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comparison galaxy.xml @ 95:a0c848f00363 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5903fd8076687ad01a7cf0a522b954106ac6579a
author fubar
date Wed, 24 Apr 2024 03:25:23 +0000
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94:acbacaf0efe3 95:a0c848f00363
1 <?xml version="1.0"?>
2 <root>
3 <metadata>
4 <general>
5 <defaultLocation></defaultLocation>
6 <zipOut>true</zipOut>
7 <analytics>false</analytics>
8 <primary_color>#0d233f</primary_color>
9 <secondary_color>#721e63</secondary_color>
10 <tertiary_color>#135560</tertiary_color>
11 <quaternary_color>#ffb11d</quaternary_color>
12 <font_size>10</font_size>
13 <session_name>New test session</session_name>
14 </general>
15 <galaxyUrl>http://localhost:8080</galaxyUrl>
16 </metadata>
17 <assembly>
18 <metadata>
19 <genomes>
20 <genome path="/tmp/tmpaivwlly7/files/2/6/5/dataset_265ba9ba-75c3-49ca-be12-7c34a7b56380.dat" label="Merlin" useuri="no">
21 <metadata>
22
23 <dataset id="e3f2f10afcaf3f83"
24 hid="1"
25 size="171.6 KB"
26 edam_format="format_1929"
27 file_ext="fasta"
28 dname = "Merlin"
29 />
30 <history
31 user_email="planemo@galaxyproject.org"
32 user_id="1"
33 display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>
34 id="e3f2f10afcaf3f83"
35 />
36 <metadata
37 dbkey="?"
38 data_lines="2881"
39 sequences="1"
40 />
41 <tool
42 tool_id="upload1"
43 tool_version="1.1.7"
44 />
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/tmpaivwlly7/files/8/d/6/dataset_8d6c2542-1af4-4bd1-ab96-98e31f60a542.dat" ext="gff3" label="merlin.gff3" useuri="no">
54 <metadata>
55
56 <dataset id="6e131a28d20492ec" hid="2"
57 size="5.0 KB"
58 edam_format="format_1975"
59 file_ext="gff3" />
60 <history id="e3f2f10afcaf3f83"
61 user_email="planemo@galaxyproject.org"
62 user_id="1"
63 display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>
64
65 <metadata
66 dbkey="?"
67 data_lines="9"
68 comment_lines="10"
69 columns="9"
70 column_names="[]"
71 delimiter="__tc__"
72 attributes="23"
73 />
74 <tool
75 tool_id="upload1"
76 tool_version="1.1.7"
77 />
78 </metadata>
79 </trackFile>
80 </files>
81 <options>
82 <style>
83 <type>LinearBasicDisplay</type>
84 <trackShowLabels>false</trackShowLabels>
85 <trackShowDescriptions>false</trackShowDescriptions>
86 </style>
87 <gff>
88 </gff>
89 </options>
90 </track>
91 <track cat="Assembly properties" format="bigwig" visibility="default_on">
92 <files>
93 <trackFile path="/tmp/tmpaivwlly7/files/b/e/0/dataset_be0fc51e-5417-47ca-bfd0-6bc92397dbd5.dat" ext="bigwig" label="merlin.bw" useuri="no">
94 <metadata>
95
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98 edam_format="format_3006"
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100 <history id="e3f2f10afcaf3f83"
101 user_email="planemo@galaxyproject.org"
102 user_id="1"
103 display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>
104
105 <metadata
106 dbkey="?"
