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comparison test-data/gff3/test.xml @ 25:1cfc579079a6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
author iuc
date Tue, 29 Jan 2019 05:34:16 -0500
parents ff11d442feed
children 112eb40ba6cf
comparison
equal deleted inserted replaced
24:fa30df9b79c2 25:1cfc579079a6
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/tmpnh6QWY/files/000/dataset_5.dat"> 6 <genome path="/tmp/tmpWtvfKr/files/000/dataset_5.dat">
7 <metadata> 7 <metadata>
8 <dataset id="7b55dbb89df8f4e5" hid="1" 8 <dataset id="7b55dbb89df8f4e5" 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="54f2a3a23292eb07"
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="hg17" 17 dbkey="?"
18 data_lines="2881" 18 data_lines="2881"
19 sequences="1" 19 sequences="1"
20 /> 20 />
21 <tool 21 <tool
22 tool_id="upload1" 22 tool_id="upload1"
23 tool_version="1.1.4" 23 tool_version="1.1.6"
24 /> 24 />
25 </metadata> 25 </metadata>
26 </genome> 26 </genome>
27 </genomes> 27 </genomes>
28 <general> 28 <general>
29 <defaultLocation></defaultLocation> 29 <defaultLocation></defaultLocation>
30 <trackPadding>20</trackPadding> 30 <trackPadding>20</trackPadding>
31 31
35 <show_nav>true</show_nav> 35 <show_nav>true</show_nav>
36 <show_overview>true</show_overview> 36 <show_overview>true</show_overview>
37 <show_menu>true</show_menu> 37 <show_menu>true</show_menu>
38 <hideGenomeOptions>false</hideGenomeOptions> 38 <hideGenomeOptions>false</hideGenomeOptions>
39 </general> 39 </general>
40 <galaxyUrl>http://localhost:8080</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/tmpnh6QWY/files/000/dataset_6.dat" ext="gff3" label="A.gff"> 45 <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_6.dat" ext="gff3" label="A.gff">
46 <metadata> 46 <metadata>
47 <dataset id="fa6d20d0fb68383f" hid="2" 47 <dataset id="fa6d20d0fb68383f" 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="54f2a3a23292eb07"
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="hg17" 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 column_names="" 60 column_names=""
61 delimiter="__tc__" 61 delimiter="__tc__"
62 attributes="6" 62 attributes="6"
63 /> 63 />
64 <tool 64 <tool
65 tool_id="upload1" 65 tool_id="upload1"
66 tool_version="1.1.4" 66 tool_version="1.1.6"
67 /> 67 />
68 </metadata> 68 </metadata>
69 </trackFile> 69 </trackFile>
70 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_7.dat" ext="gff3" label="B.gff"> 70 <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_7.dat" ext="gff3" label="B.gff">
71 <metadata> 71 <metadata>
72 <dataset id="683bc220e21425bb" hid="3" 72 <dataset id="683bc220e21425bb" hid="3"
73 size="2.3 KB" 73 size="2.3 KB"
74 edam_format="format_1975" 74 edam_format="format_1975"
75 file_ext="gff3" /> 75 file_ext="gff3" />
76 <history id="54f2a3a23292eb07" 76 <history id="54f2a3a23292eb07"
77 user_email="test@bx.psu.edu" 77 user_email="test@bx.psu.edu"
78 user_id="2" 78 user_id="2"
79 display_name="test_history"/> 79 display_name="test_history"/>
80 <metadata 80 <metadata
81 dbkey="hg17" 81 dbkey="?"
82 data_lines="27" 82 data_lines="27"
83 comment_lines="19" 83 comment_lines="19"
84 columns="9" 84 columns="9"
85 column_names="" 85 column_names=""
86 delimiter="__tc__" 86 delimiter="__tc__"
87 attributes="6" 87 attributes="6"
88 /> 88 />
89 <tool 89 <tool
90 tool_id="upload1" 90 tool_id="upload1"
91 tool_version="1.1.4" 91 tool_version="1.1.6"
92 /> 92 />
93 </metadata> 93 </metadata>
94 </trackFile> 94 </trackFile>
95 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_8.dat" ext="gff3" label="C.gff"> 95 <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_8.dat" ext="gff3" label="C.gff">
96 <metadata> 96 <metadata>
97 <dataset id="a90a30fafe298e1e" hid="4" 97 <dataset id="a90a30fafe298e1e" hid="4"
98 size="2.3 KB" 98 size="2.3 KB"
99 edam_format="format_1975" 99 edam_format="format_1975"
100 file_ext="gff3" /> 100 file_ext="gff3" />
101 <history id="54f2a3a23292eb07" 101 <history id="54f2a3a23292eb07"
102 user_email="test@bx.psu.edu" 102 user_email="test@bx.psu.edu"
103 user_id="2" 103 user_id="2"
104 display_name="test_history"/> 104 display_name="test_history"/>
105 <metadata 105 <metadata
106 dbkey="hg17" 106 dbkey="?"
