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API Reference

Get details of an app revision

get https://cavatica-api.sbgenomics.com/v2

/apps/{app_id}/{revision_number}

For general information on the API, including formatting, parameters, and pagination, please see the API Overview.

This call allows you to obtain a particular revision of a tool, which is not necessarily the most recent version.

https://cavatica-api.sbgenomics.com/v2/apps/{app_id}/{revision_number}

👍

app_ids

Recall from the API Overview that the app_id has the form {project_owner}\{project}\{app_short_name}\{revision_number}

You can get the app_id for an app by making the call to list all apps available to you

Request

Example request

GET /v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0 HTTP/1.1
Host: cavatica-api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74

curl  -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://cavatica-api.sbgenomics.com/v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0/raw"

Header Fields

NameDescription
X-SBG-Auth-Token
required		Your CAVATICA authentication token.

Path parameters

NameDescription
app_idThe ID for the app you are querying. It can be obtained by making the call to list all apps available to you
revision_numberThe integer denoting the revision of the app.

Query parameters

NameData typeDescription
fieldsstringSelector specifying a subset of fields to include in the response.

Response

See a list of CAVATICA-specific response codes that may be contained in the body of the response.

Example response body

{
	"href": "https://api.sbgenomics.com/v2/apps/admin/sbg-public-data/RSEM BAM2WIG/4",
	"id": "admin/sbg-public-data/rsem-bam2wig-1-2-31/4",
	"project": "admin/sbg-public-data",
	"name": "RSEM BAM2WIG",
	"revision": 4,
	"raw": {
		"id": "https://api.sbgenomics.com/v2/apps/admin/sbg-public-data/rsem-bam2wig-1-2-31/4/raw/",
		"sbg:modifiedOn": 1476979693,
		"inputs": [
			{
				"description": "Can be either in SAM/BAM/CRAM format. Must be sorted.",
				"label": "Sorted alignment file",
				"type": [
					"File"
				],
				"sbg:fileTypes": "BAM, SAM, CRAM",
				"inputBinding":
					{ "position": 0, "separate": true, "sbg:cmdInclude": true },
				"sbg:stageInput": "copy",
				"id": "#sorted_alignment_file"
			},
			{
				"description": "If this is set, RSEM will not look for “ZW” tag and each alignment appeared in the BAM file has weight 1. Set this if your BAM file is not generated by RSEM.",
				"label": "No fractional weight",
				"sbg:category": "Options",
				"type": [
					"null",
					"boolean"
				],
				"id": "#no_fractional_weight",
				"inputBinding":
					{ "prefix": "--no-fractional-weight", "position": 3, "separate": true, "sbg:cmdInclude": true },
				"sbg:toolDefaultValue": "off"
			}
		],
		"sbg:cmdPreview": "rsem-bam2wig /path/to/aligned_file.bam aligned_file.wiggle_plot.wig aligned_file.wiggle_plot",
		"sbg:latestRevision": 4,
		"sbg:revisionsInfo": [
{ "sbg:revisionNotes": null, "sbg:revision": 0, "sbg:modifiedOn": 1476979693, "sbg:modifiedBy": "admin" }
,
{ "sbg:revisionNotes": null, "sbg:revision": 1, "sbg:modifiedOn": 1476979693, "sbg:modifiedBy": "admin" }
,
{ "sbg:revisionNotes": null, "sbg:revision": 2, "sbg:modifiedOn": 1476979693, "sbg:modifiedBy": "admin" }
,
