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comparison jbrowse2.xml @ 88:efd1d41f11b4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
author fubar
date Sun, 14 Apr 2024 03:49:10 +0000
parents de8fb46bc3ef
children 408781c080fc
comparison
equal deleted inserted replaced
87:de8fb46bc3ef 88:efd1d41f11b4
1 <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_12" profile="22.05"> 1 <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_14" profile="22.05">
2 <description>genome browser</description> 2 <description>genome browser</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edamInc"/> 6 <expand macro="edamInc"/>
97 </metadata> 97 </metadata>
98 </genome> 98 </genome>
99 #else 99 #else
100 <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.name}" useuri="no"> 100 <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.name}" useuri="no">
101 <metadata> 101 <metadata>
102 #if $uglyTestingHack != "enabled": 102
103 <dataset id="${__app__.security.encode_id($assembly.reference_genome.genome.id)}" 103 <dataset id="${__app__.security.encode_id($assembly.reference_genome.genome.id)}"
104 hid="${assembly.reference_genome.genome.hid}" 104 hid="${assembly.reference_genome.genome.hid}"
105 size="${assembly.reference_genome.genome.get_size(nice_size=True)}" 105 size="${assembly.reference_genome.genome.get_size(nice_size=True)}"
106 edam_format="${assembly.reference_genome.genome.datatype.edam_format}" 106 edam_format="${assembly.reference_genome.genome.datatype.edam_format}"
107 file_ext="${assembly.reference_genome.genome.ext}" 107 file_ext="${assembly.reference_genome.genome.ext}"
133 /> 133 />
134 <tool 134 <tool
135 tool_id="${assembly.reference_genome.genome.creating_job.tool_id}" 135 tool_id="${assembly.reference_genome.genome.creating_job.tool_id}"
136 tool_version="${assembly.reference_genome.genome.creating_job.tool_version}" 136 tool_version="${assembly.reference_genome.genome.creating_job.tool_version}"
137 /> 137 />
138 #end if 138
139 </metadata> 139 </metadata>
140 </genome> 140 </genome>
141 #end if 141 #end if
142 </genomes> 142 </genomes>
143
144 </metadata> 143 </metadata>
145 <tracks> 144 <tracks>
146 #for $tg in $assembly.track_groups: 145 #for $tg in $assembly.track_groups:
147 #for $track in $tg.data_tracks: 146 #for $track in $tg.data_tracks:
147 #set input_exists = "False"
148 #if $track.data_format.useuri.insource == "uri": 148 #if $track.data_format.useuri.insource == "uri":
149 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> 149 #if $track.data_format.useuri.annouri:
150 <files> 150 #set input_exists = "True"
151 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" 151 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
152 label="${track.data_format.useuri.annoname}" useuri="yes"> 152 <files>
153 <metadata> 153 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}"
154 <dataset id = "${track.data_format.useuri.annouri}" /> 154 label="${track.data_format.useuri.annoname}" useuri="yes">
155 </metadata> 155 <metadata>
156 </trackFile> 156 <dataset id = "${track.data_format.useuri.annouri}" />
157 </files> 157 </metadata>
158 </trackFile>
159 </files>
160 #end if
158 #else if $track.data_format.useuri.insource == "history": 161 #else if $track.data_format.useuri.insource == "history":
159 #if $track.data_format.useuri.annotation: 162 #if $track.data_format.useuri.annotation:
163 #set input_exists = "True"
160 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> 164 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
161 <files> 165 <files>
162 #for $dataset in $track.data_format.useuri.annotation: 166 #for $dataset in $track.data_format.useuri.annotation:
163 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no"> 167 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no">
164 <metadata> 168 <metadata>
165 #if $uglyTestingHack != "enabled": 169
166 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" 170 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
167 size="${dataset.get_size(nice_size=True)}" 171 size="${dataset.get_size(nice_size=True)}"
168 edam_format="${dataset.datatype.edam_format}" 172 edam_format="${dataset.datatype.edam_format}"
169 file_ext="${dataset.ext}" /> 173 file_ext="${dataset.ext}" />
170 <history id="${__app__.security.encode_id($dataset.history_id)}" 174 <history id="${__app__.security.encode_id($dataset.history_id)}"
192 /> 196 />
193 <tool 197 <tool
194 tool_id="${dataset.creating_job.tool_id}" 198 tool_id="${dataset.creating_job.tool_id}"
195 tool_version="${dataset.creating_job.tool_version}" 199 tool_version="${dataset.creating_job.tool_version}"
196 /> 200 />
197 #end if
198 </metadata> 201 </metadata>
199 </trackFile> 202 </trackFile>
200 #end for 203 #end for
201 </files> 204 </files>
202 #end if 205 #end if
206 #end if
207 #if $input_exists == "True":