107 data_lines="27" 107 data_lines="27"
108 comment_lines="19" 108 comment_lines="19"
109 columns="9" 109 columns="9"
110 column_names="" 110 column_names=""
111 delimiter="__tc__" 111 delimiter="__tc__"
112 attributes="6" 112 attributes="6"
113 /> 113 />
114 <tool 114 <tool
115 tool_id="upload1" 115 tool_id="upload1"
116 tool_version="1.1.4" 116 tool_version="1.1.6"
117 /> 117 />
118 </metadata> 118 </metadata>
119 </trackFile> 119 </trackFile>
120 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_9.dat" ext="gff3" label="D.gff"> 120 <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_9.dat" ext="gff3" label="D.gff">
121 <metadata> 121 <metadata>
122 <dataset id="b842d972534ccb3e" hid="5" 122 <dataset id="b842d972534ccb3e" hid="5"
123 size="2.3 KB" 123 size="2.3 KB"
124 edam_format="format_1975" 124 edam_format="format_1975"
125 file_ext="gff3" /> 125 file_ext="gff3" />
126 <history id="54f2a3a23292eb07" 126 <history id="54f2a3a23292eb07"
127 user_email="test@bx.psu.edu" 127 user_email="test@bx.psu.edu"
128 user_id="2" 128 user_id="2"
129 display_name="test_history"/> 129 display_name="test_history"/>
130 <metadata 130 <metadata
131 dbkey="hg17" 131 dbkey="?"
132 data_lines="27" 132 data_lines="27"
133 comment_lines="19" 133 comment_lines="19"
134 columns="9" 134 columns="9"
135 column_names="" 135 column_names=""
136 delimiter="__tc__" 136 delimiter="__tc__"
137 attributes="6" 137 attributes="6"
138 /> 138 />
139 <tool 139 <tool
140 tool_id="upload1" 140 tool_id="upload1"
141 tool_version="1.1.4" 141 tool_version="1.1.6"
142 /> 142 />
143 </metadata> 143 </metadata>
144 </trackFile> 144 </trackFile>
145 </files> 145 </files>
146 146
169 </gff> 169 </gff>
170 </options> 170 </options>
171 </track> 171 </track>
172 <track cat="Ignore Scale" format="gene_calls" visibility="default_off"> 172 <track cat="Ignore Scale" format="gene_calls" visibility="default_off">
173 <files> 173 <files>
174 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff"> 174 <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff">
175 <metadata> 175 <metadata>
176 <dataset id="5449172d6ff5669b" hid="6" 176 <dataset id="5449172d6ff5669b" hid="6"
177 size="2.3 KB" 177 size="2.3 KB"
178 edam_format="format_1975" 178 edam_format="format_1975"
179 file_ext="gff3" /> 179 file_ext="gff3" />
180 <history id="54f2a3a23292eb07" 180 <history id="54f2a3a23292eb07"
181 user_email="test@bx.psu.edu" 181 user_email="test@bx.psu.edu"
182 user_id="2" 182 user_id="2"
183 display_name="test_history"/> 183 display_name="test_history"/>
184 <metadata 184 <metadata
185 dbkey="hg17" 185 dbkey="?"
186 data_lines="27" 186 data_lines="27"
187 comment_lines="19" 187 comment_lines="19"
188 columns="9" 188 columns="9"
189 column_names="" 189 column_names=""
190 delimiter="__tc__" 190 delimiter="__tc__"
191 attributes="6" 191 attributes="6"
192 /> 192 />
193 <tool 193 <tool
194 tool_id="upload1" 194 tool_id="upload1"
195 tool_version="1.1.4" 195 tool_version="1.1.6"
196 /> 196 />
197 </metadata> 197 </metadata>
198 </trackFile> 198 </trackFile>
199 </files> 199 </files>
200 200
223 </gff> 223 </gff>
224 </options> 224 </options>
225 </track> 225 </track>
226 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 226 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
227 <files> 227 <files>
228 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff"> 228 <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff">
229 <metadata> 229 <metadata>
230 <dataset id="5449172d6ff5669b" hid="6" 230 <dataset id="5449172d6ff5669b" hid="6"
231 size="2.3 KB" 231 size="2.3 KB"
232 edam_format="format_1975" 232 edam_format="format_1975"
233 file_ext="gff3" /> 233 file_ext="gff3" />
234 <history id="54f2a3a23292eb07" 234 <history id="54f2a3a23292eb07"
235 user_email="test@bx.psu.edu" 235 user_email="test@bx.psu.edu"
236 user_id="2" 236 user_id="2"
237 display_name="test_history"/> 237 display_name="test_history"/>
238 <metadata 238 <metadata
239 dbkey="hg17" 239 dbkey="?"
