{"metadata":{"image":[],"title":"","description":""},"api":{"url":"","auth":"required","results":{"codes":[]},"settings":"","examples":{"codes":[]},"method":"get","params":[]},"next":{"description":"","pages":[]},"title":"Get details of an app revision","type":"endpoint","slug":"get-a-specific-revision-of-an-app","excerpt":"/apps/{app_id}/{revision_number}","body":"This call allows you to obtain a particular revision of a tool, which needn't be the most recent version.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"https://cgc-api.sbgenomics.com/v2/apps/{app_id}/{revision_number}\",\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 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 denoting the revision 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\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n\\t\\\"href\\\": \\\"https://api.sbgenomics.com/v2/apps/admin/sbg-public-data/RSEM BAM2WIG/4\\\",\\n\\t\\\"id\\\": \\\"admin/sbg-public-data/rsem-bam2wig-1-2-31/4\\\",\\n\\t\\\"project\\\": \\\"admin/sbg-public-data\\\",\\n\\t\\\"name\\\": \\\"RSEM BAM2WIG\\\",\\n\\t\\\"revision\\\": 4,\\n\\t\\\"raw\\\": {\\n\\t\\t\\\"id\\\": \\\"https://api.sbgenomics.com/v2/apps/admin/sbg-public-data/rsem-bam2wig-1-2-31/4/raw/\\\",\\n\\t\\t\\\"sbg:modifiedOn\\\": 1476979693,\\n\\t\\t\\\"inputs\\\": [\\n\\t\\t\\t{\\n\\t\\t\\t\\t\\\"description\\\": \\\"Can be either in SAM/BAM/CRAM format. Must be sorted.\\\",\\n\\t\\t\\t\\t\\\"label\\\": \\\"Sorted alignment file\\\",\\n\\t\\t\\t\\t\\\"type\\\": [\\n\\t\\t\\t\\t\\t\\\"File\\\"\\n\\t\\t\\t\\t],\\n\\t\\t\\t\\t\\\"sbg:fileTypes\\\": \\\"BAM, SAM, CRAM\\\",\\n\\t\\t\\t\\t\\\"inputBinding\\\":\\n\\t\\t\\t\\t\\t{ \\\"position\\\": 0, \\\"separate\\\": true, \\\"sbg:cmdInclude\\\": true },\\n\\t\\t\\t\\t\\\"sbg:stageInput\\\": \\\"copy\\\",\\n\\t\\t\\t\\t\\\"id\\\": \\\"#sorted_alignment_file\\\"\\n\\t\\t\\t},\\n\\t\\t\\t{\\n\\t\\t\\t\\t\\\"description\\\": \\\"If this is set, RSEM will not look for “ZW” tag and each alignment appeared in the BAM file has weight 1. Set this if your BAM file is not generated by RSEM.\\\",\\n\\t\\t\\t\\t\\\"label\\\": \\\"No fractional weight\\\",\\n\\t\\t\\t\\t\\\"sbg:category\\\": \\\"Options\\\",\\n\\t\\t\\t\\t\\\"type\\\": [\\n\\t\\t\\t\\t\\t\\\"null\\\",\\n\\t\\t\\t\\t\\t\\\"boolean\\\"\\n\\t\\t\\t\\t],\\n\\t\\t\\t\\t\\\"id\\\": \\\"#no_fractional_weight\\\",\\n\\t\\t\\t\\t\\\"inputBinding\\\":\\n\\t\\t\\t\\t\\t{ \\\"prefix\\\": \\\"--no-fractional-weight\\\", \\\"position\\\": 3, \\\"separate\\\": true, \\\"sbg:cmdInclude\\\": true },\\n\\t\\t\\t\\t\\\"sbg:toolDefaultValue\\\": \\\"off\\\"\\n\\t\\t\\t}\\n\\t\\t],\\n\\t\\t\\\"sbg:cmdPreview\\\": \\\"rsem-bam2wig /path/to/aligned_file.bam aligned_file.wiggle_plot.wig aligned_file.wiggle_plot\\\",\\n\\t\\t\\\"sbg:latestRevision\\\": 4,\\n\\t\\t\\\"sbg:revisionsInfo\\\": [\\n{ \\\"sbg:revisionNotes\\\": null, \\\"sbg:revision\\\": 