208 <options>
209 <style>
210 #if str($track.data_format.data_format_select) in ["gff", "bed", "maf", "blastxml"]:
211 <type>${track.data_format.jbstyle.display}</type>
212 #if str($track.data_format.jbstyle.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
213 <trackShowLabels>${track.data_format.jbstyle.show_labels}</trackShowLabels>
214 <trackShowDescriptions>${track.data_format.jbstyle.show_descriptions}</trackShowDescriptions>
215 #end if
216 #else if str($track.data_format.data_format_select) == "vcf":
217 <type>${track.data_format.jbstyle.track_style.display}</type>
218 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
219 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels>
220 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions>
221 #end if
222
223 #end if
224 #if str($track.data_format.data_format_select) in ["bam", "cram"]:
225 <type>LinearAlignmentsDisplay</type>
226 #end if
227 #if str($track.data_format.data_format_select) in ["hic", "cool", "mcool", "scool"]:
228 <type>LinearHicDisplay</type>
229 #end if
230 </style>
231 #if str($track.data_format.data_format_select) == "bam":
232 <bam>
233 <bam_index>
234 #for $dataset in $track.data_format.useuri.annotation:
235 ${dataset.name},${dataset.metadata.bam_index}
236 #end for
237 </bam_index>
238 </bam>
239 #else if str($track.data_format.data_format_select) == "cram":
240 <cram>
241 <cram_index>
242 #for $dataset in $track.data_format.useuri.annotation:
243 ${dataset.name},${dataset.metadata.cram_index}
244 #end for
245 </cram_index>
246 </cram>
247 #else if str($track.data_format.data_format_select) == "blastxml":
248 <blast>
249 #if str($track.data_format.blast_parent) != "":
250 <parent>${track.data_format.blast_parent}</parent>
251 #end if
252 <protein>${track.data_format.is_protein}</protein>
253 <min_gap>${track.data_format.min_gap}</min_gap>
254 </blast>
255 #else if str($track.data_format.data_format_select) == "gff":
256 <gff>
257 #if $track.data_format.match_part.match_part_select == "true":
258 <match>${track.data_format.match_part.name}</match>
259 #end if
260 </gff>
261 #else if str($track.data_format.data_format_select) == "paf":
262 <paf>
263 #if $track.data_format.pafuseuri.insource == "history":
264 <genome>
265 #for $anno in $track.data_format.pafuseuri.annotation:
266 ${anno},
267 #end for
268 </genome>
269 <genome_label>
270 #for $anno in $track.data_format.pafuseuri.annotation:
271 ${anno.name},
272 #end for
273 </genome_label>
274 #else:
275 <genome>
276 #for $refgenome in $track.data_format.pafuseuri.refuri:
277 $refgenome.annotation,
278 #end for
279 </genome>
280 <genome_label>
281 #for $refgenome in $track.data_format.pafuseuri.refuri:
282 ${refgenome.annoname},
283 #end for
284 </genome_label>
285 #end if
286 </paf>
287 #else if str($track.data_format.data_format_select) == "hic":
288 <hic>
289 </hic>
290 #else if str($track.data_format.data_format_select) == "cool":
291 <cool>
292 </cool>
293 #else if str($track.data_format.data_format_select) == "bed":
294 <bed>
295 </bed>
296 #else if str($track.data_format.data_format_select) == "sparql":
297 <label>${track.data_format.label}</label>
298 <sparql>
299 <url>${track.data_format.url}</url>
300 <query>${track.data_format.query}</query>
301 <query_refnames>${track.data_format.query_refnames}</query_refnames>
302 </sparql>
303 #end if
304 </options>
305 </track>
203 #end if 306 #end if
204 #if $uglyTestingHack != "enabled":
205 <options>
206 <style>
207 #if str($track.data_format.data_format_select) in ["gff", "bed", "maf", "blastxml"]:
208 <type>${track.data_format.jbstyle.display}</type>
209 #if str($track.data_format.jbstyle.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
210 <trackShowLabels>${track.data_format.jbstyle.show_labels}</trackShowLabels>
211 <trackShowDescriptions>${track.data_format.jbstyle.show_descriptions}</trackShowDescriptions>
212 #end if
213 #else if str($track.data_format.data_format_select) == "vcf":
214 <type>${track.data_format.jbstyle.track_style.display}</type>
215 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
216 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels>
217 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions>
218 #end if
219
220 #end if
221 #if str($track.data_format.data_format_select) in ["bam", "cram"]:
222 <type>LinearAlignmentsDisplay</type>
223 #end if
224 #if str($track.data_format.data_format_select) in ["hic", "cool", "mcool", "scool"]:
225 <type>LinearHicDisplay</type>
226 #end if
227 </style>
228 #if str($track.data_format.data_format_select) == "bam":
229 <bam>
230 <bam_index>
231 #for $dataset in $track.data_format.useuri.annotation:
232 ${dataset.name},${dataset.metadata.bam_index}
233 #end for
234 </bam_index>
235 </bam>
236 #else if str($track.data_format.data_format_select) == "cram":
237 <cram>
