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comparison test-data/gff3/test.xml @ 34:9de82b4963e6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
author iuc
date Wed, 11 Sep 2019 09:40:36 -0400
parents 2bb2e07a7a21
children
comparison
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33:0ae74c70b267 34:9de82b4963e6
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <root> 2 <root>
3 <metadata> 3 <metadata>
4 <gencode>11</gencode> 4 <gencode>11</gencode>
5 <genomes> 5 <genomes>
6 <genome path="/tmp/tmpTx5wXw/files/000/dataset_5.dat"> 6 <genome path="/tmp/tmpqkd9zdgq/files/b/f/a/dataset_bfad32fe-cc05-405c-965c-6fe9b7a36908.dat">
7 <metadata> 7 <metadata>
8 <dataset id="7b55dbb89df8f4e5" hid="1" 8 <dataset id="b842d972534ccb3e" hid="1"
9 size="171.6 KB" 9 size="171.6 KB"
10 edam_format="format_1929" 10 edam_format="format_1929"
11 file_ext="fasta" /> 11 file_ext="fasta" />
12 <history id="54f2a3a23292eb07" 12 <history id="8155e4b4bf1581ff"
13 user_email="test@bx.psu.edu" 13 user_email="test@bx.psu.edu"
14 user_id="2" 14 user_id="2"
15 display_name="test_history"/> 15 display_name="test_history"/>
16 <metadata 16 <metadata
17 dbkey="?" 17 dbkey="?"
40 <galaxyUrl>http://localhost</galaxyUrl> 40 <galaxyUrl>http://localhost</galaxyUrl>
41 </metadata> 41 </metadata>
42 <tracks> 42 <tracks>
43 <track cat="Auto Coloured" format="gene_calls" visibility="default_off"> 43 <track cat="Auto Coloured" format="gene_calls" visibility="default_off">
44 <files> 44 <files>
45 <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_6.dat" ext="gff3" label="gff3/A.gff"> 45 <trackFile path="/tmp/tmpqkd9zdgq/files/7/6/2/dataset_7625da24-6a53-41c2-a7fc-c5c9719deccc.dat" ext="gff3" label="A.gff">
46 <metadata> 46 <metadata>
47 <dataset id="fa6d20d0fb68383f" hid="2" 47 <dataset id="5449172d6ff5669b" hid="2"
48 size="2.3 KB" 48 size="2.3 KB"
49 edam_format="format_1975" 49 edam_format="format_1975"
50 file_ext="gff3" /> 50 file_ext="gff3" />
51 <history id="54f2a3a23292eb07" 51 <history id="8155e4b4bf1581ff"
52 user_email="test@bx.psu.edu" 52 user_email="test@bx.psu.edu"
53 user_id="2" 53 user_id="2"
54 display_name="test_history"/> 54 display_name="test_history"/>
55 <metadata 55 <metadata
56 dbkey="?" 56 dbkey="?"
57 data_lines="27" 57 data_lines="27"
58 comment_lines="19" 58 comment_lines="19"
59 columns="9" 59 columns="9"
60 delimiter="__tc__" 60 delimiter="__tc__"
61 attributes="6" 61 attributes="6"
62 /> 62 />
63 <tool 63 <tool
64 tool_id="upload1" 64 tool_id="upload1"
65 tool_version="1.1.6" 65 tool_version="1.1.6"
66 /> 66 />
67 </metadata> 67 </metadata>
68 </trackFile> 68 </trackFile>
69 <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_7.dat" ext="gff3" label="gff3/B.gff"> 69 <trackFile path="/tmp/tmpqkd9zdgq/files/c/f/c/dataset_cfcde690-dc99-4152-87ef-0936eb90f2ca.dat" ext="gff3" label="B.gff">
70 <metadata> 70 <metadata>
71 <dataset id="683bc220e21425bb" hid="3" 71 <dataset id="9ce08b2254e4d5ed" hid="3"
72 size="2.3 KB" 72 size="2.3 KB"
73 edam_format="format_1975" 73 edam_format="format_1975"
74 file_ext="gff3" /> 74 file_ext="gff3" />
75 <history id="54f2a3a23292eb07" 75 <history id="8155e4b4bf1581ff"
76 user_email="test@bx.psu.edu" 76 user_email="test@bx.psu.edu"
77 user_id="2" 77 user_id="2"
78 display_name="test_history"/> 78 display_name="test_history"/>
79 <metadata 79 <metadata
80 dbkey="?" 80 dbkey="?"