{ "sbg:revisionNotes": "Updated description.", "sbg:revision": 3, "sbg:modifiedOn": 1476979693, "sbg:modifiedBy": "admin" }
,
{ "sbg:revisionNotes": null, "sbg:revision": 4, "sbg:modifiedOn": 1476979693, "sbg:modifiedBy": "admin" }
],
"hints": [
{ "value": 1, "class": "sbg:CPURequirement" }
,
{ "value": 1000, "class": "sbg:MemRequirement" }
,
{ "dockerImageId": "67d3a6c01e91234f43c8ef809c2a245a75bf7d5a52762823cdc3b2e784de576c", "class": "DockerRequirement", "dockerPull": "images.sbgenomics.com/uros_sipetic/rsem:1.2.31" }
],
"stdin": "",
"sbg:links": [
{ "label": "RSEM Homepage", "id": "http://deweylab.github.io/RSEM/" }
,
{ "label": "RSEM Source Code", "id": "https://github.com/deweylab/RSEM" }
,
{ "label": "RSEM Download", "id": "https://github.com/deweylab/RSEM/archive/v1.2.31.tar.gz" }
,
{ "label": "RSEM Publications", "id": "https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323" }
,
{ "label": "RSEM Documentation", "id": "http://deweylab.github.io/RSEM/README.html" }
],
"stdout": "",
"description": "RSEM BAM2WIG generates a wiggle plot representing the expected number of reads overlapping each position in the genome/transcript from the sorted genome/transcript BAM file output.\n\n###Common issues###\nNone",
"sbg:validationErrors": [],
"sbg:image_url": null,
"sbg:toolkitVersion": "1.2.31",
"sbg:toolkit": "RSEM",
"requirements": [
{
"id": "#cwl-js-engine",
"class": "ExpressionEngineRequirement",
"requirements": [
{ "class": "DockerRequirement", "dockerPull": "rabix/js-engine" }
]
}
],
"sbg:id": "admin/sbg-public-data/rsem-bam2wig-1-2-31/4",
"sbg:categories": [
"Converters",
"Plotting-and-Rendering",
"RNA"
],
"sbg:toolAuthor": "Bo Li, Colin Dewey",
"temporaryFailCodes": [],
"label": "RSEM BAM2WIG",
"sbg:createdBy": "admin",
"class": "CommandLineTool",
"sbg:project": "admin/sbg-public-data",
"sbg:sbgMaintained": false,
"sbg:revision": 4,
"baseCommand": [
"rsem-bam2wig"
],
"sbg:contributors": [
"admin"
],
"sbg:createdOn": 1476979693,
"successCodes": [],
"sbg:modifiedBy": "admin",
"sbg:license": "GNU General Public License v3.0 only",
"arguments": [
{
"position": 1,
"valueFrom": {
"engine": "#cwl-js-engine",
"script": "{\n var str = $job.inputs.sorted_alignment_file.path.split('/').pop().split('.')\n x = \"\"\n for (i=0; i<str.length-1; i++) {\n if (i<str.length-2)
{\n x = x + str[i] + '.'\n } else {\n x = x + str[i]\n }\n }\n return x + \".wiggle_plot.wig\"\n}",
"class": "Expression"
},
"separate": true
},
{
"position": 2,
"valueFrom": {
"engine": "#cwl-js-engine",
"script": "{\n var str = $job.inputs.sorted_alignment_file.path.split('/').pop().split('.')\n x = \"\"\n for (i=0; i<str.length-1; i++) {\n if (i<str.length-2) {n x = x + str[i] + '.'n }
else
{\n x = x + str[i]\n }
\n }\n return x + \".wiggle_plot\"\n}",
"class": "Expression"
},
"separate": true
}
],
"outputs": [
{
"description": "Output wiggle file.",
"label": "Output wiggle file",
"type": [
"null",
"File"
],
"sbg:fileTypes": "WIG",
"outputBinding":
{ "glob": "*.wig", "sbg:inheritMetadataFrom": "#sorted_alignment_file" }
,
"id": "#rsem_bam_to_wiggle_plot_file"
}
],
"sbg:job": {
"allocatedResources":
{ "mem": 1000, "cpu": 1 }
,
"inputs": {
"no_fractional_weight": false,
"sorted_alignment_file":
{ "size": 0, "path": "/path/to/aligned_file.bam", "secondaryFiles": [], "class": "File" }
}
}
}
}
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