Miscellaneous |
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 |