{"__v":10,"_id":"569433cfd8c04d1700e5ae0c","category":{"__v":92,"_id":"55faf9aa17b9d00d00969f49","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"],"project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","sync":{"url":"","isSync":false},"reference":true,"createdAt":"2015-09-17T17:34:34.937Z","from_sync":false,"order":26,"slug":"api","title":"API Reference"},"parentDoc":null,"project":"55faf11ba62ba1170021a9a7","user":"554340dfb7f4540d00fcef1d","version":{"__v":35,"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","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"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":["56a604bcfe3e780d00c5069a","56a605d8d222d20d00500dbf","56a60c7bfe3e780d00c506a3"],"next":{"pages":[],"description":""},"createdAt":"2016-01-11T22:59:27.377Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"examples":{"codes":[]},"method":"get","results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":true,"order":53,"body":"This call returns information about the specified app. The 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}\",\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\\nIf the `revision_number` field is omitted, the latest revision of the app is returned\\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 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\\\"\",\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  },\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 CGC-specific response codes that may be contained in the body of the response.](doc:api-status-codes) \n\n###Example response body\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"href\\\": \\\"https://cgc-api.sbgenomics.com/v2/apps/rfranklin/my-project/cummerbundqc/0\\\",\\n  \\\"id\\\": \\\"rfranklin/my-project/cummerbundqc/0\\\",\\n  \\\"project\\\": \\\"rfranklin/my-project\\\",\\n  \\\"name\\\": \\\"CummeRbundQC\\\",\\n  \\\"revision\\\": 0,\\n  \\\"raw\\\": {\\n    \\\"sbg:toolAuthor\\\": \\\"Cole Trapnell/University of Washington\\\",\\n    \\\"sbg:project\\\": \\\"rfranklin/my-project\\\",\\n    \\\"requirements\\\": [],\\n    \\\"id\\\": \\\"https://cgc-api.sbgenomics.com/rfranklin/my-project/cummerbundqc/0/raw/\\\",\\n    \\\"sbg:toolkit\\\": \\\"CummeRbund\\\",\\n    \\\"sbg:revision\\\": 0,\\n    \\\"sbg:toolkitVersion\\\": \\\"2.8.2\\\",\\n    \\\"stdout\\\": \\\"\\\",\\n    \\\"outputs\\\": [\\n      {\\n        \\\"outputBinding\\\": {\\n          \\\"glob\\\": \\\"*.zip\\\",\\n          \\\"sbg:metadata\\\": {},\\n          \\\"sbg:inheritMetadataFrom\\\": \\\"#cuffdiff_zip\\\"\\n        },\\n        \\\"type\\\": [\\n          \\\"null\\\",\\n          \\\"File\\\"\\n        ],\\n        \\\"sbg:fileTypes\\\": \\\"ZIP\\\",\\n        \\\"description\\\": \\\"Downloadable zipped report.\\\",\\n        \\\"id\\\": \\\"#archive\\\",\\n        \\\"label\\\": \\\"Report archive\\\"\\n      },\\n      {\\n        \\\"outputBinding\\\": {\\n          \\\"glob\\\": \\\"*.b64html\\\",\\n          \\\"sbg:metadata\\\": {},\\n          \\\"sbg:inheritMetadataFrom\\\": \\\"#cuffdiff_zip\\\"\\n        },\\n        \\\"type\\\": [\\n          \\\"null\\\",\\n          \\\"File\\\"\\n        ],\\n        \\\"sbg:fileTypes\\\": \\\"B64HTML\\\",\\n        \\\"description\\\": \\\"Base64 encoded HTML report prepared for easy viewing.