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comparison x/galaxy.xml @ 131:69c6ea16c148 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 3cf9ec268c0719caf060b7d6bf5c0159909c348a
author fubar
date Sat, 12 Oct 2024 23:11:22 +0000
parents fbabf7498471
children
comparison
equal deleted inserted replaced
130:e188a9d25ed2 131:69c6ea16c148
1 <?xml version="1.0"?>
2 <root>
3 <metadata>
4 <general>
5 <defaultLocation></defaultLocation>
6 <zipOut>true</zipOut>
7 <bpPerPx>50</bpPerPx>
8 <analytics>false</analytics>
9 <primary_color>#0d233f</primary_color>
10 <secondary_color>#721e63</secondary_color>
11 <tertiary_color>#135560</tertiary_color>
12 <quaternary_color>#ffb11d</quaternary_color>
13 <font_size>10</font_size>
14 <session_name>New test session</session_name>
15 </general>
16 <galaxyUrl>http://localhost:8080</galaxyUrl>
17 </metadata>
18 <assembly>
19 <metadata>
20 <genomes>
21 <genome path="/tmp/tmpus622kw5/files/7/4/8/dataset_748d2461-ea0f-4e92-b129-e680b76d4c81.dat" label="Merlin" useuri="no">
22 <metadata>
23
24 <dataset id="801225f8dc4ca2f7"
25 hid="1"
26 size="171.6 KB"
27 edam_format="format_1929"
28 file_ext="fasta"
29 dname = "Merlin"
30 />
31 <history
32 user_email="planemo@galaxyproject.org"
33 user_id="1"
34 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
35 id="801225f8dc4ca2f7"
36 />
37 <metadata
38 dbkey="?"
39 data_lines="2881"
40 sequences="1"
41 />
42 <tool
43 tool_id="upload1"
44 tool_version="1.1.7"
45 />
46 </metadata>
47 </genome>
48 </genomes>
49 </metadata>
50 <tracks>
51 <track cat="Assembly properties" format="gff" visibility="default_on">
52 <files>
53 <trackFile path="/tmp/tmpus622kw5/files/b/7/d/dataset_b7de2a4d-8123-493d-99ad-6f251912ae1c.dat" ext="gff3" label="merlin.gff3" useuri="no">
54 <metadata>
55 <dataset id="f899122287bdd0b2" hid="2"
56 size="5.0 KB"
57 edam_format="format_1975"
58 file_ext="gff3" />
59 <history id="801225f8dc4ca2f7"
60 user_email="planemo@galaxyproject.org"
61 user_id="1"
62 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
63 <metadata
64 dbkey="?"
65 data_lines="9"
66 comment_lines="10"
67 columns="9"
68 column_names="[]"
69 delimiter="__tc__"
70 attributes="23"
71 />
72 <tool
73 tool_id="upload1"
74 tool_version="1.1.7"
75 />
76 </metadata>
77 </trackFile>
78 </files>
79 <options>
80 <style>
81 <type>LinearBasicDisplay</type>
82 <trackShowLabels>false</trackShowLabels>
83 <trackShowDescriptions>false</trackShowDescriptions>
84 </style>
85 <gff>
86 </gff>
87 </options>
88 </track>
89 <track cat="Assembly properties" format="bigwig" visibility="default_on">
90 <files>
91 <trackFile path="/tmp/tmpus622kw5/files/b/5/2/dataset_b523b4bc-c4b6-4eb0-a914-364fb4f91db4.dat" ext="bigwig" label="merlin.bw" useuri="no">
92 <metadata>
93 <dataset id="78cc944b7b4634f8" hid="3"
94 size="81.6 KB"
95 edam_format="format_3006"
96 file_ext="bigwig" />
97 <history id="801225f8dc4ca2f7"
98 user_email="planemo@galaxyproject.org"
99 user_id="1"
100 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
101 <metadata
102 dbkey="?"
