{"_id":"5774f48d50a4121900e4a2b8","__v":3,"user":"575e85ac41c8ba0e00259a44","version":{"_id":"5773dcfc255e820e00e1cd50","__v":26,"project":"5773dcfc255e820e00e1cd4d","createdAt":"2016-06-29T14:36:44.812Z","releaseDate":"2016-06-29T14:36:44.812Z","categories":["5773dcfc255e820e00e1cd51","5773df36904b0c0e00ef05ff","577baf92451b1e0e006075ac","577bb183b7ee4a0e007c4e8d","577ce77a1cf3cb0e0048e5ea","577d11865fd4de0e00cc3dab","578e62792c3c790e00937597","578f4fd98335ca0e006d5c84","578f5e5c3d04570e00976ebb","57bc35f7531e000e0075d118","57f801b3760f3a1700219ebb","5804d55d1642890f00803623","581c8d55c0dc651900aa9350","589dcf8ba8c63b3b00c3704f","594cebadd8a2f7001b0b53b2","59a562f46a5d8c00238e309a","5a2aa096e25025003c582b58","5a2e79566c771d003ca0acd4","5a3a5166142db90026f24007","5a3a52b5bcc254001c4bf152","5a3a574a2be213002675c6d2","5a3a66bb2be213002675cb73","5a3a6e4854faf60030b63159","5c8a68278e883901341de571","5cb9971e57bf020024523c7b","5cbf1683e2a36d01d5012ecd"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"githubsync":"","project":"5773dcfc255e820e00e1cd4d","category":{"_id":"5773df36904b0c0e00ef05ff","version":"5773dcfc255e820e00e1cd50","__v":0,"project":"5773dcfc255e820e00e1cd4d","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-06-29T14:46:14.277Z","from_sync":false,"order":12,"slug":"api","title":"Cavatica API"},"parentDoc":null,"metadata":{"title":"","description":"","image":[]},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-06-30T10:29:33.170Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","examples":{"codes":[]},"method":"get","auth":"required","params":[],"url":""},"isReference":false,"order":64,"body":"This call returns information about the specified app revision, as raw CWL. The call differs from the call to [ `GET` a specific revision of an app](doc:get-details-of-an-app-revision) by returning a JSON object that is the CWL description of the app revision. \n\nThe 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.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"https://cavatica-api.sbgenomics.com/v2/apps/{app_id}/raw\",\n      \"language\": \"text\",\n      \"name\": \"API path\"\n    }\n  ]\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"success\",\n  \"body\": \"Recall from the [API Overview](doc:the-api#section-identifying-projects-users-apps-files-tasks-and-inputs) that the `app_id` has the form `{project_owner}\\\\{project}\\\\{app_short_name}\\\\{revision_number}`\\n\\nYou can get the `app_id` for an app by making the call to [list all apps available to you](doc:list-all-apps-available-to-you)\",\n  \"title\": \"app_ids\"\n}\n[/block]\n##Request\n\n###Example request\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"GET /v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0/raw HTTP/1.1\\nHost: cavatica-api.sbgenomics.com\\nX-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74\\n\",\n      \"language\": \"http\",\n      \"name\": null\n    },\n    {\n      \"code\": \"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\\\"\",\n      \"language\": \"curl\",\n      \"name\": \"cURL\"\n    }\n  ],\n  \"sidebar\": true\n}\n[/block]\n###Header Fields\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Name\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"`X-SBG-Auth-Token`\\n_required_\",\n    \"0-1\": \"Your Cavatica [authentication token](doc:get-your-authentication-token).