0, \\\"sbg:modifiedOn\\\": 1476979693, \\\"sbg:modifiedBy\\\": \\\"admin\\\" }\\n,\\n{ \\\"sbg:revisionNotes\\\": null, \\\"sbg:revision\\\": 1, \\\"sbg:modifiedOn\\\": 1476979693, \\\"sbg:modifiedBy\\\": \\\"admin\\\" }\\n,\\n{ \\\"sbg:revisionNotes\\\": null, \\\"sbg:revision\\\": 2, \\\"sbg:modifiedOn\\\": 1476979693, \\\"sbg:modifiedBy\\\": \\\"admin\\\" }\\n,\\n{ \\\"sbg:revisionNotes\\\": \\\"Updated description.\\\", \\\"sbg:revision\\\": 3, \\\"sbg:modifiedOn\\\": 1476979693, \\\"sbg:modifiedBy\\\": \\\"admin\\\" }\\n,\\n{ \\\"sbg:revisionNotes\\\": null, \\\"sbg:revision\\\": 4, \\\"sbg:modifiedOn\\\": 1476979693, \\\"sbg:modifiedBy\\\": \\\"admin\\\" }\\n],\\n\\\"hints\\\": [\\n{ \\\"value\\\": 1, \\\"class\\\": \\\"sbg:CPURequirement\\\" }\\n,\\n{ \\\"value\\\": 1000, \\\"class\\\": \\\"sbg:MemRequirement\\\" }\\n,\\n{ \\\"dockerImageId\\\": \\\"67d3a6c01e92210f43c8ef809c2a245a75bf7d5a52762823cdc3b2e784de576c\\\", \\\"class\\\": \\\"DockerRequirement\\\", \\\"dockerPull\\\": \\\"images.sbgenomics.com/uros_sipetic/rsem:1.2.31\\\" }\\n],\\n\\\"stdin\\\": \\\"\\\",\\n\\\"sbg:links\\\": [\\n{ \\\"label\\\": \\\"RSEM Homepage\\\", \\\"id\\\": \\\"http://deweylab.github.io/RSEM/\\\" }\\n,\\n{ \\\"label\\\": \\\"RSEM Source Code\\\", \\\"id\\\": \\\"https://github.com/deweylab/RSEM\\\" }\\n,\\n{ \\\"label\\\": \\\"RSEM Download\\\", \\\"id\\\": \\\"https://github.com/deweylab/RSEM/archive/v1.2.31.tar.gz\\\" }\\n,\\n{ \\\"label\\\": \\\"RSEM Publications\\\", \\\"id\\\": \\\"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323\\\" }\\n,\\n{ \\\"label\\\": \\\"RSEM Documentation\\\", \\\"id\\\": \\\"http://deweylab.github.io/RSEM/README.html\\\" }\\n],\\n\\\"stdout\\\": \\\"\\\",\\n\\\"description\\\": \\\"RSEM BAM2WIG generates a wiggle plot representing the expected number of reads overlapping each position in the genome/transcript from the sorted genome/transcript BAM file output.\\\\n\\\\n###Common issues###\\\\nNone\\\",\\n\\\"sbg:validationErrors\\\": [],\\n\\\"sbg:image_url\\\": null,\\n\\\"sbg:toolkitVersion\\\": \\\"1.2.31\\\",\\n\\\"sbg:toolkit\\\": \\\"RSEM\\\",\\n\\\"requirements\\\": [\\n{\\n\\\"id\\\": \\\"#cwl-js-engine\\\",\\n\\\"class\\\": \\\"ExpressionEngineRequirement\\\",\\n\\\"requirements\\\": [\\n{ \\\"class\\\": \\\"DockerRequirement\\\", \\\"dockerPull\\\": \\\"rabix/js-engine\\\" }\\n]\\n}\\n],\\n\\\"sbg:id\\\": \\\"admin/sbg-public-data/rsem-bam2wig-1-2-31/4\\\",\\n\\\"sbg:categories\\\": [\\n\\\"Converters\\\",\\n\\\"Plotting-and-Rendering\\\",\\n\\\"RNA\\\"\\n],\\n\\\"sbg:toolAuthor\\\": \\\"Bo Li, Colin Dewey\\\",\\n\\\"temporaryFailCodes\\\": [],\\n\\\"label\\\": \\\"RSEM BAM2WIG\\\",\\n\\\"sbg:createdBy\\\": \\\"admin\\\",\\n\\\"class\\\": \\\"CommandLineTool\\\",\\n\\\"sbg:project\\\": \\\"admin/sbg-public-data\\\",\\n\\\"sbg:sbgMaintained\\\": false,\\n\\\"sbg:revision\\\": 