238 <cram_index>
239 #for $dataset in $track.data_format.useuri.annotation:
240 ${dataset.name},${dataset.metadata.cram_index}
241 #end for
242 </cram_index>
243 </cram>
244 #else if str($track.data_format.data_format_select) == "blastxml":
245 <blast>
246 #if str($track.data_format.blast_parent) != "":
247 <parent>${track.data_format.blast_parent}</parent>
248 #end if
249 <protein>${track.data_format.is_protein}</protein>
250 <min_gap>${track.data_format.min_gap}</min_gap>
251 </blast>
252 #else if str($track.data_format.data_format_select) == "gff":
253 <gff>
254 #if $track.data_format.match_part.match_part_select == "true":
255 <match>${track.data_format.match_part.name}</match>
256 #end if
257 </gff>
258 #else if str($track.data_format.data_format_select) == "paf":
259 <paf>
260 #if $track.data_format.pafuseuri.insource == "history":
261 <genome>
262 #for $anno in $track.data_format.pafuseuri.annotation:
263 ${anno},
264 #end for
265 </genome>
266 <genome_label>
267 #for $anno in $track.data_format.pafuseuri.annotation:
268 ${anno.name},
269 #end for
270 </genome_label>
271 #else:
272 <genome>
273 #for $refgenome in $track.data_format.pafuseuri.refuri:
274 $refgenome.annotation,
275 #end for
276 </genome>
277 <genome_label>
278 #for $refgenome in $track.data_format.pafuseuri.refuri:
279 ${refgenome.annoname},
280 #end for
281 </genome_label>
282 #end if
283 </paf>
284 #else if str($track.data_format.data_format_select) == "hic":
285 <hic>
286 </hic>
287 #else if str($track.data_format.data_format_select) == "cool":
288 <cool>
289 </cool>
290 #else if str($track.data_format.data_format_select) == "bed":
291 <bed>
292 </bed>
293 #else if str($track.data_format.data_format_select) == "sparql":
294 <label>${track.data_format.label}</label>
295 <sparql>
296 <url>${track.data_format.url}</url>
297 <query>${track.data_format.query}</query>
298 <query_refnames>${track.data_format.query_refnames}</query_refnames>
299 </sparql>
300 #end if
301 </options>
302 #end if
303 </track>
304 #end for 307 #end for
305 #end for 308 #end for
306 </tracks> 309 </tracks>
307 </assembly> 310 </assembly>
308 #end for 311 #end for
309 #end if 312 #end if
310 </root> 313 </root>
311 ]]></configfile> 314 ]]></configfile>
312 </configfiles> 315 </configfiles>
313 <inputs> 316 <inputs>
314 <repeat name="assemblies" min="1" title="Genome Assembly" help="When too many genomes are never enough"> 317 <repeat name="assemblies" min="1" title="Genome reference to provide display coordinates for this set of tracks"
318 help="JBrowse2 can show a set of tracks for each of multiple genome reference fasta files">
315 <conditional name="reference_genome"> 319 <conditional name="reference_genome">
316 <param help="Select a built in, history or remote tabix URI for the reference track" 320 <param help="Select a built in, history or remote tabix URI for the reference track"
317 label="Reference genome source" name="genome_type_select" type="select"> 321 label="Reference genome source" name="genome_type_select" type="select">
318 <option selected="True" value="indexed">Use a built-in genome</option> 322 <option selected="True" value="indexed">Use a Galaxy server built-in genome</option>
319 <option value="history">Use a genome from history</option> 323 <option value="history">Use a genome fasta file from the current history</option>
320 <option value="uri">URI for a reference as tabix with predictable index file URI</option> 324 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as tabix bgzip with predictable index file URI</option>
321 </param> 325 </param>
322 <when value="indexed"> 326 <when value="indexed">
323 <param 327 <param
324 help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome" 328 help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome"
325 label="Select a built in reference genome or custom genome" 329 label="Select a built in reference genome or custom genome"
378 <option value="paf">PAF - approximate mapping positions between two set of sequences</option> 382 <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
379 <option value="vcf">VCF SNP track</option> 383 <option value="vcf">VCF SNP track</option>
380 </param> 384 </param>
381 <when value="blastxml"> 385 <when value="blastxml">
382 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> 386 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
383
384 <param label="Features used in Blast Search" 387 <param label="Features used in Blast Search"
385 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature 388 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature
386 IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, 389 IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this,
387 blastp results on a protein sequence don't need this." 390 blastp results on a protein sequence don't need this."
