Get raw CWL for an app

/apps/{app_id}/raw

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 the Platform by a project member, or a publicly available app that has been copied to the project.

Path

https://api.sb.biodatacatalyst.nhlbi.nih.gov/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

HTTP

GET /v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/raw HTTP/1.1
Host: api.sb.biodatacatalyst.nhlbi.nih.gov
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74

cURL

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

Header Fields

Name	Description
X-SBG-Auth-Token required	Your authentication token.

Path parameters

Name	Description
app_id	The ID for the app you are querying. It can be obtained by making the call to list all apps available to you

Query parameters

Name	Data type	Description
fields	string	Selector specifying a subset of fields to include in the response.

Response

See a list of 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.

JSON

{
  "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/rfranklin/bamtools:2.4.0"
    },
    {
      "value": 1,
      "class": "sbg:CPURequirement"
    },
    {
      "value": 1000,
      "class": "sbg:MemRequirement"
    }
  ],
  "sbg:copyOf": "jsmith/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://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"
}