4,\\n\\\"baseCommand\\\": [\\n\\\"rsem-bam2wig\\\"\\n],\\n\\\"sbg:contributors\\\": [\\n\\\"admin\\\"\\n],\\n\\\"sbg:createdOn\\\": 1476979693,\\n\\\"successCodes\\\": [],\\n\\\"sbg:modifiedBy\\\": \\\"admin\\\",\\n\\\"sbg:license\\\": \\\"GNU General Public License v3.0 only\\\",\\n\\\"arguments\\\": [\\n{\\n\\\"position\\\": 1,\\n\\\"valueFrom\\\": {\\n\\\"engine\\\": \\\"#cwl-js-engine\\\",\\n\\\"script\\\": \\\"{\\\\n var str = $job.inputs.sorted_alignment_file.path.split('/').pop().split('.')\\\\n x = \\\\\\\"\\\\\\\"\\\\n for (i=0; i<str.length-1; i++) {\\\\n if (i<str.length-2)\\n{\\\\n x = x + str[i] + '.'\\\\n } else {\\\\n x = x + str[i]\\\\n }\\\\n }\\\\n return x + \\\\\\\".wiggle_plot.wig\\\\\\\"\\\\n}\\\",\\n\\\"class\\\": \\\"Expression\\\"\\n},\\n\\\"separate\\\": true\\n},\\n{\\n\\\"position\\\": 2,\\n\\\"valueFrom\\\": {\\n\\\"engine\\\": \\\"#cwl-js-engine\\\",\\n\\\"script\\\": \\\"{\\\\n var str = $job.inputs.sorted_alignment_file.path.split('/').pop().split('.')\\\\n x = \\\\\\\"\\\\\\\"\\\\n for (i=0; i<str.length-1; i++) {\\\\n if (i<str.length-2) {n x = x + str[i] + '.'n }\\nelse\\n{\\\\n x = x + str[i]\\\\n }\\n\\\\n }\\\\n return x + \\\\\\\".wiggle_plot\\\\\\\"\\\\n}\\\",\\n\\\"class\\\": \\\"Expression\\\"\\n},\\n\\\"separate\\\": true\\n}\\n],\\n\\\"outputs\\\": [\\n{\\n\\\"description\\\": \\\"Output wiggle file.\\\",\\n\\\"label\\\": \\\"Output wiggle file\\\",\\n\\\"type\\\": [\\n\\\"null\\\",\\n\\\"File\\\"\\n],\\n\\\"sbg:fileTypes\\\": \\\"WIG\\\",\\n\\\"outputBinding\\\":\\n{ \\\"glob\\\": \\\"*.wig\\\", \\\"sbg:inheritMetadataFrom\\\": \\\"#sorted_alignment_file\\\" }\\n,\\n\\\"id\\\": \\\"#rsem_bam_to_wiggle_plot_file\\\"\\n}\\n],\\n\\\"sbg:job\\\": {\\n\\\"allocatedResources\\\":\\n{ \\\"mem\\\": 1000, \\\"cpu\\\": 1 }\\n,\\n\\\"inputs\\\": {\\n\\\"no_fractional_weight\\\": false,\\n\\\"sorted_alignment_file\\\":\\n{ \\\"size\\\": 0, \\\"path\\\": \\\"/path/to/aligned_file.bam\\\", \\\"secondaryFiles\\\": [], \\\"class\\\": \\\"File\\\" }\\n}\\n}\\n}\\n}\",\n      \"language\": \"json\"\n    }\n  ],\n  \"sidebar\": true\n}\n[/block]","updates":["56a6177fb28bc217005039bf"],"order":65,"isReference":true,"hidden":false,"sync_unique":"","link_url":"","link_external":false,"_id":"56328edb38f8aa0d00d30f95","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"],"_id":"55faf11ba62ba1170021a9aa","releaseDate":"2015-09-17T16:58:03.490Z","createdAt":"2015-09-17T16:58:03.490Z","project":"55faf11ba62ba1170021a9a7","__v":46},"__v":13,"project":"55faf11ba62ba1170021a9a7","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":32,"from_sync":false,"reference":true,"_id":"55faf9aa17b9d00d00969f49","project":"55faf11ba62ba1170021a9a7","createdAt":"2015-09-17T17:34:34.937Z","version":"55faf11ba62ba1170021a9aa","__v":92},"createdAt":"2015-10-29T21:25:47.935Z","githubsync":"","parentDoc":null,"user":"554340dfb7f4540d00fcef1d"}

