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comparison test-data/gff3/test.xml @ 45:665c4f3e48ae draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
author iuc
date Wed, 15 Nov 2017 15:14:41 -0500
parents c1451868f8d4
children c6fd9fbd50e7
comparison
equal deleted inserted replaced
44:86728aa7f499 45:665c4f3e48ae
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>test-data/merlin.fa</genome> 6 <genome path="/tmp/tmpnh6QWY/files/000/dataset_5.dat">
7 <metadata>
8 <dataset id="7b55dbb89df8f4e5" hid="1"
9 size="171.6 KB"
10 edam_format="format_1929"
11 file_ext="fasta" />
12 <history id="54f2a3a23292eb07"
13 user_email="test@bx.psu.edu"
14 user_id="2"
15 display_name="test_history"/>
16 <metadata
17 dbkey="hg17"
18 data_lines="2881"
19 sequences="1"
20 />
21 <tool
22 tool_id="upload1"
23 tool_version="1.1.4"
24 />
25 </metadata>
26 </genome>
7 </genomes> 27 </genomes>
8 <general> 28 <general>
9 <defaultLocation></defaultLocation> 29 <defaultLocation></defaultLocation>
10 <trackPadding>20</trackPadding> 30 <trackPadding>20</trackPadding>
11 31
15 <show_nav>true</show_nav> 35 <show_nav>true</show_nav>
16 <show_overview>true</show_overview> 36 <show_overview>true</show_overview>
17 <show_menu>true</show_menu> 37 <show_menu>true</show_menu>
18 <hideGenomeOptions>false</hideGenomeOptions> 38 <hideGenomeOptions>false</hideGenomeOptions>
19 </general> 39 </general>
40 <galaxyUrl>http://localhost:8080</galaxyUrl>
20 </metadata> 41 </metadata>
21 <tracks> 42 <tracks>
22 <track cat="Auto Coloured" format="gene_calls" visibility="default_off"> 43 <track cat="Auto Coloured" format="gene_calls" visibility="default_off">
23 <files> 44 <files>
24 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/> 45 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_6.dat" ext="gff3" label="A.gff">
25 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/> 46 <metadata>
26 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/> 47 <dataset id="fa6d20d0fb68383f" hid="2"
27 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/> 48 size="2.3 KB"
28 </files> 49 edam_format="format_1975"
29 50 file_ext="gff3" />
30 <options> 51 <history id="54f2a3a23292eb07"
31 <style> 52 user_email="test@bx.psu.edu"
32 <className>feature</className> 53 user_id="2"
33 <description>note,description</description> 54 display_name="test_history"/>
34 <label>name,id</label> 55 <metadata
35 <height>100px</height> 56 dbkey="hg17"
57 data_lines="27"
58 comment_lines="19"
59 columns="9"
60 column_names=""
61 delimiter="__tc__"
62 attributes="6"
63 />
64 <tool
65 tool_id="upload1"
66 tool_version="1.1.4"
67 />
68 </metadata>
69 </trackFile>
70 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_7.dat" ext="gff3" label="B.gff">
71 <metadata>
72 <dataset id="683bc220e21425bb" hid="3"
73 size="2.3 KB"
74 edam_format="format_1975"
75 file_ext="gff3" />
76 <history id="54f2a3a23292eb07"
77 user_email="test@bx.psu.edu"
78 user_id="2"
79 display_name="test_history"/>
80 <metadata
81 dbkey="hg17"
82 data_lines="27"
83 comment_lines="19"
84 columns="9"
85 column_names=""
86 delimiter="__tc__"
87 attributes="6"
88 />
89 <tool
90 tool_id="upload1"
91 tool_version="1.1.4"
92 />
93 </metadata>
94 </trackFile>
95 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_8.dat" ext="gff3" label="C.gff">
96 <metadata>
97 <dataset id="a90a30fafe298e1e" hid="4"
98 size="2.3 KB"
99 edam_format="format_1975"
100 file_ext="gff3" />
101 <history id="54f2a3a23292eb07"
102 user_email="test@bx.psu.edu"
103 user_id="2"
104 display_name="test_history"/>
105 <metadata
106 dbkey="hg17"
107 data_lines="27"
108 comment_lines="19"
109 columns="9"
110 column_names=""
111 delimiter="__tc__"
112 attributes="6"
113 />
114 <tool
115 tool_id="upload1"
116 tool_version="1.1.4"
117 />
118 </metadata>
119 </trackFile>
120 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_9.dat" ext="gff3" label="D.gff">
121 <metadata>
122 <dataset id="b842d972534ccb3e" hid="5"
123 size="2.3 KB"
