macro="track_visibility" /> 407 <expand macro="track_visibility" />
393 </when> 408 </when>
394 <when value="bigwig"> 409 <when value="bigwig">
395 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> 410 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
396 <expand macro="track_visibility" /> 411 <expand macro="track_visibility" />