\",\n    \"h-2\": \"\"\n  },\n  \"cols\": 2,\n  \"rows\": 1\n}\n[/block]\n###Path parameters\n[block:parameters]\n{\n  \"data\": {\n    \"0-0\": \"`app_id`\",\n    \"h-0\": \"Name\",\n    \"h-1\": \"Description\",\n    \"0-1\": \"The ID for the app you are querying. It can be obtained by making the call to [list all apps available to you](doc:list-all-apps-available-to-you)\",\n    \"1-0\": \"`revision number`\",\n    \"1-1\": \"The integer that is the revision number of the app\"\n  },\n  \"cols\": 2,\n  \"rows\": 2\n}\n[/block]\n###Query parameters\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Name\",\n    \"h-1\": \"Data type\",\n    \"h-2\": \"Description\",\n    \"0-0\": \"`fields`\",\n    \"0-1\": \"string\",\n    \"0-2\": \"Selector specifying a subset of fields to include in the response.\"\n  },\n  \"cols\": 3,\n  \"rows\": 1\n}\n[/block]\n##Response\n\n[See a list of Cavatica-specific response codes that may be contained in the body of the response.](doc:api-status-codes) \n\n###Example response body\nNote that this call returns the full CWL description of the app.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"successCodes\\\": [],\\n  \\\"sbg:homepage\\\": \\\"https://github.com/pezmaster31/bamtools/wiki\\\",\\n  \\\"sbg:validationErrors\\\": [],\\n  \\\"sbg:sbgMaintained\\\": false,\\n  \\\"temporaryFailCodes\\\": [],\\n  \\\"requirements\\\": [],\\n  \\\"sbg:latestRevision\\\": 0,\\n  \\\"description\\\": \\\"BamTools Merge merges multiple BAM files into a single file.\\\",\\n  \\\"sbg:job\\\": {\\n    \\\"inputs\\\": {\\n      \\\"region\\\": \\\"chr1\\\",\\n      \\\"input_bam_files\\\": [\\n        {\\n          \\\"path\\\": \\\"1.bam\\\"\\n        },\\n        {\\n          \\\"path\\\": \\\"2.bam\\\"\\n        }\\n      ]\\n    },\\n    \\\"allocatedResources\\\": {\\n      \\\"cpu\\\": 1,\\n      \\\"mem\\\": 1000\\n    }\\n  },\\n  \\\"sbg:toolAuthor\\\": \\\"Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg\\\",\\n  \\\"hints\\\": [\\n    {\\n      \\\"dockerImageId\\\": \\\"f808163d4cd3\\\",\\n      \\\"class\\\": \\\"DockerRequirement\\\",\\n      \\\"dockerPull\\\": \\\"images.sbgenomics.com/markop/bamtools:2.4.0\\\"\\n    },\\n    {\\n      \\\"value\\\": 1,\\n      \\\"class\\\": \\\"sbg:CPURequirement\\\"\\n    },\\n    {\\n      \\\"value\\\": 1000,\\n      \\\"class\\\": \\\"sbg:MemRequirement\\\"\\n    }\\n  ],\\n  \\\"sbg:copyOf\\\": \\\"djordje_klisic/public-apps-by-seven-bridges/bamtools-merge-2-4-0/0\\\",\\n  \\\"sbg:createdOn\\\": 1452181866,\\n  \\\"arguments\\\": [\\n    {\\n      \\\"position\\\": 1,\\n      \\\"prefix\\\": \\\"-out\\\",\\n      \\\"separate\\\": true,\\n      \\\"valueFrom\\\": \\\"merged.bam\\\"\\n    }\\n  ],\\n  \\\"outputs\\\": [\\n    {\\n      \\\"sbg:fileTypes\\\": \\\"BAM\\\",\\n      \\\"id\\\": \\\"#output_bam_file\\\",\\n      \\\"outputBinding\\\": {\\n        \\\"glob\\\": \\\"merged.bam\\\",\\n        \\\"sbg:metadata\\\": {},\\n        \\\"sbg:inheritMetadataFrom\\\": \\\"#input_bams\\\"\\n      },\\n      \\\"description\\\": \\\"Output BAM file.