| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.5+galaxy7 (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 | 1.16.5 | 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 |
| findutils | 4.6.0 | 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_0|category: Default track_groups_0|data_tracks_0|data_format|annotation: ['bed/test-3.bed', 'bed/test-6.bed'] reference_genome|genome_type_select: history standalone: False reference_genome|genome: merlin.fa track_groups_0|data_tracks_0|data_format|data_format_select: gene_calls gencode: 11 uglyTestingHack: enabled |
attributes: name |
merlin.fa bed/test-3.bed bed/test-6.bed name |
| Test-4 |
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-5 |
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-6 |
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|track_config|canvas_options|transcriptType: transcript track_groups_0|data_tracks_0|data_format|track_config|track_class: JBrowse/View/Track/CanvasFeatures 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 track_groups_0|data_tracks_0|data_format|track_config|canvas_options|subParts: exon track_groups_0|data_tracks_0|data_format|track_config|canvas_options|impliedUTRs: True uglyTestingHack: enabled |
attributes: name |
merlin.fa gff3/1.gff name |
| Test-7 |
track_groups_0|category: With custom track config track_groups_0|data_tracks_0|data_format|jb_custom_config|option_0|opt_value|val_type: text track_groups_0|data_tracks_0|data_format|annotation: gff3/1.gff track_groups_0|data_tracks_0|data_format|jb_custom_config|option_3|opt_key: style.strandArrow reference_genome|genome_type_select: history track_groups_0|data_tracks_0|data_format|jb_custom_config|option_2|opt_value|val_type: float track_groups_0|data_tracks_0|data_format|jb_custom_config|option_2|opt_key: maxFeatureScreenDensity track_groups_0|data_tracks_0|data_format|jb_custom_config|option_3|opt_value|val: False track_groups_0|data_tracks_0|data_format|jb_custom_config|option_1|opt_value|val: 150 track_groups_0|data_tracks_0|data_format|jb_custom_config|option_0|opt_key: displayMode 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|jb_custom_config|option_0|opt_value|val: collapsed track_groups_0|data_tracks_0|data_format|jb_custom_config|option_3|opt_value|val_type: boolean track_groups_0|data_tracks_0|data_format|data_format_select: gene_calls gencode: 11 track_groups_0|data_tracks_0|data_format|jb_custom_config|option_1|opt_value|val_type: integer track_groups_0|data_tracks_0|data_format|jb_custom_config|option_2|opt_value|val: 0.1 track_groups_0|data_tracks_0|data_format|jb_custom_config|option_1|opt_key: histograms.height uglyTestingHack: enabled |
attributes: name |
merlin.fa gff3/1.gff name |
| Test-8 |
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-9 |
gencode: 1 standalone: False reference_genome|genome_type_select: indexed uglyTestingHack: enabled |
attributes: name |
name |
| Test-10 |
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 |