{"metadata":{"image":[],"title":"","description":""},"api":{"url":"","auth":"required","params":[],"results":{"codes":[]},"settings":"","examples":{"codes":[]},"method":"get"},"next":{"description":"","pages":[]},"title":"Get raw CWL for an app revision","type":"endpoint","slug":"get-raw-cwl-for-an-app-revision","excerpt":"/apps/{app_id}/{revision_number}/raw","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-a-specific-revision-of-an-app) 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 the CGC 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://cgc-api.sbgenomics.com/v2/apps/{app_id}/raw\",\n      \"language\": \"text\",\n      \"name\": \"Path\"\n    }\n  ]\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"success\",\n  \"body\": \"Recall from the [API Overview](http://docs.cancergenomicscloud.org/v1.0/docs/the-cgc-api#section-identifying-projects-users-apps-files-and-tasks) 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: cgc-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://cgc-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 CGC [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 CGC-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://cgc-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]","updates":[],"order":67,"isReference":true,"hidden":false,"sync_unique":"","link_url":"","link_external":false,"_id":"5694f301c5c5ce0d00058e68","parentDoc":null,"__v":0,"createdAt":"2016-01-12T12:35:13.213Z","githubsync":"","version":{"version":"1.0","version_clean":"1.0.0","codename":"","is_stable":true,"is_beta":true,"is_hidden":false,"is_deprecated":false,"categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77","59a555bccdbd85001bfb1442","5a2a81f688574d001e9934f5","5b080c8d7833b20003ddbb6f","5c222bed4bc358002f21459a","5c22412594a2a5005cc9e919","5c41ae1c33592700190a291e","5c8a525e2ba7b2003f9b153c","5cbf14d58c79c700ef2b502e","5db6f03a6e187c006f667fa4","5f894c7d3b0894006477ca01","6176d5bf8f59c6001038c2f7"],"_id":"55faf11ba62ba1170021a9aa","releaseDate":"2015-09-17T16:58:03.490Z","createdAt":"2015-09-17T16:58:03.490Z","project":"55faf11ba62ba1170021a9a7","__v":48},"project":"55faf11ba62ba1170021a9a7","user":"554340dfb7f4540d00fcef1d","category":{"sync":{"isSync":false,"url":""},"pages":["56312d239ead230d00a188f2","56312e0d82d96a0d00b0fb08","56315777fc94aa0d00e9b553","56315b779ead230d00a1894a","5631657c9c25801700dac34f","56317884fc94aa0d00e9b586","56318386c3b04b0d00ba9bb9","563240ccdcc27a170082363b","563240dfbddb091700ad5e82","563240edfe9acd1900cc1d10","56324504fa40240d007c8d5f","56324b30c3b04b0d00ba9c96","563273ae45f2cb0d006be3fa","563273c08c9cda0d0025266d","563273cc38f8aa0d00d30f55","563273d838f8aa0d00d30f59","5632740945f2cb0d006be3fc","56327411df556c0d00cd0905","5632741b8c9cda0d0025266f","563274ea10b6040d008793d8","5632757cdf556c0d00cd0908","563275b710b6040d008793da","563275f938f8aa0d00d30f60","5632762fb904a10d0032f6fc","5632767110b6040d008793dd","563276c0b904a10d0032f700","5632770162c48a0d00334d53","5632843d8c9cda0d00252698","5632846e62c48a0d00334d78","56328a7e49e16d0d00122420","56328aaf49e16d0d00122425","56328b2238f8aa0d00d30f88","56328b6c8c9cda0d002526a2","56328c0710b6040d008793ff","56328c3710b6040d00879401","56328c5938f8aa0d00d30f8c","56328c90b904a10d0032f722","56328cc449e16d0d0012242a","56328ce68c9cda0d002526a8","56328d1338f8aa0d00d30f8e","56328d5810b6040d00879407","56328d7cdf556c0d00cd092f","56328d9a10b6040d00879409","56328db438f8aa0d00d30f92","56328dd762c48a0d00334d8b","56328df649e16d0d0012242d","56328e1edf556c0d00cd0931","56328e4662c48a0d00334d8e","56328e5edf556c0d00cd0933","56328e8f8c9cda0d002526ab","56328eb3b904a10d0032f72a","56328edb38f8aa0d00d30f95","56328ef210b6040d0087940d","56328f148c9cda0d002526ad","56328f2962c48a0d00334d90","56328f54b904a10d0032f72c","56328f6c38f8aa0d00d30f98","56328f858c9cda0d002526af","56328fae62c48a0d00334d95","56328fd838f8aa0d00d30f9c","5637f069ee0ee60d0024ec18","5641ffaa9417b40d00c0fc35","564355240d9748190079dea9","5644cfeb2c74cf1900da4831","56450f856b0ca50d00f6bd8f","56706537cbb2fb0d00f7c7dd","567065bc3d29830d00376213","56706fc2cbb2fb0d00f7c87e","568bf5a1e662f40d00eee866","568c0699e662f40d00eee881","568cff0274c77f2d00d56d51","568d10f58602880d001ce277","568d2abc37b636250036b904","568d343413c5ad0d00b34efb","568d593a8602880d001ce2d3","568e64135e12fb0d00325160","568e66f05e12fb0d00325162","568e78aa5e12fb0d0032517a","569433cfd8c04d1700e5ae0c","56943723d8c04d1700e5ae14","5694393b3e9d080d00f0655d","5694e6cf953b810d008f91bc","5694f301c5c5ce0d00058e68","569502ef9797fa1900f704e7","5695063bcaa32519009c40b3","569511cccaa32519009c40d9","569557e2fcb1032d0089dfe2","569562fefcb1032d0089dfee","56956428fe18811700c9c058","569639b87596a90d0014e5a3","56a90197e590350d004b5103","56a9021e9ec7660d002e08c2"],"title":"API Reference","slug":"api","order":33,"from_sync":false,"reference":true,"_id":"55faf9aa17b9d00d00969f49","project":"55faf11ba62ba1170021a9a7","createdAt":"2015-09-17T17:34:34.937Z","version":"55faf11ba62ba1170021a9aa","__v":92}}