\\\",\\n        \\\"id\\\": \\\"#html\\\",\\n        \\\"label\\\": \\\"Report\\\"\\n      }\\n    ],\\n    \\\"inputs\\\": [\\n      {\\n        \\\"sbg:category\\\": \\\"Input files\\\",\\n        \\\"type\\\": [\\n          \\\"File\\\"\\n        ],\\n        \\\"sbg:fileTypes\\\": \\\"ZIP\\\",\\n        \\\"id\\\": \\\"#cuffdiff_zip\\\",\\n        \\\"description\\\": \\\"Zipped list of output tracking, tab delimited and INFO files.\\\",\\n        \\\"inputBinding\\\": {\\n          \\\"prefix\\\": \\\"--cuffzip\\\",\\n          \\\"separate\\\": true,\\n          \\\"sbg:cmdInclude\\\": true\\n        },\\n        \\\"label\\\": \\\"Archive of Cuffdiff output files\\\"\\n      },\\n      {\\n        \\\"sbg:category\\\": \\\"Basic Options\\\",\\n        \\\"type\\\": [\\n          \\\"null\\\",\\n          \\\"float\\\"\\n        ],\\n        \\\"id\\\": \\\"#dispersion_threshold\\\",\\n        \\\"description\\\": \\\"Changing this parameter sets threshold for the genes that are displayed on dispersion plot, namely it removes from the plot all genes that have dispersion lower than this value.\\\",\\n        \\\"sbg:toolDefaultValue\\\": \\\"0.01\\\",\\n        \\\"inputBinding\\\": {\\n          \\\"prefix\\\": \\\"--dispthreshold\\\",\\n          \\\"separate\\\": true,\\n          \\\"sbg:cmdInclude\\\": true\\n        },\\n        \\\"label\\\": \\\"Dispersion plot threshold\\\"\\n      },\\n      {\\n        \\\"sbg:category\\\": \\\"Basic Options\\\",\\n        \\\"type\\\": [\\n          \\\"null\\\",\\n          \\\"float\\\"\\n        ],\\n        \\\"id\\\": \\\"#density_threshold\\\",\\n        \\\"description\\\": \\\"Changing this parameter sets threshold for the genes that are displayed on both density plots. It removes from the plots all genes that have FPKM value lower than this value.\\\",\\n        \\\"sbg:toolDefaultValue\\\": \\\"0.0001\\\",\\n        \\\"inputBinding\\\": {\\n          \\\"prefix\\\": \\\"--densthreshold\\\",\\n          \\\"separate\\\": true,\\n          \\\"sbg:cmdInclude\\\": true\\n        },\\n        \\\"label\\\": \\\"Density plot threshold\\\"\\n      },\\n      {\\n        \\\"sbg:category\\\": \\\"Basic Options\\\",\\n        \\\"type\\\": [\\n          \\\"null\\\",\\n          \\\"boolean\\\"\\n        ],\\n        \\\"id\\\": \\\"#thresholds_off\\\",\\n        \\\"description\\\": \\\"Set this parameter in case you don't want to eliminate lower expressed genes on dispersion and density plots. Be aware that this would cause plots to be stretched in order to show these low values for dispersion and FPKM.\\\",\\n        \\\"sbg:toolDefaultValue\\\": \\\"False\\\",\\n        \\\"inputBinding\\\": {\\n          \\\"prefix\\\": \\\"--thresholdsoff\\\",\\n          \\\"separate\\\": true,\\n          \\\"sbg:cmdInclude\\\": true\\n        },\\n        \\\"label\\\": \\\"Turn off thresholds\\\"\\n      }\\n    ],\\n    \\\"hints\\\": [\\n      {\\n        \\\"class\\\": \\\"DockerRequirement\\\",\\n        \\\"dockerImageId\\\": \\\"0c4541b52eb7\\\",\\n        \\\"dockerPull\\\": \\\"images.sbgenomics.com/ana_d/cummerbund-qc:2.8.2--1.0\\\"\\n      },\\n      {\\n        \\\"class\\\": \\\"sbg:CPURequirement\\\",\\n        \\\"value\\\": 8\\n      },\\n      {\\n        \\\"class\\\": \\\"sbg:MemRequirement\\\",\\n        \\\"value\\\": 6000\\n      }\\n    ],\\n    \\\"sbg:modifiedOn\\\": 1448366962,\\n    \\\"sbg:latestRevision\\\": 0,\\n    \\\"sbg:id\\\": \\\"rfranklin/my-project/cummerbundqc/0\\\",\\n    \\\"sbg:job\\\": {\\n      \\\"inputs\\\": {\\n        \\\"cuffdiff_zip\\\": {\\n          \\\"class\\\": \\\"File\\\",\\n          \\\"size\\\": 0,\\n          \\\"path\\\": \\\"cuffdiff_zip.ext\\\",\\n          \\\"secondaryFiles\\\": []\\n        },\\n        \\\"density_threshold\\\": 0,\\n        \\\"dispersion_threshold\\\": 0,\\n        \\\"thresholds_off\\\": true\\n      },\\n      \\\"allocatedResources\\\": {\\n        \\\"cpu\\\": 8,\\n        \\\"mem\\\": 6000\\n      }\\n    },\\n    \\\"sbg:cmdPreview\\\": \\\"python /opt/cummerbund-qc.py --cuffzip cuffdiff_zip.ext --dispthreshold 0 --densthreshold 0 --thresholdsoff  cuffdiff_zip.ext\\\",\\n    \\\"description\\\": \\\"CummeRbundQC assesses the quality of a differential expression analysis performed with Cuffdiff. It accepts differential expression results in the form of a cuffdiff.zip folder as input and produces a report with charts that can be viewed on Seven Bridges platform or downloaded to your local drive. \\\\n\\\\nCummeRbundQC is built on top of CummeRbund v. 2.8.2. CummeRbundQC incorporates the \\\\\\\"Global Statistics and Quality Control\\\\\\\" graphs described in the CummeRbund manual. These visualizations provide an overview of the relationships among the replicates and help in detecting over-dispersion in samples.\\\",\\n    \\\"sbg:links\\\": [\\n      {\\n        \\\"id\\\": \\\"http://bioconductor.org/packages/release/bioc/html/cummeRbund.html\\\",\\n        \\\"label\\\": \\\"Homepage\\\"\\n      },\\n      {\\n        \\\"id\\\": \\\"http://bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf\\\",\\n        \\\"label\\\": \\\"Manual\\\"\\n      },\\n      {\\n        \\\"id\\\": \\\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/\\\",\\n        \\\"label\\\": \\\"Publication\\\"\\n      }\\n    ],\\n    \\\"temporaryFailCodes\\\": [],\\n    \\\"successCodes\\\": [],\\n    \\\"sbg:contributors\\\": [\\n      \\\"rfranklin\\\"\\n    ],\\n    \\\"label\\\": \\\"CummeRbundQC\\\",\\n    \\\"sbg:sbgMaintained\\\": false,\\n    \\\"baseCommand\\\": [\\n      \\\"python\\\",\\n      \\\"/opt/cummerbund-qc.py\\\"\\n    ],\\n    \\\"sbg:createdBy\\\": \\\"rfranklin\\\",\\n    \\\"class\\\": \\\"CommandLineTool\\\",\\n    \\\"sbg:modifiedBy\\\": \\\"rfranklin\\\",\\n    \\\"sbg:validationErrors\\\": [],\\n    \\\"sbg:revisionsInfo\\\": [\\n      {\\n        \\\"sbg:modifiedBy\\\": \\\"rfranklin\\\",\\n        \\\"sbg:modifiedOn\\\": 1448366962,\\n        \\\"sbg:revision\\\": 0\\n      }\\n    ],\\n    \\\"sbg:categories\\\": [\\n      \\\"Differential-Expression\\\",\\n      \\\"Plotting-and-Rendering\\\"\\n    ],\\n    \\\"arguments\\\": [],\\n    \\\"stdin\\\": \\\"\\\",\\n    \\\"sbg:license\\\": \\\"Artistic License 2.0\\\",\\n    \\\"sbg:createdOn\\\": 1448366962\\n  }\\n}\",\n      \"language\": \"json\"\n    }\n  ],\n  \"sidebar\": true\n}\n[/block]","excerpt":"/apps/{app_id}","slug":"get-details-of-an-app","type":"endpoint","title":"Get details of an app"}

getGet details of an app

/apps/{app_id}