240 data_lines="27" 240 data_lines="27"
241 comment_lines="19" 241 comment_lines="19"
242 columns="9" 242 columns="9"
243 column_names="" 243 column_names=""
244 delimiter="__tc__" 244 delimiter="__tc__"
245 attributes="6" 245 attributes="6"
246 /> 246 />
247 <tool 247 <tool
248 tool_id="upload1" 248 tool_id="upload1"
249 tool_version="1.1.4" 249 tool_version="1.1.6"
250 /> 250 />
251 </metadata> 251 </metadata>
252 </trackFile> 252 </trackFile>
253 </files> 253 </files>
254 254
283 </gff> 283 </gff>
284 </options> 284 </options>
285 </track> 285 </track>
286 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 286 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
287 <files> 287 <files>
288 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff"> 288 <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff">
289 <metadata> 289 <metadata>
290 <dataset id="5449172d6ff5669b" hid="6" 290 <dataset id="5449172d6ff5669b" hid="6"
291 size="2.3 KB" 291 size="2.3 KB"
292 edam_format="format_1975" 292 edam_format="format_1975"
293 file_ext="gff3" /> 293 file_ext="gff3" />
294 <history id="54f2a3a23292eb07" 294 <history id="54f2a3a23292eb07"
295 user_email="test@bx.psu.edu" 295 user_email="test@bx.psu.edu"
296 user_id="2" 296 user_id="2"
297 display_name="test_history"/> 297 display_name="test_history"/>
298 <metadata 298 <metadata
299 dbkey="hg17" 299 dbkey="?"
300 data_lines="27" 300 data_lines="27"
301 comment_lines="19" 301 comment_lines="19"
302 columns="9" 302 columns="9"
303 column_names="" 303 column_names=""
304 delimiter="__tc__" 304 delimiter="__tc__"
305 attributes="6" 305 attributes="6"
306 /> 306 />
307 <tool 307 <tool
308 tool_id="upload1" 308 tool_id="upload1"
309 tool_version="1.1.4" 309 tool_version="1.1.6"
310 /> 310 />
311 </metadata> 311 </metadata>
312 </trackFile> 312 </trackFile>
313 </files> 313 </files>
314 314
343 </gff> 343 </gff>
344 </options> 344 </options>
345 </track> 345 </track>
346 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 346 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
347 <files> 347 <files>
348 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff"> 348 <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff">
349 <metadata> 349 <metadata>
350 <dataset id="5449172d6ff5669b" hid="6" 350 <dataset id="5449172d6ff5669b" hid="6"
351 size="2.3 KB" 351 size="2.3 KB"
352 edam_format="format_1975" 352 edam_format="format_1975"
353 file_ext="gff3" /> 353 file_ext="gff3" />
354 <history id="54f2a3a23292eb07" 354 <history id="54f2a3a23292eb07"
355 user_email="test@bx.psu.edu" 355 user_email="test@bx.psu.edu"
356 user_id="2" 356 user_id="2"
357 display_name="test_history"/> 357 display_name="test_history"/>
358 <metadata 358 <metadata
359 dbkey="hg17" 359 dbkey="?"
360 data_lines="27" 360 data_lines="27"
361 comment_lines="19" 361 comment_lines="19"
362 columns="9" 362 columns="9"
363 column_names="" 363 column_names=""
364 delimiter="__tc__" 364 delimiter="__tc__"
365 attributes="6" 365 attributes="6"
366 /> 366 />
367 <tool 367 <tool
368 tool_id="upload1" 368 tool_id="upload1"
369 tool_version="1.1.4" 369 tool_version="1.1.6"
370 /> 370 />
371 </metadata> 371 </metadata>
372 </trackFile> 372 </trackFile>
373 </files> 373 </files>
374 374
405 </gff> 405 </gff>
406 </options> 406 </options>
407 </track> 407 </track>
408 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 408 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
409 <files> 409 <files>
410 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff"> 410 <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff">
411 <metadata> 411 <metadata>
412 <dataset id="5449172d6ff5669b" hid="6" 412 <dataset id="5449172d6ff5669b" hid="6"
413 size="2.3 KB" 413 size="2.3 KB"
414 edam_format="format_1975" 414 edam_format="format_1975"
415 file_ext="gff3" /> 415 file_ext="gff3" />
416 <history id="54f2a3a23292eb07" 416 <history id="54f2a3a23292eb07"
417 user_email="test@bx.psu.edu" 417 user_email="test@bx.psu.edu"
418 user_id="2" 418 user_id="2"
419 display_name="test_history"/> 419 display_name="test_history"/>
420 <metadata 420 <metadata
421 dbkey="hg17" 421 dbkey="?"