124 edam_format="format_1975"
125 file_ext="gff3" />
126 <history id="54f2a3a23292eb07"
127 user_email="test@bx.psu.edu"
128 user_id="2"
129 display_name="test_history"/>
130 <metadata
131 dbkey="hg17"
132 data_lines="27"
133 comment_lines="19"
134 columns="9"
135 column_names=""
136 delimiter="__tc__"
137 attributes="6"
138 />
139 <tool
140 tool_id="upload1"
141 tool_version="1.1.4"
142 />
143 </metadata>
144 </trackFile>
145 </files>
146
147 <options>
148 <style>
149 <overridePlugins>False</overridePlugins>
150 <overrideDraggable>False</overrideDraggable>
151 <className>feature</className>
152 <description>note,description</description>
153 <label>product,name,id</label>
154 <height>10px</height>
155 <maxHeight>600</maxHeight>
36 </style> 156 </style>
37 <scaling> 157 <scaling>
38 <method>ignore</method> 158 <method>ignore</method>
39 <scheme> 159 <scheme>
40 <color>__auto__</color> 160 <color>__auto__</color>
49 </gff> 169 </gff>
50 </options> 170 </options>
51 </track> 171 </track>
52 <track cat="Ignore Scale" format="gene_calls" visibility="default_off"> 172 <track cat="Ignore Scale" format="gene_calls" visibility="default_off">
53 <files> 173 <files>
54 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/> 174 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
55 </files> 175 <metadata>
56 176 <dataset id="5449172d6ff5669b" hid="6"
57 <options> 177 size="2.3 KB"
58 <style> 178 edam_format="format_1975"
59 <className>feature</className> 179 file_ext="gff3" />
60 <description>note,description</description> 180 <history id="54f2a3a23292eb07"
61 <label>name,id</label> 181 user_email="test@bx.psu.edu"
62 <height>100px</height> 182 user_id="2"
183 display_name="test_history"/>
184 <metadata
185 dbkey="hg17"
186 data_lines="27"
187 comment_lines="19"
188 columns="9"
189 column_names=""
190 delimiter="__tc__"
191 attributes="6"
192 />
193 <tool
194 tool_id="upload1"
195 tool_version="1.1.4"
196 />
197 </metadata>
198 </trackFile>
199 </files>
200
201 <options>
202 <style>
203 <overridePlugins>False</overridePlugins>
204 <overrideDraggable>False</overrideDraggable>
205 <className>feature</className>
206 <description>note,description</description>
207 <label>product,name,id</label>
208 <height>10px</height>
209 <maxHeight>600</maxHeight>
63 </style> 210 </style>
64 <scaling> 211 <scaling>
65 <method>ignore</method> 212 <method>ignore</method>
66 <scheme> 213 <scheme>
67 <color>#ff00ff</color> 214 <color>#ff00ff</color>
76 </gff> 223 </gff>
77 </options> 224 </options>
78 </track> 225 </track>
79 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 226 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
80 <files> 227 <files>
81 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/> 228 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
82 </files> 229 <metadata>
83 230 <dataset id="5449172d6ff5669b" hid="6"
84 <options> 231 size="2.3 KB"
85 <style> 232 edam_format="format_1975"
86 <className>feature</className> 233 file_ext="gff3" />
87 <description>note,description</description> 234 <history id="54f2a3a23292eb07"
88 <label>name,id</label> 235 user_email="test@bx.psu.edu"
89 <height>100px</height> 236 user_id="2"
237 display_name="test_history"/>
238 <metadata
239 dbkey="hg17"
240 data_lines="27"
241 comment_lines="19"
242 columns="9"
243 column_names=""
244 delimiter="__tc__"
245 attributes="6"
246 />
247 <tool
248 tool_id="upload1"
249 tool_version="1.1.4"
250 />
251 </metadata>
252 </trackFile>
253 </files>
254
255 <options>
256 <style>
257 <overridePlugins>False</overridePlugins>
258 <overrideDraggable>False</overrideDraggable>
259 <className>feature</className>
260 <description>note,description</description>
261 <label>product,name,id</label>
262 <height>10px</height>
263 <maxHeight>600</maxHeight>
90 </style> 264 </style>
91 <scaling> 265 <scaling>
92 <method>score</method> 266 <method>score</method>
93 <algo>linear</algo> 267 <algo>linear</algo>
94 <scales> 268 <scales>
109 </gff> 283 </gff>
