Mercurial > repos > gga > apollo_create_or_update

comparison test-data/dataset_1_files/jbrowse.conf @ 10:d72192ec8e39 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
author gga
date Mon, 02 Dec 2019 05:46:45 -0500
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9:29ce13734a5c 10:d72192ec8e39
1 #### JBrowse main configuration file
2
3 ## uncomment the section below to customize this browser's title and description
4 # [aboutThisBrowser]
5 # title = <i>Oryza sativa</i>
6 # description = Browser for O. sativa transcripts and RNA-seq data,
7 # produced by the Smith laboratory at Example State University.
8
9 ## uncomment and edit the example below to configure a faceted track selector
10 # [trackSelector]
11 # type = Faceted
12 # displayColumns =
13 # + label
14 # + key
15 # + organism
16 # + technique
17 ## optionally sort the faceted track selector by column (use the names from displayColumns)
18 # initialSortColumn=label
19 ## optionally give different names to some of the data facets using renameFacets
20 # [trackSelector.renameFacets]
21 # submission = Submission ID
22 # developmental-stage = Conditions
23 # cell-line = Cell Line
24 # key = Dataset
25 # label = Track
26
27 ## uncomment this section to get hierarchical trackselector options
28 # [trackSelector]
29 ## optionally turn off sorting for the hierarchical track selector
30 # sortHierarchical = false
31 ## set collapsed categories for the hierarchical track selector
32 # collapsedCategories = Reference sequence,Quantitative / XY Plot
33 ## set category ordering in the hierarchical track selector
34 # categoryOrder = BAM, Transcripts, Quantitative/Density, VCF
35
36 ## configure where to get metadata about tracks. always indexes the
37 ## `metadata` part of each track config, but this can be used to load
38 ## additional metadata from CSV or JSON urls
39 # [trackMetadata]
40 # sources = data/trackMetadata.csv
41
42
43 [GENERAL]
44
45
46 ## add a document.domain to set the same-origin policy
47 # documentDomain=foobar.com
48
49 ## use classic jbrowse menu with file instead of track and genome
50 #classicMenu = true
51
52 ## hide open genome option
53 #hideGenomeOptions = true
54
55 ## enable or disable high resolution rendering for canvas features. set to auto, disabled, or numerical scaling factor. default: 2
56 # highResolutionMode=auto
57
58 ## uncomment to change the default sort order of the reference
59 ## sequence dropdown
60 # refSeqOrder = length descending
61
62 ## Uncomment to prevent HTML tracks from displaying gene subfeatures (enabled by default)
63 # inferHTMLSubfeatures = false
64
65 ## to set a default data directory other than 'data', uncomment and
66 ## edit the line below
67 # dataRoot = data
68
69 ## optionally add more include statements to load and merge in more
70 ## configuration files
71 include = {dataRoot}/trackList.json
72 include += {dataRoot}/tracks.conf
73 # include += ../url/of/my/other/config.json
74 # include += another_config.conf
75
76 ## uncomment and edit the example below to enable one or more
77 ## JBrowse plugins
78 # [ plugins.MyPlugin ]
79 # location = plugins/MyPlugin
80 # [ plugins.AnotherPlugin ]
81 # location = ../plugin/dir/someplace/else
82
83 ## edit the datasets list below to add datasets to the jbrowse dataset
84 ## selector
85
86 # [datasets.volvox]
87 # url = ?data=sample_data/json/volvox
88 # name = Volvox Example
89
90 # [datasets.modencode]
91 # url = ?data=sample_data/json/modencode
92 # name = MODEncode Example
93
94 # [datasets.yeast]
95 # url = ?data=sample_data/json/yeast
96 # name = Yeast Example
97 [ plugins.BlastView ]
98 location = ../plugin/BlastView/
99 [ plugins.GCContent ]
100 location = ../plugin/GCContent/
101 [ plugins.ComboTrackSelector ]
102 location = ../plugin/ComboTrackSelector/
103 [ plugins.MultiBigWig ]
104 location = ../plugin/MultiBigWig/
105 [ plugins.bookmarks ]
106 location = ../plugin/bookmarks/
107 [ plugins.NeatCanvasFeatures ]
108 location = ../plugin/NeatCanvasFeatures/
109 [ plugins.NeatHTMLFeatures ]
110 location = ../plugin/NeatHTMLFeatures/