422 data_lines="27" 422 data_lines="27"
423 comment_lines="19" 423 comment_lines="19"
424 columns="9" 424 columns="9"
425 column_names="" 425 column_names=""
426 delimiter="__tc__" 426 delimiter="__tc__"
427 attributes="6" 427 attributes="6"
428 /> 428 />
429 <tool 429 <tool
430 tool_id="upload1" 430 tool_id="upload1"
431 tool_version="1.1.4" 431 tool_version="1.1.6"
432 /> 432 />
433 </metadata> 433 </metadata>
434 </trackFile> 434 </trackFile>
435 </files> 435 </files>
436 436
467 </gff> 467 </gff>
468 </options> 468 </options>
469 </track> 469 </track>
470 <track cat="Realistic" format="gene_calls" visibility="default_off"> 470 <track cat="Realistic" format="gene_calls" visibility="default_off">
471 <files> 471 <files>
472 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_11.dat" ext="gff3" label="interpro.gff"> 472 <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_11.dat" ext="gff3" label="interpro.gff">
473 <metadata> 473 <metadata>
474 <dataset id="9ce08b2254e4d5ed" hid="7" 474 <dataset id="9ce08b2254e4d5ed" hid="7"
475 size="103.3 KB" 475 size="103.3 KB"
476 edam_format="format_1975" 476 edam_format="format_1975"
477 file_ext="gff3" /> 477 file_ext="gff3" />
478 <history id="54f2a3a23292eb07" 478 <history id="54f2a3a23292eb07"
479 user_email="test@bx.psu.edu" 479 user_email="test@bx.psu.edu"
480 user_id="2" 480 user_id="2"
481 display_name="test_history"/> 481 display_name="test_history"/>
482 <metadata 482 <metadata
483 dbkey="hg17" 483 dbkey="?"
484 data_lines="556" 484 data_lines="556"
485 comment_lines="2" 485 comment_lines="2"
486 columns="9" 486 columns="9"
487 column_names="" 487 column_names=""
488 delimiter="__tc__" 488 delimiter="__tc__"
489 attributes="11" 489 attributes="11"
490 /> 490 />
491 <tool 491 <tool
492 tool_id="upload1" 492 tool_id="upload1"
493 tool_version="1.1.4" 493 tool_version="1.1.6"
494 /> 494 />
495 </metadata> 495 </metadata>
496 </trackFile> 496 </trackFile>
497 </files> 497 </files>
498 498
521 </gff> 521 </gff>
522 </options> 522 </options>
523 </track> 523 </track>
524 <track cat="Realistic" format="gene_calls" visibility="default_off"> 524 <track cat="Realistic" format="gene_calls" visibility="default_off">
525 <files> 525 <files>
526 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_12.dat" ext="gff3" label="2.gff"> 526 <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_12.dat" ext="gff3" label="2.gff">
527 <metadata> 527 <metadata>
528 <dataset id="80b8022ff3f677b7" hid="8" 528 <dataset id="80b8022ff3f677b7" hid="8"
529 size="326 bytes" 529 size="326 bytes"
530 edam_format="format_1975" 530 edam_format="format_1975"
531 file_ext="gff3" /> 531 file_ext="gff3" />
532 <history id="54f2a3a23292eb07" 532 <history id="54f2a3a23292eb07"
533 user_email="test@bx.psu.edu" 533 user_email="test@bx.psu.edu"
534 user_id="2" 534 user_id="2"
535 display_name="test_history"/> 535 display_name="test_history"/>
536 <metadata 536 <metadata
537 dbkey="hg17" 537 dbkey="?"
538 data_lines="3" 538 data_lines="3"
539 comment_lines="3" 539 comment_lines="3"
540 columns="9" 540 columns="9"
541 column_names="" 541 column_names=""
542 delimiter="__tc__" 542 delimiter="__tc__"
543 attributes="4" 543 attributes="4"
544 /> 544 />
545 <tool 545 <tool
546 tool_id="upload1" 546 tool_id="upload1"
547 tool_version="1.1.4" 547 tool_version="1.1.6"
548 /> 548 />
549 </metadata> 549 </metadata>
550 </trackFile> 550 </trackFile>
551 </files> 551 </files>
552 552
579 </tracks> 579 </tracks>
580 <plugins 580 <plugins
581 ComboTrackSelector="" 581 ComboTrackSelector=""
582 Bookmarks="" 582 Bookmarks=""
583 GCContent="" 583 GCContent=""
584 BlastView="True"
584 theme="" 585 theme=""
585 /> 586 />
586 </root> 587 </root>