110 </options> 284 </options>
111 </track> 285 </track>
112 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 286 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
113 <files> 287 <files>
114 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/> 288 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
115 </files> 289 <metadata>
116 290 <dataset id="5449172d6ff5669b" hid="6"
117 <options> 291 size="2.3 KB"
118 <style> 292 edam_format="format_1975"
119 <className>feature</className> 293 file_ext="gff3" />
120 <description>note,description</description> 294 <history id="54f2a3a23292eb07"
121 <label>name,id</label> 295 user_email="test@bx.psu.edu"
122 <height>100px</height> 296 user_id="2"
297 display_name="test_history"/>
298 <metadata
299 dbkey="hg17"
300 data_lines="27"
301 comment_lines="19"
302 columns="9"
303 column_names=""
304 delimiter="__tc__"
305 attributes="6"
306 />
307 <tool
308 tool_id="upload1"
309 tool_version="1.1.4"
310 />
311 </metadata>
312 </trackFile>
313 </files>
314
315 <options>
316 <style>
317 <overridePlugins>False</overridePlugins>
318 <overrideDraggable>False</overrideDraggable>
319 <className>feature</className>
320 <description>note,description</description>
321 <label>product,name,id</label>
322 <height>10px</height>
323 <maxHeight>600</maxHeight>
123 </style> 324 </style>
124 <scaling> 325 <scaling>
125 <method>score</method> 326 <method>score</method>
126 <algo>linear</algo> 327 <algo>linear</algo>
127 <scales> 328 <scales>
142 </gff> 343 </gff>
143 </options> 344 </options>
144 </track> 345 </track>
145 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 346 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
146 <files> 347 <files>
147 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/> 348 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
148 </files> 349 <metadata>
149 350 <dataset id="5449172d6ff5669b" hid="6"
150 <options> 351 size="2.3 KB"
151 <style> 352 edam_format="format_1975"
152 <className>feature</className> 353 file_ext="gff3" />
153 <description>note,description</description> 354 <history id="54f2a3a23292eb07"
154 <label>name,id</label> 355 user_email="test@bx.psu.edu"
155 <height>100px</height> 356 user_id="2"
357 display_name="test_history"/>
358 <metadata
359 dbkey="hg17"
360 data_lines="27"
361 comment_lines="19"
362 columns="9"
363 column_names=""
364 delimiter="__tc__"
365 attributes="6"
366 />
367 <tool
368 tool_id="upload1"
369 tool_version="1.1.4"
370 />
371 </metadata>
372 </trackFile>
373 </files>
374
375 <options>
376 <style>
377 <overridePlugins>False</overridePlugins>
378 <overrideDraggable>False</overrideDraggable>
379 <className>feature</className>
380 <description>note,description</description>
381 <label>product,name,id</label>
382 <height>10px</height>
383 <maxHeight>600</maxHeight>
156 </style> 384 </style>
157 <scaling> 385 <scaling>
158 <method>score</method> 386 <method>score</method>
159 <algo>linear</algo> 387 <algo>linear</algo>
160 <scales> 388 <scales>
177 </gff> 405 </gff>
178 </options> 406 </options>
179 </track> 407 </track>
180 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 408 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
181 <files> 409 <files>
182 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/> 410 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
183 </files> 411 <metadata>
184 412 <dataset id="5449172d6ff5669b" hid="6"
185 <options> 413 size="2.3 KB"
186 <style> 414 edam_format="format_1975"
187 <className>feature</className> 415 file_ext="gff3" />
188 <description>note,description</description> 416 <history id="54f2a3a23292eb07"
189 <label>name,id</label> 417 user_email="test@bx.psu.edu"
190 <height>100px</height> 418 user_id="2"
419 display_name="test_history"/>
420 <metadata
421 dbkey="hg17"
422 data_lines="27"
423 comment_lines="19"
424 columns="9"
425 column_names=""
426 delimiter="__tc__"
427 attributes="6"
428 />
429 <tool
430 tool_id="upload1"
431 tool_version="1.1.4"
432 />