103 />
104 <tool
105 tool_id="upload1"
106 tool_version="1.1.7"
107 />
108 </metadata>
109 </trackFile>
110 </files>
111 <options>
112 <style>
113 <type>LinearWiggleDisplay</type>
114 <color>#135560</color>
115 <autoscale>globalsd</autoscale>
116 <resolution>1</resolution>
117 <summaryScoreMode>whiskers</summaryScoreMode>
118 <filled>true</filled>
119 <scaleType>linear</scaleType>
120 <displayCrossHatches>true</displayCrossHatches>
121 <minScore></minScore>
122 <maxScore></maxScore>
123 </style>
124 </options>
125 </track>
126 <track cat="Assembly properties" format="bed" visibility="default_on">
127 <files>
128 <trackFile path="/tmp/tmpus622kw5/files/b/1/3/dataset_b132250a-57b0-4f00-a94b-be3b7b14fa98.dat" ext="bed" label="test-6.bed" useuri="no">
129 <metadata>
130 <dataset id="3628324a9a091ab7" hid="4"
131 size="180 bytes"
132 edam_format="format_3003"
133 file_ext="bed" />
134 <history id="801225f8dc4ca2f7"
135 user_email="planemo@galaxyproject.org"
136 user_id="1"
137 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
138 <metadata
139 dbkey="?"
140 data_lines="3"
141 comment_lines="0"
142 columns="6"
143 column_names="[]"
144 delimiter="__tc__"
145 chromCol="1"
146 startCol="2"
147 endCol="3"
148 strandCol="6"
149 viz_filter_cols="[4]"
150 />
151 <tool
152 tool_id="upload1"
153 tool_version="1.1.7"
154 />
155 </metadata>
156 </trackFile>
157 </files>
158 <options>
159 <style>
160 <type>LinearBasicDisplay</type>
161 <trackShowLabels>false</trackShowLabels>
162 <trackShowDescriptions>false</trackShowDescriptions>
163 </style>
164 <bed>
165 <usebedscore>false</usebedscore>
166 </bed>
167 </options>
168 </track>
169 <track cat="Assembly properties" format="vcf" visibility="default_on">
170 <files>
171 <trackFile path="/tmp/tmpus622kw5/files/4/9/6/dataset_49609184-5279-4c15-8e1a-b492552a02ff.dat" ext="vcf" label="merlin.vcf" useuri="no">
172 <metadata>
173 <dataset id="7e78e1a21bf444fa" hid="5"
174 size="1.5 KB"
175 edam_format="format_3016"
176 file_ext="vcf" />
177 <history id="801225f8dc4ca2f7"
178 user_email="planemo@galaxyproject.org"
179 user_id="1"
180 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
181 <metadata
182 dbkey="?"
183 data_lines="5"
184 comment_lines="18"
185 columns="12"
186 column_names="[]"
187 delimiter="__tc__"
188 viz_filter_cols="[5]"
189 sample_names="[NA00001,NA00002,NA00003]"
190 />
191 <tool
192 tool_id="upload1"
193 tool_version="1.1.7"
194 />
195 </metadata>
196 </trackFile>
197 </files>
198 <options>
199 <style>
200 <type>LinearVariantDisplay</type>
201 <trackShowLabels>false</trackShowLabels>
202 <trackShowDescriptions>false</trackShowDescriptions>
203 </style>
204 </options>
205 </track>
206 <track cat="Assembly properties" format="cram" visibility="default_on">
207 <files>
208 <trackFile path="/tmp/tmpus622kw5/files/8/6/5/dataset_86597dfb-d461-4ef9-9eb6-c8262351f18c.dat" ext="cram" label="merlin.cram" useuri="no">
209 <metadata>
210 <dataset id="80ac834e53a3892f" hid="6"
211 size="10.9 KB"
212 edam_format="format_3462"
213 file_ext="cram" />
214 <history id="801225f8dc4ca2f7"
215 user_email="planemo@galaxyproject.org"
216 user_id="1"
217 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
218 <metadata
219 dbkey="?"
220 cram_version="3.0"
221 cram_index="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
222 />
223 <tool
224 tool_id="upload1"
225 tool_version="1.1.7"
226 />
227 </metadata>
228 </trackFile>
229 </files>
230 <options>
231 <style>
232 <type>LinearAlignmentsDisplay</type>
233 </style>
234 <cram>
235 <cram_index>
236 /tmp/tmpus622kw5/files/8/6/5/dataset_86597dfb-d461-4ef9-9eb6-c8262351f18c.dat ~ /tmp/tmpus622kw5/files/_metadata_files/c/d/8/metadata_cd855eb8-90c3-478b-af5d-47ba048c1765.dat,
237 </cram_index>
238 </cram>
239 </options>
240 </track>
241 <track cat="Assembly properties" format="bam" visibility="default_on">
242 <files>
243 <trackFile path="/tmp/tmpus622kw5/files/d/6/8/dataset_d6878dfb-6c11-4673-a348-d7c441e5c7db.dat" ext="bam" label="merlin-sample.bam" useuri="no">
244 <metadata>
245 <dataset id="64ba8fadcb1fc688" hid="7"
246 size="13.0 KB"
247 edam_format="format_2572"
248 file_ext="bam" />
249 <history id="801225f8dc4ca2f7"
250 user_email="planemo@galaxyproject.org"
251 user_id="1"
252 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
253 <metadata
254 dbkey="?"
