Mercurial > repos > iuc > jbrowse2

comparison test-data/out/02_remote/galaxy.xml @ 0:61add3f58f26 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
author iuc
date Thu, 02 Oct 2025 10:19:44 +0000
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-1:000000000000 0:61add3f58f26
1 <?xml version="1.0"?>
2 <root>
3 <metadata>
4 <general>
5 <analytics>false</analytics>
6 <primary_color>#0d233f</primary_color>
7 <secondary_color>#721e63</secondary_color>
8 <tertiary_color>#135560</tertiary_color>
9 <quaternary_color>#ffb11d</quaternary_color>
10 <font_size>10</font_size>
11 </general>
12 <galaxyUrl>http://localhost:8080</galaxyUrl>
13 </metadata>
14 <assembly>
15 <genome path="https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz" label="hg19" remote="true">
16 <metadata />
17 </genome>
18 <defaultLocation></defaultLocation>
19 <tracks>
20 <track cat="Default" format="wiggle" visibility="default_on">
21
22
23 <files>
24 <trackFile path="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw" ext="bigwig" label="SKBR3 pacbio coverage (NGMLR)" remote="true">
25 <metadata>
26 </metadata>
27 </trackFile>
28 </files>
29
30 <options>
31 <style>
32 <display>LinearWiggleDisplay</display>
33
34
35
36 <renderer>xyplot</renderer>
37 </style>
38
39
40
41 <wiggle>
42 </wiggle>
43 </options>
44 </track>
45 <track cat="Default" format="wiggle" visibility="default_on">
46
47
48 <files>
49 <trackFile path="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw" ext="bigwig" label="SKBR3 pacbio coverage (NGMLR)" remote="true">
50 <metadata>
51 </metadata>
52 </trackFile>
53 </files>
54
55 <options>
56 <style>
57 <display>MultiLinearWiggleDisplay</display>
58
59
60
61 <renderer>multirowxy</renderer>
62 </style>
63
64
65 <multitrack type="boolean">True</multitrack>
66
67 <wiggle>
68 </wiggle>
69 </options>
70 </track>
71 <track cat="Default" format="pileup" visibility="default_on">
72
73
74 <files>
75 <trackFile path="https://s3.amazonaws.com/1000genomes/phase3/data/NA12878/exome_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam" ext="bam" label="NA12878 Exome" remote="true">
76 <metadata>
77 </metadata>
78 </trackFile>
79 </files>
80
81 <options>
82 <style>
83 <display>LinearAlignmentsDisplay</display>
84
85
86
87 </style>
88
89
90
91 <pileup>
92 </pileup>
93 </options>
94 </track>
95 <track cat="Default" format="cram" visibility="default_on">
96
97
98 <files>
99 <trackFile path="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/alzheimers_isoseq/hq_isoforms.fasta.cram" ext="cram" label="hg_isoforms.fasta_cram" remote="true">
100 <metadata>
101 </metadata>
102 </trackFile>
103 </files>
104
105 <options>
106 <style>
107 <display>LinearAlignmentsDisplay</display>
108
109
110
111 </style>
112
113
114
115 <cram>
116 </cram>
117 </options>
118 </track>
119 <track cat="Default" format="hic" visibility="default_on">
120
121
122 <files>
123 <trackFile path="https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic" ext="hic" label="hg_isoforms.fasta_cram" remote="true">
124 <metadata>
125 </metadata>
126 </trackFile>
127 </files>
128
129 <options>
130 <style>
131 <display>LinearHicDisplay</display>
132
133
134
135 </style>
136
137
138
139 <hic>
140 </hic>
141 </options>
142 </track>
143 <track cat="Default" format="vcf" visibility="default_on">
144
145
146 <files>
147 <trackFile path="https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/vcf/nstd175.GRCh37.variant_call.vcf.gz" ext="vcf,vcf_bgzip" label="HG002 dbVar variant calls" remote="true">
148 <metadata>
149 </metadata>
150 </trackFile>
151 </files>
152
153 <options>
154 <style>
155 <display>LinearVariantDisplay</display>
156
157
158
159 </style>
160
161
162
163 </options>
164 </track>
165 <track cat="Default" format="vcf" visibility="default_on">
166
167
168 <files>
169 <trackFile path="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/COLO829/truthset_somaticSVs_COLO829.vcf" ext="vcf,vcf_bgzip" label="truthset_somaticSVs_COLO829" remote="true">
170 <metadata>
171 </metadata>
172 </trackFile>
173 </files>
174
175 <options>
176 <style>
177 <display>LinearVariantDisplay</display>
178
179
180
181 </style>
182
183
184
185 </options>
186 </track>
187 <track cat="Default" format="gene_calls" visibility="default_on">
188
189
190 <files>
191 <trackFile path="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gencode/gencode.v36lift37.annotation.sort.gff3.gz" ext="gff,gff3,bed" label="Gencode v36 (GRCh37 liftover)" remote="true">
192 <metadata>
193 </metadata>
194 </trackFile>
195 </files>
196
197 <options>
198 <style>
199 <display>LinearBasicDisplay</display>
200
201 <show_labels type="boolean">true</show_labels>
202 <show_descriptions type="boolean">true</show_descriptions>
203 <labels_name>jexl:get(feature,'name') || get(feature,'id')</labels_name>
204 <descriptions_name>jexl:get(feature,'note') || get(feature,'description')</descriptions_name>
205 <display_mode>normal</display_mode>
206 <max_height type="integer">600</max_height>
207
208
209 </style>
210
211 <formatdetails>
212 <depth>1</depth>
213 </formatdetails>
214
215
216 <gff>
217 <index>false</index>
218 </gff>
219 </options>
220 </track>
221 <track cat="Default" format="gene_calls" visibility="default_on">
222
223
224 <files>
225 <trackFile path="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/mappability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz" ext="gff,gff3,bed" label="wgEncodeDukeMapabilityRegionsExcludable" remote="true">
226 <metadata>
227 </metadata>
228 </trackFile>
229 </files>
230
231 <options>
232 <style>
233 <display>LinearBasicDisplay</display>
234
235 <show_labels type="boolean">true</show_labels>
236 <show_descriptions type="boolean">true</show_descriptions>
237 <labels_name>jexl:get(feature,'name') || get(feature,'id')</labels_name>
238 <descriptions_name>jexl:get(feature,'note') || get(feature,'description')</descriptions_name>
239 <display_mode>normal</display_mode>
240 <max_height type="integer">600</max_height>
241
242
243 </style>
244
245 <formatdetails>
246 <depth>1</depth>
247 </formatdetails>
248
249
250 <gff>
251 <index>false</index>
252 </gff>
253 </options>
254 </track>
255 </tracks>
256 </assembly>
257 </root>