{"metadata":{"image":[],"title":"","description":""},"api":{"url":"","auth":"required","settings":"","examples":{"codes":[]},"method":"get","params":[],"results":{"codes":[]}},"next":{"description":"","pages":[]},"title":"Get raw CWL for an app","type":"endpoint","slug":"get-raw-cwl-for-an-app","excerpt":"/apps/{app_id}/raw\n\nFor general information on the API, including formatting, parameters, and pagination, please see the [API Overview](the-api).","body":"This call returns information about the specified app, as raw CWL. The call differs from the call to [ `GET` details of an app](doc:get-details-of-an-app) by returning a JSON object that is the CWL. \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\\nNote that if you omit `revision_number`, the API will return the latest app revision.\\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/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/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 },\n \"cols\": 2,\n \"rows\": 1\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>","updates":[],"order":65,"isReference":false,"hidden":false,"sync_unique":"","link_url":"","link_external":false,"_id":"5774f41750a4121900e4a2b6","user":"575e85ac41c8ba0e00259a44","githubsync":"","parentDoc":null,"project":"5773dcfc255e820e00e1cd4d","__v":4,"createdAt":"2016-06-30T10:27:35.814Z","version":{"version":"1.0","version_clean":"1.0.0","codename":"","is_stable":true,"is_beta":false,"is_hidden":false,"is_deprecated":false,"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","5dc15666a4f788004c5fd7d7","5eaff69e844d67003642a020","5eb00899b36ba5002d35b0c1","5eb0172be179b70073dc936e","5eb01b42b36ba5002d35ebba","5eb01f202654a20136813093","5eb918ef149186021c9a76c8","5f0839d3f4b24e005ebbbc29","5f893e508c9862002d0614a9","6024033e2b2f6f004dfe994c"],"_id":"5773dcfc255e820e00e1cd50","__v":36,"createdAt":"2016-06-29T14:36:44.812Z","releaseDate":"2016-06-29T14:36:44.812Z","project":"5773dcfc255e820e00e1cd4d"},"category":{"sync":{"isSync":false,"url":""},"pages":[],"title":"Cavatica API","slug":"api","order":19,"from_sync":false,"reference":false,"_id":"5773df36904b0c0e00ef05ff","createdAt":"2016-06-29T14:46:14.277Z","version":"5773dcfc255e820e00e1cd50","__v":0,"project":"5773dcfc255e820e00e1cd4d"}}
getGet raw CWL for an app
/apps/{app_id}/raw
For general information on the API, including formatting, parameters, and pagination, please see the [API Overview](the-api).