Repository revision
25:1cfc579079a6

Repository 'jbrowse'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/jbrowse

JBrowse tool metadata
Miscellaneous
JBrowse
genome browser
jbrowse
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0
1.16.1+galaxy0
python '${__tool_directory__}/jbrowse.py' --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.1
jbrowse
Requirements (dependencies defined in the <requirements> tag set)
name version type
jbrowse 1.16.1 package
python 2.7 package
biopython 1.72 package
bcbiogff 0.6.4 package
samtools 1.9 package
pyyaml 3.13 package
tabix 0.2.6 package
Functional tests
name inputs outputs required files
Test-1 standalone: False
gencode: 1
reference_genome|genome: merlin.fa
reference_genome|genome_type_select: history
uglyTestingHack: enabled
attributes: name
merlin.fa
name
Test-2 standalone: False
gencode: 11
reference_genome|genome: merlin.fa
reference_genome|genome_type_select: history
uglyTestingHack: enabled
attributes: name
merlin.fa
name
Test-3 track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|color_scheme|score_scheme: opacity
track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_score_select: score
track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_scheme|color|color_select: manual
track_groups_3|data_tracks_1|data_format|match_part|match_part_select: True
track_groups_1|data_tracks_0|data_format|jbcolor_scale|color_score|color|color_select: manual
track_groups_2|data_tracks_2|data_format|annotation: gff3/1.gff
track_groups_2|data_tracks_0|data_format|match_part|match_part_select: False
track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|score_scaling: linear
track_groups_2|data_tracks_2|data_format|match_part|match_part_select: False
track_groups_1|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select: none
track_groups_3|data_tracks_0|data_format|match_part|match_part_select: False
reference_genome|genome: merlin.fa
track_groups_2|data_tracks_1|data_format|data_format_select: gene_calls
track_groups_3|data_tracks_1|data_format|jbcolor_scale|color_score|color_score_select: none
track_groups_0|data_tracks_0|data_format|annotation: ['gff3/A.gff', 'gff3/B.gff', 'gff3/C.gff', 'gff3/D.gff']
track_groups_1|data_tracks_0|data_format|match_part|match_part_select: False
track_groups_0|data_tracks_0|data_format|data_format_select: gene_calls
track_groups_1|data_tracks_0|data_format|jbcolor_scale|color_score|color|style_color: #ff00ff
gencode: 11
track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scales|scale_select: manual
track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|score_scaling: linear
reference_genome|genome_type_select: history
track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scales|maximum: 1000
track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scales|scale_select: manual
track_groups_2|data_tracks_3|data_format|match_part|match_part_select: False
track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|score_scales|scale_select: automatic
track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_scheme|color|style_color: #ff0000
track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scaling: linear
track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|color_scheme|color|color_select: automatic
track_groups_2|category: Scaled Colour
track_groups_1|category: Ignore Scale
track_groups_2|data_tracks_2|data_format|data_format_select: gene_calls
track_groups_2|data_tracks_3|data_format|data_format_select: gene_calls
track_groups_3|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select: none
track_groups_2|data_tracks_0|data_format|data_format_select: gene_calls
track_groups_0|category: Auto Coloured
track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select: score
track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|color_scheme|score_scheme: opacity
track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scales|minimum: 0
track_groups_3|data_tracks_1|data_format|match_part|name: cDNA_match
track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|color_score_select: score
track_groups_2|data_tracks_0|data_format|annotation: gff3/1.gff
track_groups_1|data_tracks_0|data_format|annotation: gff3/1.gff
track_groups_3|data_tracks_1|data_format|data_format_select: gene_calls
track_groups_3|data_tracks_1|data_format|annotation: gff3/2.gff
track_groups_3|data_tracks_0|data_format|data_format_select: gene_calls
track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_score_select: score
track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|score_scales|scale_select: automatic
track_groups_3|data_tracks_0|data_format|annotation: gff3/interpro.gff
track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scales|minimum: 0
track_groups_2|data_tracks_1|data_format|annotation: gff3/1.gff
track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select: none
standalone: False