\\\",\\n      \\\"type\\\": [\\n        \\\"File\\\"\\n      ],\\n      \\\"label\\\": \\\"Output BAM file\\\"\\n    }\\n  ],\\n  \\\"sbg:categories\\\": [\\n    \\\"SAM/BAM-Processing\\\"\\n  ],\\n  \\\"sbg:contributors\\\": [\\n    \\\"RFranklin\\\"\\n  ],\\n  \\\"sbg:links\\\": [\\n    {\\n      \\\"id\\\": \\\"https://github.com/pezmaster31/bamtools\\\",\\n      \\\"label\\\": \\\"Homepage\\\"\\n    },\\n    {\\n      \\\"id\\\": \\\"https://github.com/pezmaster31/bamtools/wiki\\\",\\n      \\\"label\\\": \\\"Wiki\\\"\\n    }\\n  ],\\n  \\\"stdout\\\": \\\"\\\",\\n  \\\"stdin\\\": \\\"\\\",\\n  \\\"sbg:project\\\": \\\"RFranklin/my-project\\\",\\n  \\\"inputs\\\": [\\n    {\\n      \\\"sbg:fileTypes\\\": \\\"BAM\\\",\\n      \\\"id\\\": \\\"#input_bam_files\\\",\\n      \\\"inputBinding\\\": {\\n        \\\"sbg:cmdInclude\\\": true,\\n        \\\"prefix\\\": \\\"-in\\\",\\n        \\\"separate\\\": true,\\n        \\\"itemSeparator\\\": null,\\n        \\\"position\\\": 0\\n      },\\n      \\\"description\\\": \\\"The input BAM files.\\\",\\n      \\\"label\\\": \\\"Input BAM files\\\",\\n      \\\"type\\\": [\\n        {\\n          \\\"type\\\": \\\"array\\\",\\n          \\\"items\\\": \\\"File\\\"\\n        }\\n      ],\\n      \\\"sbg:category\\\": \\\"Input & Output\\\"\\n    },\\n    {\\n      \\\"id\\\": \\\"#region\\\",\\n      \\\"inputBinding\\\": {\\n        \\\"sbg:cmdInclude\\\": true,\\n        \\\"position\\\": 2,\\n        \\\"separate\\\": true,\\n        \\\"prefix\\\": \\\"-region\\\"\\n      },\\n      \\\"description\\\": \\\"A region of interest (e.g. \\\\\\\"chr1:500..chr3:1500\\\\\\\"). See the documentation for more info.\\\",\\n      \\\"label\\\": \\\"Region of interest\\\",\\n      \\\"type\\\": [\\n        \\\"null\\\",\\n        \\\"string\\\"\\n      ],\\n      \\\"sbg:category\\\": \\\"Input & Output\\\"\\n    }\\n  ],\\n  \\\"label\\\": \\\"BamTools Merge\\\",\\n  \\\"sbg:createdBy\\\": \\\"RFranklin\\\",\\n  \\\"baseCommand\\\": [\\n    \\\"/opt/bamtools/bin/bamtools\\\",\\n    \\\"merge\\\"\\n  ],\\n  \\\"sbg:toolkitVersion\\\": \\\"2.4.0\\\",\\n  \\\"sbg:id\\\": \\\"RFranklin/my-project/bamtools-merge-2-4-0/0\\\",\\n  \\\"sbg:license\\\": \\\"The MIT License\\\",\\n  \\\"sbg:revision\\\": 0,\\n  \\\"sbg:cmdPreview\\\": \\\"/opt/bamtools/bin/bamtools merge -in 1.bam -in 2.bam -out merged.bam -region chr1\\\",\\n  \\\"sbg:modifiedOn\\\": 1452181866,\\n  \\\"id\\\": \\\"https://cavatica-api.sbgenomics.com/RFranklin/my-project/bamtools-merge-2-4-0/0/raw/\\\",\\n  \\\"class\\\": \\\"CommandLineTool\\\",\\n  \\\"sbg:modifiedBy\\\": \\\"RFranklin\\\",\\n  \\\"sbg:revisionsInfo\\\": [\\n    {\\n      \\\"sbg:modifiedBy\\\": \\\"RFranklin\\\",\\n      \\\"sbg:modifiedOn\\\": 1452181866,\\n      \\\"sbg:revision\\\": 0\\n    }\\n  ],\\n  \\\"sbg:toolkit\\\": \\\"BamTools\\\"\\n}\",\n      \"language\": \"json\"\n    }\n  ],\n  \"sidebar\": true\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n<hr>","excerpt":"/apps/{app_id}/{revision_number}/raw\n\nFor general information on the API, including formatting, parameters, and pagination, please see the [API Overview](the-api).","slug":"get-raw-cwl-for-an-app-revision","type":"endpoint","title":"Get raw CWL for an app revision"}

getGet raw CWL for an app revision

/apps/{app_id}/{revision_number}/raw For general information on the API, including formatting, parameters, and pagination, please see the [API Overview](the-api).