This call returns information about the specified app. The 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. [block:code] { "codes": [ { "code": "https://cgc-api.sbgenomics.com/v2/apps/{app_id}", "language": "text", "name": "Path" } ] } [/block] [block:callout] { "type": "success", "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\nIf the `revision_number` field is omitted, the latest revision of the app is returned\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 HTTP/1.1\nHost: cgc-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://cgc-api.sbgenomics.com/v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0\"", "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 CGC [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)" }, "cols": 2, "rows": 1 } [/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 CGC-specific response codes that may be contained in the body of the response.](doc:api-status-codes) ###Example response body [block:code] { "codes": [ { "code": "{\n \"href\": \"https://cgc-api.sbgenomics.com/v2/apps/rfranklin/my-project/cummerbundqc/0\",\n \"id\": \"rfranklin/my-project/cummerbundqc/0\",\n \"project\": \"rfranklin/my-project\",\n \"name\": \"CummeRbundQC\",\n \"revision\": 0,\n \"raw\": {\n \"sbg:toolAuthor\": \"Cole Trapnell/University of Washington\",\n \"sbg:project\": \"rfranklin/my-project\",\n \"requirements\": [],\n \"id\": \"https://cgc-api.sbgenomics.com/rfranklin/my-project/cummerbundqc/0/raw/\",\n \"sbg:toolkit\": \"CummeRbund\",\n \"sbg:revision\": 0,\n \"sbg:toolkitVersion\": \"2.8.2\",\n \"stdout\": \"\",\n \"outputs\": [\n {\n \"outputBinding\": {\n \"glob\": \"*.zip\",\n \"sbg:metadata\": {},\n \"sbg:inheritMetadataFrom\": \"#cuffdiff_zip\"\n },\n \"type\": [\n \"null\",\n \"File\"\n ],\n \"sbg:fileTypes\": \"ZIP\",\n \"description\": \"Downloadable zipped report.\",\n \"id\": \"#archive\",\n \"label\": \"Report archive\"\n },\n {\n \"outputBinding\": {\n \"glob\": \"*.b64html\",\n \"sbg:metadata\": {},\n \"sbg:inheritMetadataFrom\": \"#cuffdiff_zip\"\n },\n \"type\": [\n \"null\",\n \"File\"\n ],\n \"sbg:fileTypes\": \"B64HTML\",\n \"description\": \"Base64 encoded HTML report prepared for easy viewing.\",\n \"id\": \"#html\",\n \"label\": \"Report\"\n }\n ],\n \"inputs\": [\n {\n \"sbg:category\": \"Input files\",\n \"type\": [\n \"File\"\n ],\n \"sbg:fileTypes\": \"ZIP\",\n \"id\": \"#cuffdiff_zip\",\n \"description\": \"Zipped list of output tracking, tab delimited and INFO files.\",\n \"inputBinding\": {\n \"prefix\": \"--cuffzip\",\n \"separate\": true,\n \"sbg:cmdInclude\": true\n },\n \"label\": \"Archive of Cuffdiff output files\"\n },\n {\n \"sbg:category\": \"Basic Options\",\n \"type\": [\n \"null\",\n \"float\"\n ],\n \"id\": \"#dispersion_threshold\",\n \"description\": \"Changing this parameter sets threshold for the genes that are displayed on dispersion plot, namely it removes from the plot all genes that have dispersion lower than this value.\",\n \"sbg:toolDefaultValue\": \"0.01\",\n \"inputBinding\": {\n \"prefix\": \"--dispthreshold\",\n \"separate\": true,\n \"sbg:cmdInclude\": true\n },\n \"label\": \"Dispersion plot threshold\"\n },\n {\n \"sbg:category\": \"Basic Options\",\n \"type\": [\n \"null\",\n \"float\"\n ],\n \"id\": \"#density_threshold\",\n \"description\": \"Changing this parameter sets threshold for the genes that are displayed on both density plots. It removes from the plots all genes that have FPKM value lower than this value.