255 columns="12"
256 column_names="[QNAME,FLAG,RNAME,POS,MAPQ,CIGAR,MRNM,MPOS,ISIZE,SEQ,QUAL,OPT]"
257 bam_version="1.3"
258 sort_order="coordinate"
259 read_groups="[]"
260 reference_names="[Merlin]"
261 reference_lengths="[172788]"
262 bam_index="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
263 />
264 <tool
265 tool_id="upload1"
266 tool_version="1.1.7"
267 />
268 </metadata>
269 </trackFile>
270 </files>
271 <options>
272 <style>
273 <type>LinearAlignmentsDisplay</type>
274 </style>
275 <bam>
276 <bam_index>
277 /tmp/tmpus622kw5/files/d/6/8/dataset_d6878dfb-6c11-4673-a348-d7c441e5c7db.dat ~ /tmp/tmpus622kw5/files/_metadata_files/8/9/f/metadata_89f41037-55f2-4252-9884-5eba8bd4e748.dat,
278 </bam_index>
279 </bam>
280 </options>
281 </track>
282 <track cat="Assembly properties" format="maf" visibility="default_on">
283 <files>
284 <trackFile path="/tmp/tmpus622kw5/files/f/e/c/dataset_feca1abe-d55a-4ade-a506-1e1f99e76cb3.dat" ext="maf" label="merlinlastz.maf" useuri="no">
285 <metadata>
286 <dataset id="d64497191f3f5d7f" hid="8"
287 size="1.5 KB"
288 edam_format="format_3008"
289 file_ext="maf" />
290 <history id="801225f8dc4ca2f7"
291 user_email="planemo@galaxyproject.org"
292 user_id="1"
293 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
294 <metadata
295 dbkey="?"
296 data_lines="0"
297 species="[Merlin,Merlin1,Merlin2,Merlin3,Merlin4,Merlin5,Merlin6]"
298 blocks="6"
299 species_chromosomes="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
300 maf_index="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
301 />
302 <tool
303 tool_id="upload1"
304 tool_version="1.1.7"
305 />
306 </metadata>
307 </trackFile>
308 </files>
309 <options>
310 <style>
311 <type>LinearBasicDisplay</type>
312 <trackShowLabels>false</trackShowLabels>
313 <trackShowDescriptions>false</trackShowDescriptions>
314 </style>
315 </options>
316 </track>
317 <track cat="Assembly properties" format="blastxml" visibility="default_on">
318 <files>
319 <trackFile path="/tmp/tmpus622kw5/files/3/6/5/dataset_365aaf8d-17be-44d6-93c7-dc4952ef511b.dat" ext="blastxml" label="merlin.blastxml" useuri="no">
320 <metadata>
321 <dataset id="3a8027169fd7c75d" hid="9"
322 size="1.6 MB"
323 edam_format="format_3331"
324 file_ext="blastxml" />
325 <history id="801225f8dc4ca2f7"
326 user_email="planemo@galaxyproject.org"
327 user_id="1"
328 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
329 <metadata
330 dbkey="?"