This call returns information about the specified app revision, as raw CWL. The call differs from the call to [ `GET` a specific revision of an app](doc:get-details-of-an-app-revision) by returning a JSON object that is the CWL description of the app revision. 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. [block:code] { "codes": [ { "code": "https://cavatica-api.sbgenomics.com/v2/apps/{app_id}/raw", "language": "text", "name": "API path" } ] } [/block] [block:callout] { "type": "success", "body": "Recall from the [API Overview](doc:the-api#section-identifying-projects-users-apps-files-tasks-and-inputs) that the `app_id` has the form `{project_owner}\\{project}\\{app_short_name}\\{revision_number}`\n\nYou can get the `app_id` for an app by making the call to [list all apps available to you](doc:list-all-apps-available-to-you)", "title": "app_ids" } [/block] ##Request ###Example request [block:code] { "codes": [ { "code": "GET /v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0/raw HTTP/1.1\nHost: cavatica-api.sbgenomics.com\nX-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74\n", "language": "http", "name": null }, { "code": "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\"", "language": "curl", "name": "cURL" } ], "sidebar": true } [/block] ###Header Fields [block:parameters] { "data": { "h-0": "Name", "h-1": "Description", "0-0": "`X-SBG-Auth-Token`\n_required_", "0-1": "Your Cavatica [authentication token](doc:get-your-authentication-token).", "h-2": "" }, "cols": 2, "rows": 1 } [/block] ###Path parameters [block:parameters] { "data": { "0-0": "`app_id`", "h-0": "Name", "h-1": "Description", "0-1": "The ID for the app you are querying. It can be obtained by making the call to [list all apps available to you](doc:list-all-apps-available-to-you)", "1-0": "`revision number`", "1-1": "The integer that is the revision number of the app" }, "cols": 2, "rows": 2 } [/block] ###Query parameters [block:parameters] { "data": { "h-0": "Name", "h-1": "Data type", "h-2": "Description", "0-0": "`fields`", "0-1": "string", "0-2": "Selector specifying a subset of fields to include in the response." }, "cols": 3, "rows": 1 } [/block] ##Response [See a list of Cavatica-specific response codes that may be contained in the body of the response.](doc:api-status-codes) ###Example response body Note that this call returns the full CWL description of the app. [block:code] { "codes": [ { "code": "{\n \"successCodes\": [],\n \"sbg:homepage\": \"https://github.com/pezmaster31/bamtools/wiki\",\n \"sbg:validationErrors\": [],\n \"sbg:sbgMaintained\": false,\n \"temporaryFailCodes\": [],\n \"requirements\": [],\n \"sbg:latestRevision\": 0,\n \"description\": \"BamTools Merge merges multiple BAM files into a single file.