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API Reference

Get raw CWL for an app

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

/apps/{app_id}/raw

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

This call returns information about the specified app, as raw CWL. The call differs from the call to GET details of an app by returning a JSON object that is the CWL.

The app should be one in a project that you can access; this could be an app that has been uploaded to CAVATICA by a project member, or a publicly available app that has been copied to the project.

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

👍

app_ids

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

Note that if you omit revision_number, the API will return the latest app revision.

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/raw 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/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

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

Note that this call returns the full CWL description of the app.

{
  "successCodes": [],
  "sbg:homepage": "https://github.com/pezmaster31/bamtools/wiki",
  "sbg:validationErrors": [],
  "sbg:sbgMaintained": false,
  "temporaryFailCodes": [],
  "requirements": [],
  "sbg:latestRevision": 0,
  "description": "BamTools Merge merges multiple BAM files into a single file.",
  "sbg:job": {
    "inputs": {
      "region": "chr1",
      "input_bam_files": [
        {
          "path": "1.bam"
        },
        {
          "path": "2.bam"
        }
      ]
    },
    "allocatedResources": {
      "cpu": 1,
      "mem": 1000
    }
  },
  "sbg:toolAuthor": "Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg",
  "hints": [
    {
      "dockerImageId": "f808163d4cd3",
      "class": "DockerRequirement",
      "dockerPull": "images.sbgenomics.com/markop/bamtools:2.4.0"
    },
    {
      "value": 1,
      "class": "sbg:CPURequirement"
    },
    {
      "value": 1000,
      "class": "sbg:MemRequirement"
    }
  ],
  "sbg:copyOf": "djordje_klisic/public-apps-by-seven-bridges/bamtools-merge-2-4-0/0",
  "sbg:createdOn": 1452181866,
  "arguments": [
    {
      "position": 1,
      "prefix": "-out",
      "separate": true,
      "valueFrom": "merged.bam"
    }
  ],
  "outputs": [
    {
      "sbg:fileTypes": "BAM",
      "id": "#output_bam_file",
      "outputBinding": {
        "glob": "merged.bam",
        "sbg:metadata": {},
        "sbg:inheritMetadataFrom": "#input_bams"
      },
      "description": "Output BAM file.",
      "type": [
        "File"
      ],
      "label": "Output BAM file"
    }
  ],
  "sbg:categories": [
    "SAM/BAM-Processing"
  ],
  "sbg:contributors": [
    "RFranklin"
  ],
  "sbg:links": [
    {
      "id": "https://github.com/pezmaster31/bamtools",
      "label": "Homepage"
    },
    {
      "id": "https://github.com/pezmaster31/bamtools/wiki",
      "label": "Wiki"
    }
  ],
  "stdout": "",
  "stdin": "",
  "sbg:project": "RFranklin/my-project",
  "inputs": [
    {
      "sbg:fileTypes": "BAM",
      "id": "#input_bam_files",
      "inputBinding": {
        "sbg:cmdInclude": true,
        "prefix": "-in",
        "separate": true,
        "itemSeparator": null,
        "position": 0
      },
      "description": "The input BAM files.",
      "label": "Input BAM files",
      "type": [
        {
          "type": "array",
          "items": "File"
        }
      ],
      "sbg:category": "Input & Output"
    },
    {
      "id": "#region",
      "inputBinding": {
        "sbg:cmdInclude": true,
        "position": 2,
        "separate": true,
        "prefix": "-region"
      },
      "description": "A region of interest (e.g. \"chr1:500..chr3:1500\"). See the documentation for more info.",
      "label": "Region of interest",
      "type": [
        "null",
        "string"
      ],
      "sbg:category": "Input & Output"
    }
  ],
  "label": "BamTools Merge",
  "sbg:createdBy": "RFranklin",
  "baseCommand": [
    "/opt/bamtools/bin/bamtools",
    "merge"
  ],
  "sbg:toolkitVersion": "2.4.0",
  "sbg:id": "RFranklin/my-project/bamtools-merge-2-4-0/0",
  "sbg:license": "The MIT License",
  "sbg:revision": 0,
  "sbg:cmdPreview": "/opt/bamtools/bin/bamtools merge -in 1.bam -in 2.bam -out merged.bam -region chr1",
  "sbg:modifiedOn": 1452181866,
  "id": "https://cavatica-api.sbgenomics.com/RFranklin/my-project/bamtools-merge-2-4-0/0/raw/",
  "class": "CommandLineTool",
  "sbg:modifiedBy": "RFranklin",
  "sbg:revisionsInfo": [
    {
      "sbg:modifiedBy": "RFranklin",
      "sbg:modifiedOn": 1452181866,
      "sbg:revision": 0
    }
  ],
  "sbg:toolkit": "BamTools"
}
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