331 data_lines="20455"
332 />
333 <tool
334 tool_id="upload1"
335 tool_version="1.1.7"
336 />
337 </metadata>
338 </trackFile>
339 </files>
340 <options>
341 <style>
342 <type>LinearBasicDisplay</type>
343 <trackShowLabels>false</trackShowLabels>
344 <trackShowDescriptions>false</trackShowDescriptions>
345 </style>
346 <blast>
347 <parent>None</parent>
348 <protein>false</protein>
349 <min_gap>10</min_gap>
350 </blast>
351 </options>
352 </track>
353 <track cat="Assembly properties" format="bam" visibility="default_on">
354 <files>
355 <trackFile path="/tmp/tmpus622kw5/files/c/d/9/dataset_cd94dba1-9bb2-4c84-ba3b-a9b269faf031.dat" ext="zip" label="files_0Xfile_data" useuri="no">
356 <metadata>
357 <dataset id="df6e27cbb08754e3" hid="10"
358 size="275.3 KB"
359 edam_format="format_2333"
360 file_ext="zip" />
361 <history id="801225f8dc4ca2f7"
362 user_email="planemo@galaxyproject.org"
363 user_id="1"
364 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
365 <metadata
366 dbkey="?"
367 />
368 <tool
369 tool_id="upload1"
370 tool_version="1.1.7"
371 />
372 </metadata>
373 </trackFile>
374 </files>
375 <options>
376 <style>
377 <type>LinearAlignmentsDisplay</type>
378 </style>
379 <bam>
380 <bam_index>
381 /tmp/tmpus622kw5/files/c/d/9/dataset_cd94dba1-9bb2-4c84-ba3b-a9b269faf031.dat ~ ,
382 </bam_index>
383 </bam>
384 </options>
385 </track>
386 </tracks>
387 </assembly>
388 <assembly>
389 <metadata>
390 <genomes>
391 <genome path="/tmp/tmpus622kw5/files/a/e/2/dataset_ae2fbecc-5b2d-4783-9ff9-dc4c0827a344.dat" label="dm3.fa" useuri="no">
392 <metadata>
393
394 <dataset id="47bf7b7c957123a5"
395 hid="11"
396 size="27.2 MB"
397 edam_format="format_1929"
398 file_ext="fasta"
399 dname = "dm3.fa"
400 />
401 <history
402 user_email="planemo@galaxyproject.org"
403 user_id="1"
404 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
405 id="801225f8dc4ca2f7"
406 />
407 <metadata
408 dbkey="?"
409 data_lines="401577"
410 sequences="1"
411 />
412 <tool
413 tool_id="upload1"
414 tool_version="1.1.7"
415 />
416 </metadata>
417 </genome>
418 </genomes>
419 </metadata>
420 <tracks>
421 <track cat="Assembly properties" format="cool" visibility="default_on">
422 <files>
423 <trackFile path="/tmp/tmpus622kw5/files/5/2/8/dataset_528eb872-92fa-4d06-bda9-b8c3522f6b50.dat" ext="cool" label="dm3test.cool" useuri="no">
424 <metadata>
425 <dataset id="b78501a0735fb2a5" hid="12"
426 size="250.1 KB"
427 edam_format="format_3590"
428 file_ext="cool" />
429 <history id="801225f8dc4ca2f7"
430 user_email="planemo@galaxyproject.org"
431 user_id="1"
432 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
433 <metadata
434 dbkey="?"
435 />
436 <tool
437 tool_id="upload1"
438 tool_version="1.1.7"
439 />
440 </metadata>
441 </trackFile>
442 </files>
443 <options>
444 <style>
445 <type>LinearHicDisplay</type>
446 </style>
447 <cool>
448 </cool>
449 </options>
450 </track>
451 </tracks>
452 </assembly>
453 <assembly>
454 <metadata>
455 <genomes>
456 <genome path="/tmp/tmpus622kw5/files/a/d/d/dataset_add7c5ef-1f3d-4c73-9d9c-43892361ebfe.dat" label="Ppersica1.fa" useuri="no">
457 <metadata>
458
459 <dataset id="1cd311606732130f"
460 hid="13"
461 size="46.2 MB"
462 edam_format="format_1929"
463 file_ext="fasta"
464 dname = "Ppersica1.fa"
465 />
466 <history
467 user_email="planemo@galaxyproject.org"
468 user_id="1"
469 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
470 id="801225f8dc4ca2f7"
471 />
472 <metadata
473 dbkey="?"