\",\n \"sbg:toolDefaultValue\": \"0.0001\",\n \"inputBinding\": {\n \"prefix\": \"--densthreshold\",\n \"separate\": true,\n \"sbg:cmdInclude\": true\n },\n \"label\": \"Density plot threshold\"\n },\n {\n \"sbg:category\": \"Basic Options\",\n \"type\": [\n \"null\",\n \"boolean\"\n ],\n \"id\": \"#thresholds_off\",\n \"description\": \"Set this parameter in case you don't want to eliminate lower expressed genes on dispersion and density plots. Be aware that this would cause plots to be stretched in order to show these low values for dispersion and FPKM.\",\n \"sbg:toolDefaultValue\": \"False\",\n \"inputBinding\": {\n \"prefix\": \"--thresholdsoff\",\n \"separate\": true,\n \"sbg:cmdInclude\": true\n },\n \"label\": \"Turn off thresholds\"\n }\n ],\n \"hints\": [\n {\n \"class\": \"DockerRequirement\",\n \"dockerImageId\": \"0c4541b52eb7\",\n \"dockerPull\": \"images.sbgenomics.com/ana_d/cummerbund-qc:2.8.2--1.0\"\n },\n {\n \"class\": \"sbg:CPURequirement\",\n \"value\": 8\n },\n {\n \"class\": \"sbg:MemRequirement\",\n \"value\": 6000\n }\n ],\n \"sbg:modifiedOn\": 1448366962,\n \"sbg:latestRevision\": 0,\n \"sbg:id\": \"rfranklin/my-project/cummerbundqc/0\",\n \"sbg:job\": {\n \"inputs\": {\n \"cuffdiff_zip\": {\n \"class\": \"File\",\n \"size\": 0,\n \"path\": \"cuffdiff_zip.ext\",\n \"secondaryFiles\": []\n },\n \"density_threshold\": 0,\n \"dispersion_threshold\": 0,\n \"thresholds_off\": true\n },\n \"allocatedResources\": {\n \"cpu\": 8,\n \"mem\": 6000\n }\n },\n \"sbg:cmdPreview\": \"python /opt/cummerbund-qc.py --cuffzip cuffdiff_zip.ext --dispthreshold 0 --densthreshold 0 --thresholdsoff cuffdiff_zip.ext\",\n \"description\": \"CummeRbundQC assesses the quality of a differential expression analysis performed with Cuffdiff. It accepts differential expression results in the form of a cuffdiff.zip folder as input and produces a report with charts that can be viewed on Seven Bridges platform or downloaded to your local drive. \\n\\nCummeRbundQC is built on top of CummeRbund v. 2.8.2. CummeRbundQC incorporates the \\\"Global Statistics and Quality Control\\\" graphs described in the CummeRbund manual. These visualizations provide an overview of the relationships among the replicates and help in detecting over-dispersion in samples.\",\n \"sbg:links\": [\n {\n \"id\": \"http://bioconductor.org/packages/release/bioc/html/cummeRbund.html\",\n \"label\": \"Homepage\"\n },\n {\n \"id\": \"http://bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf\",\n \"label\": \"Manual\"\n },\n {\n \"id\": \"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/\",\n \"label\": \"Publication\"\n }\n ],\n \"temporaryFailCodes\": [],\n \"successCodes\": [],\n \"sbg:contributors\": [\n \"rfranklin\"\n ],\n \"label\": \"CummeRbundQC\",\n \"sbg:sbgMaintained\": false,\n \"baseCommand\": [\n \"python\",\n \"/opt/cummerbund-qc.py\"\n ],\n \"sbg:createdBy\": \"rfranklin\",\n \"class\": \"CommandLineTool\",\n \"sbg:modifiedBy\": \"rfranklin\",\n \"sbg:validationErrors\": [],\n \"sbg:revisionsInfo\": [\n {\n \"sbg:modifiedBy\": \"rfranklin\",\n \"sbg:modifiedOn\": 1448366962,\n \"sbg:revision\": 0\n }\n ],\n \"sbg:categories\": [\n \"Differential-Expression\",\n \"Plotting-and-Rendering\"\n ],\n \"arguments\": [],\n \"stdin\": \"\",\n \"sbg:license\": \"Artistic License 2.0\",\n \"sbg:createdOn\": 1448366962\n }\n}", "language": "json" } ], "sidebar": true } [/block]