81 data_lines="27" 81 data_lines="27"
82 comment_lines="19" 82 comment_lines="19"
83 columns="9" 83 columns="9"
84 delimiter="__tc__" 84 delimiter="__tc__"
85 attributes="6" 85 attributes="6"
86 /> 86 />
87 <tool 87 <tool
88 tool_id="upload1" 88 tool_id="upload1"
89 tool_version="1.1.6" 89 tool_version="1.1.6"
90 /> 90 />
91 </metadata> 91 </metadata>
92 </trackFile> 92 </trackFile>
93 <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_8.dat" ext="gff3" label="gff3/C.gff"> 93 <trackFile path="/tmp/tmpqkd9zdgq/files/1/c/4/dataset_1c41cecd-9fc6-47b5-9f0b-b7bb73498675.dat" ext="gff3" label="C.gff">
94 <metadata> 94 <metadata>
95 <dataset id="a90a30fafe298e1e" hid="4" 95 <dataset id="80b8022ff3f677b7" hid="4"
96 size="2.3 KB" 96 size="2.3 KB"
97 edam_format="format_1975" 97 edam_format="format_1975"
98 file_ext="gff3" /> 98 file_ext="gff3" />
99 <history id="54f2a3a23292eb07" 99 <history id="8155e4b4bf1581ff"
100 user_email="test@bx.psu.edu" 100 user_email="test@bx.psu.edu"
101 user_id="2" 101 user_id="2"
102 display_name="test_history"/> 102 display_name="test_history"/>
103 <metadata 103 <metadata
104 dbkey="?" 104 dbkey="?"
105 data_lines="27" 105 data_lines="27"
106 comment_lines="19" 106 comment_lines="19"
107 columns="9" 107 columns="9"
108 delimiter="__tc__" 108 delimiter="__tc__"
109 attributes="6" 109 attributes="6"
110 /> 110 />
111 <tool 111 <tool
112 tool_id="upload1" 112 tool_id="upload1"
113 tool_version="1.1.6" 113 tool_version="1.1.6"
114 /> 114 />
115 </metadata> 115 </metadata>
116 </trackFile> 116 </trackFile>
117 <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_9.dat" ext="gff3" label="gff3/D.gff"> 117 <trackFile path="/tmp/tmpqkd9zdgq/files/5/b/3/dataset_5b33c8ff-b12b-4307-a35c-92ea8571dc04.dat" ext="gff3" label="D.gff">
118 <metadata> 118 <metadata>
119 <dataset id="b842d972534ccb3e" hid="5" 119 <dataset id="b54fb481e575bccc" hid="5"
120 size="2.3 KB" 120 size="2.3 KB"
121 edam_format="format_1975" 121 edam_format="format_1975"
122 file_ext="gff3" /> 122 file_ext="gff3" />
123 <history id="54f2a3a23292eb07" 123 <history id="8155e4b4bf1581ff"
124 user_email="test@bx.psu.edu" 124 user_email="test@bx.psu.edu"
125 user_id="2" 125 user_id="2"
126 display_name="test_history"/> 126 display_name="test_history"/>
127 <metadata 127 <metadata
128 dbkey="?" 128 dbkey="?"
161 <custom_config> 161 <custom_config>
162 </custom_config> 162 </custom_config>
163 163
164 <gff> 164 <gff>
165 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> 165 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
166 <topLevelFeatures>mRNA</topLevelFeatures>
167 <index>false</index> 166 <index>false</index>
168 </gff> 167 </gff>
169 </options> 168 </options>
170 </track> 169 </track>
171 <track cat="Ignore Scale" format="gene_calls" visibility="default_off"> 170 <track cat="Ignore Scale" format="gene_calls" visibility="default_off">
172 <files> 171 <files>
173 <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff"> 172 <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
174 <metadata> 173 <metadata>
175 <dataset id="5449172d6ff5669b" hid="6" 174 <dataset id="1ae74d26531588b0" hid="6"
176 size="2.3 KB" 175 size="2.3 KB"
177 edam_format="format_1975" 176 edam_format="format_1975"
178 file_ext="gff3" /> 177 file_ext="gff3" />
179 <history id="54f2a3a23292eb07" 178 <history id="8155e4b4bf1581ff"
180 user_email="test@bx.psu.edu" 179 user_email="test@bx.psu.edu"
181 user_id="2" 180 user_id="2"
182 display_name="test_history"/> 181 display_name="test_history"/>
183 <metadata 182 <metadata
184 dbkey="?" 183 dbkey="?"