474 data_lines="598142"
475 sequences="1"
476 />
477 <tool
478 tool_id="upload1"
479 tool_version="1.1.7"
480 />
481 </metadata>
482 </genome>
483 </genomes>
484 </metadata>
485 <tracks>
486 <track cat="Assembly properties" format="paf" visibility="default_on">
487 <files>
488 <trackFile path="/tmp/tmpus622kw5/files/3/9/6/dataset_396ed6d5-d81e-4a2e-b566-1b69cf0a8ec0.dat" ext="paf" label="peach-grape-map.paf" useuri="no">
489 <metadata>
490 <dataset id="4a3497682f135c57" hid="14"
491 size="1.1 MB"
492 edam_format="format_2330"
493 file_ext="paf" />
494 <history id="801225f8dc4ca2f7"
495 user_email="planemo@galaxyproject.org"
496 user_id="1"
497 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
498 <metadata
499 dbkey="?"
500 data_lines="9291"
501 />
502 <tool
503 tool_id="upload1"
504 tool_version="1.1.7"
505 />
506 </metadata>
507 </trackFile>
508 </files>
509 <options>
510 <style>
511 </style>
512 <paf>
513 <genome>
514 /tmp/tmpus622kw5/files/e/4/4/dataset_e44ca09b-d9ff-4a99-a4cb-e50f24a66ff9.dat ~ Vvinifera1.fa,
515 </genome>
516 <useuri>
517 false
518 </useuri>
519 </paf>
520 </options>
521 </track>
522 <track cat="Assembly properties" format="paf" visibility="default_on">
523 <files>
524 <trackFile path="/tmp/tmpus622kw5/files/2/7/2/dataset_272188a9-0367-4677-9b28-ad5e84aceb99.dat" ext="paf" label="arabgrapepeach.paf" useuri="no">
525 <metadata>
526 <dataset id="edaefaa2c8238b09" hid="16"
527 size="12.8 MB"
528 edam_format="format_2330"
529 file_ext="paf" />
530 <history id="801225f8dc4ca2f7"
531 user_email="planemo@galaxyproject.org"
532 user_id="1"
533 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
534 <metadata
535 dbkey="?"
536 data_lines="129777"
537 />
538 <tool
539 tool_id="upload1"
540 tool_version="1.1.7"
541 />
542 </metadata>
543 </trackFile>
544 </files>
545 <options>
546 <style>
547 </style>
548 <paf>
549 <genome>
550 https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz ~ arabidopsis.URI,
551 https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz ~ Vvinifera1.URI,
552 </genome>
553 <useuri>
554 true
555 </useuri>
556 </paf>
557 </options>
558 </track>
559 <track cat="Assembly properties" format="paf" visibility="default_on">
560 <files>
561 <trackFile path="/tmp/tmpus622kw5/files/2/7/2/dataset_272188a9-0367-4677-9b28-ad5e84aceb99.dat" ext="paf" label="arabgrapepeach.paf" useuri="no">
562 <metadata>
563 <dataset id="edaefaa2c8238b09" hid="16"
564 size="12.8 MB"
565 edam_format="format_2330"
566 file_ext="paf" />
567 <history id="801225f8dc4ca2f7"
568 user_email="planemo@galaxyproject.org"
569 user_id="1"
570 display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
571 <metadata
572 dbkey="?"
573 data_lines="129777"
574 />
575 <tool
576 tool_id="upload1"
577 tool_version="1.1.7"
578 />
579 </metadata>
580 </trackFile>
581 </files>
582 <options>
583 <style>
584 </style>
585 <paf>
586 <genome>
587 /tmp/tmpus622kw5/files/e/4/4/dataset_e44ca09b-d9ff-4a99-a4cb-e50f24a66ff9.dat ~ Vvinifera1.fa,
588 </genome>
589 <useuri>
590 false
591 </useuri>
592 </paf>
593 </options>
594 </track>
595 </tracks>
596 </assembly>
597 <assembly>
598 <metadata>
599 <genomes>
600 <genome path="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz" label="hg38" useuri="yes">
601 <metadata>
602 <dataset
603 dname = "hg38" />
604 </metadata>
605 </genome>
606 </genomes>
607 </metadata>
608 <tracks>
609 <track cat="Assembly properties" format="hic" visibility="default_on">
610 <files>
611 <trackFile path="https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic" ext="hic"
612 label="humanhic" useuri="yes">
613 <metadata>
614 <dataset id = "https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic" />
615 </metadata>
616 </trackFile>
617 </files>
618 <options>
619 <style>
620 <type>LinearHicDisplay</type>
621 </style>
622 <hic>
623 </hic>
624 </options>
625 </track>
626 </tracks>
627 </assembly>
628 </root>