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comparison jbrowse2.xml @ 59:f807e219cec3 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9
author fubar
date Fri, 22 Mar 2024 22:04:08 +0000
parents 0e592dcaeb7f
children 81d535970196
comparison
equal deleted inserted replaced
58:0e592dcaeb7f 59:f807e219cec3
137 </metadata> 137 </metadata>
138 <tracks> 138 <tracks>
139 #for $tg in $track_groups: 139 #for $tg in $track_groups:
140 #for $track in $tg.data_tracks: 140 #for $track in $tg.data_tracks:
141 #if $track.data_format.useuri.insource == "uri": 141 #if $track.data_format.useuri.insource == "uri":
142 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> 142 <track cat="${tg.category}" format="paf" visibility="${track.data_format.track_visibility}">
143 <files> 143 <files>
144 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" label="${track.data_format.useuri.annoname}" useuri="yes"> 144 <trackFile path="${ $track.data_format.useuri.insource.annouri}" ext="paf"
145 <metadata> 145 label="${track.data_format.useuri.insource.annoname}" useuri="yes">
146 <dataset id = "${track.data_format.useuri.annouri}" /> 146 <metadata>
147 </metadata> 147 <dataset id = "${track.data_format.useuri.insource.annouri}" />
148 </trackFile> 148 </metadata>
149 </files> 149 </trackFile>
150 <options/> 150 </files>
151 </track> 151 <options/>
152 </track>
152 #else if $track.data_format.useuri.insource == "history": 153 #else if $track.data_format.useuri.insource == "history":
153 #if $track.data_format.useuri.annotation: 154 #if $track.data_format.useuri.annotation:
154 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> 155 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
155 <files> 156 <files>
156 #for $dataset in $track.data_format.useuri.annotation: 157 #for $dataset in $track.data_format.useuri.annotation:
201 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels> 202 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels>
202 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> 203 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions>
203 #end if 204 #end if
204 #end if 205 #end if
205 #if str($track.data_format.data_format_select) in ["bam", "cram"]: 206 #if str($track.data_format.data_format_select) in ["bam", "cram"]:
206 <type>"LinearAlignmentsDisplay"</type> 207 <type>LinearAlignmentsDisplay</type>
208 #end if
209 #if str($track.data_format.data_format_select) in ["paf"]:
210 <type>LinearBasicDisplay</type>
207 #end if 211 #end if
208 </style> 212 </style>
209 #if str($track.data_format.data_format_select) == "bam": 213 #if str($track.data_format.data_format_select) == "bam":
210 <bam> 214 <bam>
211 #for $dataset in $track.data_format.useuri.annotation: 215 #for $dataset in $track.data_format.useuri.annotation:
233 #end if 237 #end if
234 </gff> 238 </gff>
235 #else if str($track.data_format.data_format_select) == "paf": 239 #else if str($track.data_format.data_format_select) == "paf":
236 <paf> 240 <paf>
237 <genome> 241 <genome>
238 #for gnome in $track.data_format.synteny_genome: 242 #for refgenome in $track.data_format.pafuseuri.refgenomes:
239 $gnome, 243 $refgenome.annotation,
240 #end for 244 #end for
241 </genome> 245 </genome>
242 <genome_label> 246 <genome_label>
243 #for gnome in $track.data_format.synteny_genome: 247 #for refgenome in $track.data_format.pafuseuri.refgenomes:
244 $gnome.name, 248 $refgenome.annoname,
245 #end for 249 #end for
246 </genome_label> 250 </genome_label>
247 </paf> 251 </paf>
248 #else if str($track.data_format.data_format_select) == "hic": 252 #else if str($track.data_format.data_format_select) == "hic":
249 <hic> 253 <hic>
325 value="Default" 329 value="Default"
326 help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/> 330 help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
327 <repeat name="data_tracks" title="Annotation Track"> 331 <repeat name="data_tracks" title="Annotation Track">
328 <conditional name="data_format" label="Track Data Selection Options"> 332 <conditional name="data_format" label="Track Data Selection Options">
329 <param type="select" label="Track Type" name="data_format_select"> 333 <param type="select" label="Track Type" name="data_format_select">
330 <option value="bam">BAM Pileup track</option> 334 <option value="bam">BAM track. Recommend convert to faster BED unless mapping annotation needed</option>
331 <option value="bed">BED track</option> 335 <option value="bed">BED track</option>
332 <option value="bigwig">BigWig track</option> 336 <option value="bigwig">BigWig track</option>
333 <option value="blastxml">Blast XML track - converted to GFF</option> 337 <option value="blastxml">Blast XML track (as GFF3)</option>
338 <option value="cram">CRAM track. Currently not advantageous over BAM in Galaxy. Convert to BED like BAM.</option>
339 <option value="gff">GFF/GFF3 track</option>
334 <option value="cool">HiC as cool/mcool/scool format files</option> 340 <option value="cool">HiC as cool/mcool/scool format files</option>
335 <option value="cram">CRAM</option>
336 <option value="gff">GFF/GFF3 feature track</option>
337 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> 341 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
338 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> 342 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
339 <option value="paf">PAF - approximate mapping positions between two set of sequences</option> 343 <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
340 <option value="vcf">VCF SNP</option> 344 <option value="vcf">VCF SNP track</option>
341 </param> 345 </param>
342 <when value="blastxml"> 346 <when value="blastxml">
343 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> 347 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
344 348
345 <param label="Features used in Blast Search" 349 <param label="Features used in Blast Search"
409 <when value="bigwig"> 413 <when value="bigwig">
410 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> 414 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
411 <expand macro="track_visibility" /> 415 <expand macro="track_visibility" />
412 </when> 416 </when>
413 <when value="paf"> 417 <when value="paf">
414 <param label="Comparison genome sequence" help="Paf from these as the reference(s), using the common reference as the reads to map" 418 <expand macro="input_conditional" label="PAF format synteny mapping data" format="paf"
415 format="fasta" 419 help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/>
416 name="synteny_genome" 420 <expand macro="pafref_conditional" label="Comparison genome sequence(s)"
417 type="data" 421 format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/>
418 multiple="True"/>
419 <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with mashmap or minimap2 mapping real reference onto desired syntenic references"/>
420 <expand macro="track_visibility" /> 422 <expand macro="track_visibility" />
421 </when> 423 </when>
422 424
423 <when value="hic"> 425 <when value="hic">
424 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" /> 426 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" />