track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_scheme|color|style_color: #0000ff
track_groups_0|data_tracks_0|data_format|match_part|match_part_select: False
track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_scheme|score_scheme: opacity
track_groups_2|data_tracks_3|data_format|annotation: gff3/1.gff
track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scales|maximum: 1000
track_groups_3|category: Realistic
track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_scheme|color|color_select: manual
track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scaling: linear
track_groups_2|data_tracks_1|data_format|match_part|match_part_select: False
uglyTestingHack: enabled
track_groups_1|data_tracks_0|data_format|data_format_select: gene_calls
track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_scheme|score_scheme: opacity
track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|color_scheme|color|color_select: automatic
attributes: name
merlin.fa
gff3/A.gff
gff3/B.gff
gff3/C.gff
gff3/D.gff
gff3/1.gff
gff3/interpro.gff
gff3/2.gff
name
Test-4 track_groups_0|data_tracks_1|data_format|match_part|match_part_select: False
track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_label: Another menu item
reference_genome|genome: merlin.fa
track_groups_0|data_tracks_1|data_format|jbcolor_scale|color_score|color_score_select: none
track_groups_0|data_tracks_0|data_format|data_format_select: gene_calls
gencode: 11
track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_action: newWindow
reference_genome|genome_type_select: history
track_groups_0|data_tracks_1|data_format|annotation: gff3/1.gff
track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_title: Frame title
uglyTestingHack: enabled
track_groups_0|category: With menu or index
track_groups_0|data_tracks_0|data_format|annotation: gff3/1.gff
track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_url: https://example.com/#!/?id={name}&q={type}&z="{end}"
track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_label: Some menu item
track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_icon: dijitIconNewTask
track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_url: https://example.com/#!/?id={name}&q={type}&z="{end}"
track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_title: Frame title 2
track_groups_0|data_tracks_1|data_format|index: True
track_groups_0|data_tracks_0|data_format|match_part|match_part_select: False
standalone: False
track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select: none
track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_action: iframeDialog
track_groups_0|data_tracks_1|data_format|data_format_select: gene_calls
attributes: name
merlin.fa
gff3/1.gff
name
Test-5 track_groups_0|category: With canvas config
track_groups_0|data_tracks_0|data_format|annotation: gff3/1.gff
reference_genome|genome_type_select: history
track_groups_0|data_tracks_0|data_format|match_part|match_part_select: False
standalone: False
reference_genome|genome: merlin.fa
track_groups_0|data_tracks_0|data_format|data_format_select: gene_calls
gencode: 11
track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select: none
uglyTestingHack: enabled
attributes: name
merlin.fa
gff3/1.gff
name
Test-6 track_groups_0|category: Auto Coloured
track_groups_0|data_tracks_0|data_format|annotation: bam/merlin-sample.bam
reference_genome|genome_type_select: history
standalone: False
reference_genome|genome: merlin.fa
track_groups_0|data_tracks_0|data_format|data_format_select: pileup
gencode: 11
uglyTestingHack: enabled
attributes: name
merlin.fa
bam/merlin-sample.bam
name
Test-7 gencode: 1
standalone: False
reference_genome|genome_type_select: indexed
uglyTestingHack: enabled
attributes: name
name
Test-8 track_groups_0|category: External endpoints
reference_genome|genome_type_select: history
standalone: False
track_groups_0|data_tracks_0|data_format|label: Rest api
track_groups_0|data_tracks_1|data_format|query: DEFINE sql:select-option 'order' prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> select ?start, ?end, IF( ?faldo_type = faldo:ForwardStrandPosition, 1, IF( ?faldo_type = faldo:ReverseStrandPosition, -1, 0 ) ) as ?strand, str(?obj_type_name) as ?type, str(?label) as ?name, str(?obj_name) as ?description, ?obj as ?uniqueID, ?parent as ?parentUniqueID where { values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } }
track_groups_0|data_tracks_1|data_format|label: Sparql endpoint
reference_genome|genome: merlin.fa
track_groups_0|data_tracks_1|data_format|data_format_select: sparql
track_groups_0|data_tracks_0|data_format|data_format_select: rest
gencode: 11
track_groups_0|data_tracks_1|data_format|url: http://example.org.external/sparql/
track_groups_0|data_tracks_0|data_format|url: http://example.org.external/rest_api/
uglyTestingHack: enabled
attributes: name
merlin.fa
name