217 <custom_config> 216 <custom_config>
218 </custom_config> 217 </custom_config>
219 218
220 <gff> 219 <gff>
221 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> 220 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
222 <topLevelFeatures>mRNA</topLevelFeatures>
223 <index>false</index> 221 <index>false</index>
224 </gff> 222 </gff>
225 </options> 223 </options>
226 </track> 224 </track>
227 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 225 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
228 <files> 226 <files>
229 <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff"> 227 <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
230 <metadata> 228 <metadata>
231 <dataset id="5449172d6ff5669b" hid="6" 229 <dataset id="1ae74d26531588b0" hid="6"
232 size="2.3 KB" 230 size="2.3 KB"
233 edam_format="format_1975" 231 edam_format="format_1975"
234 file_ext="gff3" /> 232 file_ext="gff3" />
235 <history id="54f2a3a23292eb07" 233 <history id="8155e4b4bf1581ff"
236 user_email="test@bx.psu.edu" 234 user_email="test@bx.psu.edu"
237 user_id="2" 235 user_id="2"
238 display_name="test_history"/> 236 display_name="test_history"/>
239 <metadata 237 <metadata
240 dbkey="?" 238 dbkey="?"
279 <custom_config> 277 <custom_config>
280 </custom_config> 278 </custom_config>
281 279
282 <gff> 280 <gff>
283 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> 281 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
284 <topLevelFeatures>mRNA</topLevelFeatures>
285 <index>false</index> 282 <index>false</index>
286 </gff> 283 </gff>
287 </options> 284 </options>
288 </track> 285 </track>
289 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 286 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
290 <files> 287 <files>
291 <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff"> 288 <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
292 <metadata> 289 <metadata>
293 <dataset id="5449172d6ff5669b" hid="6" 290 <dataset id="1ae74d26531588b0" hid="6"
294 size="2.3 KB" 291 size="2.3 KB"
295 edam_format="format_1975" 292 edam_format="format_1975"
296 file_ext="gff3" /> 293 file_ext="gff3" />
297 <history id="54f2a3a23292eb07" 294 <history id="8155e4b4bf1581ff"
298 user_email="test@bx.psu.edu" 295 user_email="test@bx.psu.edu"
299 user_id="2" 296 user_id="2"
300 display_name="test_history"/> 297 display_name="test_history"/>
301 <metadata 298 <metadata
302 dbkey="?" 299 dbkey="?"
341 <custom_config> 338 <custom_config>
342 </custom_config> 339 </custom_config>
343 340
344 <gff> 341 <gff>
345 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> 342 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
346 <topLevelFeatures>mRNA</topLevelFeatures>
347 <index>false</index> 343 <index>false</index>
348 </gff> 344 </gff>
349 </options> 345 </options>
350 </track> 346 </track>
351 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 347 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
352 <files> 348 <files>
353 <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff"> 349 <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
354 <metadata> 350 <metadata>
355 <dataset id="5449172d6ff5669b" hid="6" 351 <dataset id="1ae74d26531588b0" hid="6"
356 size="2.3 KB" 352 size="2.3 KB"
357 edam_format="format_1975" 353 edam_format="format_1975"
358 file_ext="gff3" /> 354 file_ext="gff3" />
359 <history id="54f2a3a23292eb07" 355 <history id="8155e4b4bf1581ff"
360 user_email="test@bx.psu.edu" 356 user_email="test@bx.psu.edu"
361 user_id="2" 357 user_id="2"
362 display_name="test_history"/> 358 display_name="test_history"/>
363 <metadata 359 <metadata
364 dbkey="?" 360 dbkey="?"