\",\n \"sbg:job\": {\n \"inputs\": {\n \"region\": \"chr1\",\n \"input_bam_files\": [\n {\n \"path\": \"1.bam\"\n },\n {\n \"path\": \"2.bam\"\n }\n ]\n },\n \"allocatedResources\": {\n \"cpu\": 1,\n \"mem\": 1000\n }\n },\n \"sbg:toolAuthor\": \"Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg\",\n \"hints\": [\n {\n \"dockerImageId\": \"f808163d4cd3\",\n \"class\": \"DockerRequirement\",\n \"dockerPull\": \"images.sbgenomics.com/markop/bamtools:2.4.0\"\n },\n {\n \"value\": 1,\n \"class\": \"sbg:CPURequirement\"\n },\n {\n \"value\": 1000,\n \"class\": \"sbg:MemRequirement\"\n }\n ],\n \"sbg:copyOf\": \"djordje_klisic/public-apps-by-seven-bridges/bamtools-merge-2-4-0/0\",\n \"sbg:createdOn\": 1452181866,\n \"arguments\": [\n {\n \"position\": 1,\n \"prefix\": \"-out\",\n \"separate\": true,\n \"valueFrom\": \"merged.bam\"\n }\n ],\n \"outputs\": [\n {\n \"sbg:fileTypes\": \"BAM\",\n \"id\": \"#output_bam_file\",\n \"outputBinding\": {\n \"glob\": \"merged.bam\",\n \"sbg:metadata\": {},\n \"sbg:inheritMetadataFrom\": \"#input_bams\"\n },\n \"description\": \"Output BAM file.\",\n \"type\": [\n \"File\"\n ],\n \"label\": \"Output BAM file\"\n }\n ],\n \"sbg:categories\": [\n \"SAM/BAM-Processing\"\n ],\n \"sbg:contributors\": [\n \"RFranklin\"\n ],\n \"sbg:links\": [\n {\n \"id\": \"https://github.com/pezmaster31/bamtools\",\n \"label\": \"Homepage\"\n },\n {\n \"id\": \"https://github.com/pezmaster31/bamtools/wiki\",\n \"label\": \"Wiki\"\n }\n ],\n \"stdout\": \"\",\n \"stdin\": \"\",\n \"sbg:project\": \"RFranklin/my-project\",\n \"inputs\": [\n {\n \"sbg:fileTypes\": \"BAM\",\n \"id\": \"#input_bam_files\",\n \"inputBinding\": {\n \"sbg:cmdInclude\": true,\n \"prefix\": \"-in\",\n \"separate\": true,\n \"itemSeparator\": null,\n \"position\": 0\n },\n \"description\": \"The input BAM files.\",\n \"label\": \"Input BAM files\",\n \"type\": [\n {\n \"type\": \"array\",\n \"items\": \"File\"\n }\n ],\n \"sbg:category\": \"Input & Output\"\n },\n {\n \"id\": \"#region\",\n \"inputBinding\": {\n \"sbg:cmdInclude\": true,\n \"position\": 2,\n \"separate\": true,\n \"prefix\": \"-region\"\n },\n \"description\": \"A region of interest (e.g. \\\"chr1:500..chr3:1500\\\"). See the documentation for more info.\",\n \"label\": \"Region of interest\",\n \"type\": [\n \"null\",\n \"string\"\n ],\n \"sbg:category\": \"Input & Output\"\n }\n ],\n \"label\": \"BamTools Merge\",\n \"sbg:createdBy\": \"RFranklin\",\n \"baseCommand\": [\n \"/opt/bamtools/bin/bamtools\",\n \"merge\"\n ],\n \"sbg:toolkitVersion\": \"2.4.0\",\n \"sbg:id\": \"RFranklin/my-project/bamtools-merge-2-4-0/0\",\n \"sbg:license\": \"The MIT License\",\n \"sbg:revision\": 0,\n \"sbg:cmdPreview\": \"/opt/bamtools/bin/bamtools merge -in 1.bam -in 2.bam -out merged.bam -region chr1\",\n \"sbg:modifiedOn\": 1452181866,\n \"id\": \"https://cavatica-api.sbgenomics.com/RFranklin/my-project/bamtools-merge-2-4-0/0/raw/\",\n \"class\": \"CommandLineTool\",\n \"sbg:modifiedBy\": \"RFranklin\",\n \"sbg:revisionsInfo\": [\n {\n \"sbg:modifiedBy\": \"RFranklin\",\n \"sbg:modifiedOn\": 1452181866,\n \"sbg:revision\": 0\n }\n ],\n \"sbg:toolkit\": \"BamTools\"\n}", "language": "json" } ], "sidebar": true } [/block] <div align="right"><a href="#top">top</a></div> <hr>