diff test-data/dataset_1_files/jbrowse.conf @ 10:a46a509386d3 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset_1_files/jbrowse.conf	Mon Dec 02 05:50:13 2019 -0500
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+#### JBrowse main configuration file
+
+## uncomment the section below to customize this browser's title and description
+# [aboutThisBrowser]
+# title = <i>Oryza sativa</i>
+# description = Browser for O. sativa transcripts and RNA-seq data,
+#   produced by the Smith laboratory at Example State University.
+
+## uncomment and edit the example below to configure a faceted track selector
+# [trackSelector]
+# type = Faceted
+# displayColumns =
+#   + label
+#   + key
+#   + organism
+#   + technique
+## optionally sort the faceted track selector by column (use the names from displayColumns)
+# initialSortColumn=label
+## optionally give different names to some of the data facets using renameFacets
+# [trackSelector.renameFacets]
+# submission = Submission ID
+# developmental-stage = Conditions
+# cell-line = Cell Line
+# key = Dataset
+# label = Track
+
+## uncomment this section to get hierarchical trackselector options
+# [trackSelector]
+## optionally turn off sorting for the hierarchical track selector
+# sortHierarchical = false
+## set collapsed categories for the hierarchical track selector
+# collapsedCategories = Reference sequence,Quantitative / XY Plot
+## set category ordering in the hierarchical track selector
+# categoryOrder = BAM, Transcripts, Quantitative/Density, VCF
+
+## configure where to get metadata about tracks.  always indexes the
+## `metadata` part of each track config, but this can be used to load
+## additional metadata from CSV or JSON urls
+# [trackMetadata]
+# sources = data/trackMetadata.csv
+
+
+[GENERAL]
+
+
+## add a document.domain to set the same-origin policy
+# documentDomain=foobar.com
+
+## use classic jbrowse menu with file instead of track and genome
+#classicMenu = true
+
+## hide open genome option
+#hideGenomeOptions = true
+
+## enable or disable high resolution rendering for canvas features. set to auto, disabled, or numerical scaling factor. default: 2
+# highResolutionMode=auto
+
+## uncomment to change the default sort order of the reference
+## sequence dropdown
+# refSeqOrder = length descending
+
+## Uncomment to prevent HTML tracks from displaying gene subfeatures (enabled by default)
+# inferHTMLSubfeatures = false
+
+## to set a default data directory other than 'data', uncomment and
+## edit the line below
+# dataRoot = data
+
+## optionally add more include statements to load and merge in more
+## configuration files
+include  = {dataRoot}/trackList.json
+include += {dataRoot}/tracks.conf
+# include += ../url/of/my/other/config.json
+# include += another_config.conf
+
+## uncomment and edit the example below to enable one or more
+## JBrowse plugins
+# [ plugins.MyPlugin ]
+# location = plugins/MyPlugin
+# [ plugins.AnotherPlugin ]
+# location = ../plugin/dir/someplace/else
+
+## edit the datasets list below to add datasets to the jbrowse dataset
+## selector
+
+# [datasets.volvox]
+# url  = ?data=sample_data/json/volvox
+# name = Volvox Example
+
+# [datasets.modencode]
+# url  = ?data=sample_data/json/modencode
+# name = MODEncode Example
+
+# [datasets.yeast]
+# url  = ?data=sample_data/json/yeast
+# name = Yeast Example
+[ plugins.BlastView ]
+location = ../plugin/BlastView/
+[ plugins.GCContent ]
+location = ../plugin/GCContent/
+[ plugins.ComboTrackSelector ]
+location = ../plugin/ComboTrackSelector/
+[ plugins.MultiBigWig ]
+location = ../plugin/MultiBigWig/
+[ plugins.bookmarks ]
+location = ../plugin/bookmarks/
+[ plugins.NeatCanvasFeatures ]
+location = ../plugin/NeatCanvasFeatures/
+[ plugins.NeatHTMLFeatures ]
+location = ../plugin/NeatHTMLFeatures/