107 />
108 <tool
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110 tool_version="1.1.7"
111 />
112 </metadata>
113 </trackFile>
114 </files>
115 <options>
116 <style>
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118 </options>
119 </track>
120 <track cat="Assembly properties" format="bed" visibility="default_on">
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132 display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>
133
134 <metadata
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136 data_lines="3"
137 comment_lines="0"
138 columns="6"
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140 delimiter="__tc__"
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144 strandCol="6"
145 viz_filter_cols="[4]"
146 />
147 <tool
148 tool_id="upload1"
149 tool_version="1.1.7"
150 />
151 </metadata>
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153 </files>
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163 </track>
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165 <files>
166 <trackFile path="/tmp/tmpaivwlly7/files/b/0/a/dataset_b0a8eb96-3cb7-47e7-a004-2db7f3bdf9af.dat" ext="vcf" label="merlin.vcf" useuri="no">
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172 file_ext="vcf" />
173 <history id="e3f2f10afcaf3f83"
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176 display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>
177
178 <metadata
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180 data_lines="5"
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182 columns="12"
183 column_names="[]"
184 delimiter="__tc__"
185 viz_filter_cols="[5]"
186 sample_names="[NA00001,NA00002,NA00003]"
187 />
188 <tool
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190 tool_version="1.1.7"
191 />
192 </metadata>
193 </trackFile>
194 </files>
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201 </style>
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216 display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>
217
218 <metadata
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222 />
223 <tool
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225 tool_version="1.1.7"
226 />
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228 </trackFile>
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233 </style>
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236 /tmp/tmpaivwlly7/files/6/b/d/dataset_6bd63ebf-abbf-4225-b2a9-50021936ba0b.dat:/tmp/tmpaivwlly7/files/_metadata_files/6/d/8/metadata_6d808e2c-4839-4fbd-be66-dddc3e317c0e.dat,
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253 display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>
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255 <metadata
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257 columns="12"
258 column_names="[QNAME,FLAG,RNAME,POS,MAPQ,CIGAR,MRNM,MPOS,ISIZE,SEQ,QUAL,OPT]"
259 bam_version="1.3"
260 sort_order="coordinate"
261 read_groups="[]"
262 reference_names="[Merlin]"
263 reference_lengths="[172788]"
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265 />
266 <tool
267 tool_id="upload1"
268 tool_version="1.1.7"
269 />
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294 user_email="planemo@galaxyproject.org"
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296 display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>
297
298 <metadata
299 dbkey="?"
300 data_lines="0"
301 species="[Merlin,Merlin1,Merlin2,Merlin3,Merlin4,Merlin5,Merlin6]"
302 blocks="6"
303 species_chromosomes="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
304 maf_index="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
305 />
306 <tool
307 tool_id="upload1"
308 tool_version="1.1.7"
309 />
310 </metadata>
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312 </files>
313 <options>
314 <style>
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324 <metadata>
325
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333 display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>
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335 <metadata
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342 />
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350 <trackShowDescriptions>false</trackShowDescriptions>
351 </style>
352 <blast>
353 <parent>None</parent>
354 <protein>false</protein>
355 <min_gap>10</min_gap>
356 </blast>
357 </options>
358 </track>
359 <track cat="Assembly properties" format="bam" visibility="default_on">
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361 <trackFile path="/tmp/tmpaivwlly7/files/3/7/f/dataset_37f106fe-4670-4841-b96a-c10e28223d99.dat" ext="zip" label="files_0Xfile_data" useuri="no">
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373 <metadata
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379 />
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393 </track>
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423 />
424
425 </metadata>
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443
444 <metadata
445 dbkey="?"
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447 <tool
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450 />
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457 </style>
458 <cool>
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481 id="e3f2f10afcaf3f83"
482 />
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486 sequences="1"
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490 tool_version="1.1.7"
491 />
492
493 </metadata>
494 </genome>
495 </genomes>
496 </metadata>
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498 <track cat="Assembly properties" format="paf" visibility="default_on">
499 <files>
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511
512 <metadata
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514 data_lines="9291"
515 />
516 <tool
517 tool_id="upload1"
518 tool_version="1.1.7"
519 />
520 </metadata>
521 </trackFile>
522 </files>
523 <options>
524 <style>
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526 <paf>
527 <genome>
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529 </genome>
530 <useuri>
531 false
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556 tool_version="1.1.7"
557 />
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561 <options>
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565 <genome>
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567 </genome>
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569 false
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571 </paf>
572 </options>
573 </track>
574 </tracks>
575 </assembly>
576 <assembly>
577 <metadata>
578 <genomes>
579 <genome path="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz" label="hg38" useuri="yes">
580 <metadata>
581 <dataset
582 dname = "hg38" />
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584 </genome>
585 </genomes>
586 </metadata>
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588 <track cat="Assembly properties" format="hic" visibility="default_on">
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592 <metadata>
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600 </style>
601 <hic>
602 </hic>
603 </options>
604 </track>
605 </tracks>
606 </assembly>
607 </root>