405 <custom_config> 401 <custom_config>
406 </custom_config> 402 </custom_config>
407 403
408 <gff> 404 <gff>
409 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> 405 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
410 <topLevelFeatures>mRNA</topLevelFeatures>
411 <index>false</index> 406 <index>false</index>
412 </gff> 407 </gff>
413 </options> 408 </options>
414 </track> 409 </track>
415 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 410 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
416 <files> 411 <files>
417 <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff"> 412 <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
418 <metadata> 413 <metadata>
419 <dataset id="5449172d6ff5669b" hid="6" 414 <dataset id="1ae74d26531588b0" hid="6"
420 size="2.3 KB" 415 size="2.3 KB"
421 edam_format="format_1975" 416 edam_format="format_1975"
422 file_ext="gff3" /> 417 file_ext="gff3" />
423 <history id="54f2a3a23292eb07" 418 <history id="8155e4b4bf1581ff"
424 user_email="test@bx.psu.edu" 419 user_email="test@bx.psu.edu"
425 user_id="2" 420 user_id="2"
426 display_name="test_history"/> 421 display_name="test_history"/>
427 <metadata 422 <metadata
428 dbkey="?" 423 dbkey="?"
469 <custom_config> 464 <custom_config>
470 </custom_config> 465 </custom_config>
471 466
472 <gff> 467 <gff>
473 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> 468 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
474 <topLevelFeatures>mRNA</topLevelFeatures>
475 <index>false</index> 469 <index>false</index>
476 </gff> 470 </gff>
477 </options> 471 </options>
478 </track> 472 </track>
479 <track cat="Realistic" format="gene_calls" visibility="default_off"> 473 <track cat="Realistic" format="gene_calls" visibility="default_off">
480 <files> 474 <files>
481 <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_11.dat" ext="gff3" label="gff3/interpro.gff"> 475 <trackFile path="/tmp/tmpqkd9zdgq/files/0/3/0/dataset_030f551a-fd97-470e-ab58-328d8108783d.dat" ext="gff3" label="interpro.gff">
482 <metadata> 476 <metadata>
483 <dataset id="9ce08b2254e4d5ed" hid="7" 477 <dataset id="440a6c2b5d9efe20" hid="7"
484 size="103.3 KB" 478 size="103.3 KB"
485 edam_format="format_1975" 479 edam_format="format_1975"
486 file_ext="gff3" /> 480 file_ext="gff3" />
487 <history id="54f2a3a23292eb07" 481 <history id="8155e4b4bf1581ff"
488 user_email="test@bx.psu.edu" 482 user_email="test@bx.psu.edu"
489 user_id="2" 483 user_id="2"
490 display_name="test_history"/> 484 display_name="test_history"/>
491 <metadata 485 <metadata
492 dbkey="?" 486 dbkey="?"
525 <custom_config> 519 <custom_config>
526 </custom_config> 520 </custom_config>
527 521
528 <gff> 522 <gff>
529 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> 523 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
530 <topLevelFeatures>mRNA</topLevelFeatures>
531 <index>false</index> 524 <index>false</index>
532 </gff> 525 </gff>
533 </options> 526 </options>
534 </track> 527 </track>
535 <track cat="Realistic" format="gene_calls" visibility="default_off"> 528 <track cat="Realistic" format="gene_calls" visibility="default_off">
536 <files> 529 <files>
537 <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_12.dat" ext="gff3" label="gff3/2.gff"> 530 <trackFile path="/tmp/tmpqkd9zdgq/files/a/b/b/dataset_abb36b76-2a3a-4353-919e-13c94629303f.dat" ext="gff3" label="2.gff">
538 <metadata> 531 <metadata>
539 <dataset id="80b8022ff3f677b7" hid="8" 532 <dataset id="ea0b941dfbe636f8" hid="8"
540 size="326 bytes" 533 size="326 bytes"
541 edam_format="format_1975" 534 edam_format="format_1975"
542 file_ext="gff3" /> 535 file_ext="gff3" />
543 <history id="54f2a3a23292eb07" 536 <history id="8155e4b4bf1581ff"
544 user_email="test@bx.psu.edu" 537 user_email="test@bx.psu.edu"
545 user_id="2" 538 user_id="2"
546 display_name="test_history"/> 539 display_name="test_history"/>
547 <metadata 540 <metadata
548 dbkey="?" 541 dbkey="?"
581 <custom_config> 574 <custom_config>
582 </custom_config> 575 </custom_config>
583 576
584 <gff> 577 <gff>
585 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> 578 <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
586 <topLevelFeatures>mRNA</topLevelFeatures>
587 <match>cDNA_match</match> 579 <match>cDNA_match</match>
588 <index>false</index> 580 <index>false</index>
589 </gff> 581 </gff>
590 </options> 582 </options>
591 </track> 583 </track>