388 format="gff3" 391 format="gff3"
389 name="blast_parent" 392 name="blast_parent"
390 optional="true" 393 optional="true"
391 type="data"/> 394 type="data"/>
392
393 <param label="Minimum Gap Size" 395 <param label="Minimum Gap Size"
394 help="before a new match_part feature is created" 396 help="before a new match_part feature is created"
395 name="min_gap" 397 name="min_gap"
396 type="integer" 398 type="integer"
397 value="10" 399 value="10"
457 help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/> 459 help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/>
458 <expand macro="pafref_conditional" label="Comparison genome sequence(s)" 460 <expand macro="pafref_conditional" label="Comparison genome sequence(s)"
459 format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/> 461 format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/>
460 <expand macro="track_visibility" /> 462 <expand macro="track_visibility" />
461 </when> 463 </when>
462
463 <when value="hic"> 464 <when value="hic">
464 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" /> 465 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" />
465 <expand macro="track_visibility" /> 466 <expand macro="track_visibility" />
466 </when> 467 </when>
467 <when value="cool"> 468 <when value="cool">
562 <param name="insource" value="history"/> 563 <param name="insource" value="history"/>
563 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.blastxml"/> 564 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.blastxml"/>
564 </conditional> 565 </conditional>
565 </conditional> 566 </conditional>
566 </repeat> 567 </repeat>
568 <repeat name="data_tracks">
569 <conditional name="data_format">
570 <param name="data_format_select" value="bam"/>
571 <conditional name="useuri">
572 <param name="insource" value="history"/>
573 <param name="annotation" value=""/>
574 </conditional>
575 </conditional>
576 </repeat>
567 </repeat> 577 </repeat>
568 </repeat> 578 </repeat>
569 <repeat name="assemblies"> 579 <repeat name="assemblies">
570 <conditional name="reference_genome"> 580 <conditional name="reference_genome">
571 <param name="genome_type_select" value="history"/> 581 <param name="genome_type_select" value="history"/>
656 <has_archive_member path="merlin.vcf_3.vcf.tbi"/> 666 <has_archive_member path="merlin.vcf_3.vcf.tbi"/>
657 <has_archive_member path="merlin.cram_4.cram"/> 667 <has_archive_member path="merlin.cram_4.cram"/>
658 <has_archive_member path="merlin-sample.bam_5.bam"/> 668 <has_archive_member path="merlin-sample.bam_5.bam"/>
659 <has_archive_member path="merlinlastz.maf_6.maf.sorted.bed.gz.tbi"/> 669 <has_archive_member path="merlinlastz.maf_6.maf.sorted.bed.gz.tbi"/>
660 <has_archive_member path="merlin.blastxml_7.blastxml.gz"/> 670 <has_archive_member path="merlin.blastxml_7.blastxml.gz"/>
661 <has_archive_member path="dm3test.cool_8.cool.hic"/> 671 <has_archive_member path="dm3test.cool_9.cool.hic"/>
662 <has_archive_member path="peach-grape-map.paf_9.paf"/> 672 <has_archive_member path="peach-grape-map.paf_10.paf"/>
663 <has_archive_member path="Merlin.fa.gz.fai"/> 673 <has_archive_member path="Merlin.fa.gz.fai"/>
664 <has_archive_member path="config.json"> 674 <has_archive_member path="config.json">
665 <has_json_property_with_text property="name" text="Merlin" /> 675 <has_json_property_with_text property="name" text="Merlin" />
666 </has_archive_member> 676 </has_archive_member>
667 677