Details
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Type:
Task
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:3
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Epic Link:
Description
Situation: As part of IGBF-3181 one of the possible choices was to include a dropdown for the coverage graph analyses that would allow the user to select the output as either bigwig or bedgraph. However, the dropdown menu item appears to break BioViz Connect as when the syncappsdatabase endpoint is hit an error is returned and the apps do not appear correctly in the BioViz Connect Analyses right panel.
Task: Add the dropdown menu as an option to the Analyses right-panel.
Attachments
Issue Links
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- Closed
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Activity
App description for 38909bac-40c4-11ed-936c-008cfa5ae621
Looks like the "type" for the dropdown is TextSelection
{
"description": "Make a scaled coverage graph file in bigWig format from a bam sequence alignment file using deepTools bamCoverage version 3.3.0 with options --binSize 1. See deeptools.readthedocs.io. %INPUT%bam",
"requirements": [
{
"step_number": 0,
"max_cpu_cores": 4.0,
"memory_limit": 17179869184
}
],
"deleted": false,
"disabled": false,
"version_id": "3890ed82-40c4-11ed-936c-008cfa5ae621",
"name": "DUPLICATE Make coverage graph (bw)",
"limitChecks": {
"canRun": true,
"results": []
},
"system_id": "de",
"label": "DUPLICATE Make coverage graph (bw)",
"id": "38909bac-40c4-11ed-936c-008cfa5ae621",
"app_type": "DE",
"versions": [
{
"version": "Unversioned",
"version_id": "3890ed82-40c4-11ed-936c-008cfa5ae621"
}
],
"groups": [
{
"id": "3897f53c-40c4-11ed-936c-008cfa5ae621",
"name": "",
"label": "Inputs",
"parameters": [
{
"description": "Enter the name of your BAM file (*)",
"arguments": [],
"name": "--bam",
"type": "FileInput",
"validators": [],
"label": "Input File (BAM)",
"id": "389183c8-40c4-11ed-936c-008cfa5ae621_3898ac66-40c4-11ed-936c-008cfa5ae621",
"isVisible": true,
"required": true
},
{
"description": "Enter the name of your index file (.bai)",
"arguments": [],
"name": "",
"type": "FileInput",
"validators": [],
"label": "Input File Index (.bai)",
"id": "389183c8-40c4-11ed-936c-008cfa5ae621_3899be58-40c4-11ed-936c-008cfa5ae621",
"isVisible": true,
"required": true
}
],
"step_number": 0
},
{
"id": "38a174f4-40c4-11ed-936c-008cfa5ae621",
"name": "",
"label": "Outputs",
"parameters": [
{
"description": "Select bedgraph or bigwig for the file output",
"arguments": [
{
"name": "--outFileFormat",
"isDefault": true,
"id": "df6145d2-40d1-11ed-a1ec-008cfa5ae621",
"display": "bigwig",
"value": "bigwig"
},
{
"name": "--outFileFormat",
"isDefault": false,
"id": "df6169c2-40d1-11ed-a1ec-008cfa5ae621",
"display": "bedgraph",
"value": "bedgraph"
}
],
"name": "",
"type": "TextSelection",
"validators": [],
"label": "Select file type output",
"id": "389183c8-40c4-11ed-936c-008cfa5ae621_df611a08-40d1-11ed-a1ec-008cfa5ae621",
"isVisible": true,
"defaultValue": {
"id": "df6145d2-40d1-11ed-a1ec-008cfa5ae621",
"name": "--outFileFormat",
"value": "bigwig",
"display": "bigwig",
"isDefault": true
},
"required": true
},
{
"description": "File is output to current directory if in Home or output to Analyses if file in Community/Shared",
"arguments": [],
"name": "--outFileName",
"type": "FileOutput",
"validators": [],
"label": "Output file name",
"id": "389183c8-40c4-11ed-936c-008cfa5ae621_38a29c80-40c4-11ed-936c-008cfa5ae621",
"isVisible": true,
"defaultValue": "FILE.bigwig",
"required": true
}
],
"step_number": 0
}
],
"version": "Unversioned"
}
App IDs for the two apps that have dropdowns (they are duplicates of make scaled coverage graph and make coverage graph).
38909bac-40c4-11ed-936c-008cfa5ae621
8b67ea38-40d3-11ed-aa9e-008cfa5ae621