433 </metadata>
434 </trackFile>
435 </files>
436
437 <options>
438 <style>
439 <overridePlugins>False</overridePlugins>
440 <overrideDraggable>False</overrideDraggable>
441 <className>feature</className>
442 <description>note,description</description>
443 <label>product,name,id</label>
444 <height>10px</height>
445 <maxHeight>600</maxHeight>
191 </style> 446 </style>
192 <scaling> 447 <scaling>
193 <method>score</method> 448 <method>score</method>
194 <algo>linear</algo> 449 <algo>linear</algo>
195 <scales> 450 <scales>
212 </gff> 467 </gff>
213 </options> 468 </options>
214 </track> 469 </track>
215 <track cat="Realistic" format="gene_calls" visibility="default_off"> 470 <track cat="Realistic" format="gene_calls" visibility="default_off">
216 <files> 471 <files>
217 <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/> 472 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_11.dat" ext="gff3" label="interpro.gff">
218 </files> 473 <metadata>
219 474 <dataset id="9ce08b2254e4d5ed" hid="7"
220 <options> 475 size="103.3 KB"
221 <style> 476 edam_format="format_1975"
222 <className>feature</className> 477 file_ext="gff3" />
223 <description>note,description</description> 478 <history id="54f2a3a23292eb07"
224 <label>name,id</label> 479 user_email="test@bx.psu.edu"
225 <height>100px</height> 480 user_id="2"
481 display_name="test_history"/>
482 <metadata
483 dbkey="hg17"
484 data_lines="556"
485 comment_lines="2"
486 columns="9"
487 column_names=""
488 delimiter="__tc__"
489 attributes="11"
490 />
491 <tool
492 tool_id="upload1"
493 tool_version="1.1.4"
494 />
495 </metadata>
496 </trackFile>
497 </files>
498
499 <options>
500 <style>
501 <overridePlugins>False</overridePlugins>
502 <overrideDraggable>False</overrideDraggable>
503 <className>feature</className>
504 <description>note,description</description>
505 <label>product,name,id</label>
506 <height>10px</height>
507 <maxHeight>600</maxHeight>
226 </style> 508 </style>
227 <scaling> 509 <scaling>
228 <method>ignore</method> 510 <method>ignore</method>
229 <scheme> 511 <scheme>
230 <color>__auto__</color> 512 <color>__auto__</color>
239 </gff> 521 </gff>
240 </options> 522 </options>
241 </track> 523 </track>
242 <track cat="Realistic" format="gene_calls" visibility="default_off"> 524 <track cat="Realistic" format="gene_calls" visibility="default_off">
243 <files> 525 <files>
244 <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/> 526 <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_12.dat" ext="gff3" label="2.gff">
245 </files> 527 <metadata>
246 528 <dataset id="80b8022ff3f677b7" hid="8"
247 <options> 529 size="326 bytes"
248 <style> 530 edam_format="format_1975"
249 <className>feature</className> 531 file_ext="gff3" />
250 <description>note,description</description> 532 <history id="54f2a3a23292eb07"
251 <label>name,id</label> 533 user_email="test@bx.psu.edu"
252 <height>100px</height> 534 user_id="2"
535 display_name="test_history"/>
536 <metadata
537 dbkey="hg17"
538 data_lines="3"
539 comment_lines="3"
540 columns="9"
541 column_names=""
542 delimiter="__tc__"
543 attributes="4"
544 />
545 <tool
546 tool_id="upload1"
547 tool_version="1.1.4"
548 />
549 </metadata>
550 </trackFile>
551 </files>
552
553 <options>
554 <style>
555 <overridePlugins>False</overridePlugins>
556 <overrideDraggable>False</overrideDraggable>
557 <className>feature</className>
558 <description>note,description</description>
559 <label>product,name,id</label>
560 <height>10px</height>
561 <maxHeight>600</maxHeight>
253 </style> 562 </style>
254 <scaling> 563 <scaling>
255 <method>ignore</method> 564 <method>ignore</method>
256 <scheme> 565 <scheme>
257 <color>__auto__</color> 566 <color>__auto__</color>
266 <index>false</index> 575 <index>false</index>
267 </gff> 576 </gff>
268 </options> 577 </options>
269 </track> 578 </track>
270 </tracks> 579 </tracks>
580 <plugins
581 ComboTrackSelector=""
582 Bookmarks=""
583 GCContent=""
584 theme=""
585 />
271 </root> 586 </root>