GET STARTED

TUTORIALS

ACCESS THE CGC

MANAGE AN ANALYSIS ENVIRONMENT

COLLABORATE SECURELY

DATASETS HUB

PUBLIC PROJECTS

BRING DATA TO THE CGC

SET METADATA ASSOCIATED WITH A PRIVATE FILE

SEARCH FILES

ADD FILES TO A PROJECT

ORGANIZE FILES

ARCHIVE FILES

FIND APPS

BRING YOUR TOOLS

DOCKER

DESCRIBE YOUR TOOL (LEGACY)

TOOL WRAPPING TIPS AND TRICKS

EDIT AN APP (LEGACY)

ARCHIVE APPS

RUN AN ANALYSIS

TASK EXECUTION

REVIEW A TASK

VIEW ANALYSIS RESULTS

INTERACTIVE ANALYSIS

DOWNLOAD RESULTS

DEVELOPER TOOLS

CONNECT CLOUD STORAGE

API Hub

API CLIENTS

SB Command Line Interface

API Reference

EDIT AN APP

BULK API ACTIONS

ASYNC BULK ACTIONS

DRS API

WATCH AND LEARN

DATA CRUNCHER

SBFS (Beta)

SBFS Command Reference

getGet details of an app revision

/apps/{app_id}/{revision_number}
This call allows you to obtain a particular revision of a tool, which needn't be the most recent version. [block:code] { "codes": [ { "code": "https://cgc-api.sbgenomics.com/v2/apps/{app_id}/{revision_number}", "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\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 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/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 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)", "1-0": "`revision_number`", "1-1": "The integer denoting the revision 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 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\t\"href\": \"https://api.sbgenomics.com/v2/apps/admin/sbg-public-data/RSEM BAM2WIG/4\",\n\t\"id\": \"admin/sbg-public-data/rsem-bam2wig-1-2-31/4\",\n\t\"project\": \"admin/sbg-public-data\",\n\t\"name\": \"RSEM BAM2WIG\",\n\t\"revision\": 4,\n\t\"raw\": {\n\t\t\"id\": \"https://api.sbgenomics.com/v2/apps/admin/sbg-public-data/rsem-bam2wig-1-2-31/4/raw/\",\n\t\t\"sbg:modifiedOn\": 1476979693,\n\t\t\"inputs\": [\n\t\t\t{\n\t\t\t\t\"description\": \"Can be either in SAM/BAM/CRAM format. Must be sorted.\",\n\t\t\t\t\"label\": \"Sorted alignment file\",\n\t\t\t\t\"type\": [\n\t\t\t\t\t\"File\"\n\t\t\t\t],\n\t\t\t\t\"sbg:fileTypes\": \"BAM, SAM, CRAM\",\n\t\t\t\t\"inputBinding\":\n\t\t\t\t\t{ \"position\": 0, \"separate\": true, \"sbg:cmdInclude\": true },\n\t\t\t\t\"sbg:stageInput\": \"copy\",\n\t\t\t\t\"id\": \"#sorted_alignment_file\"\n\t\t\t},\n\t\t\t{\n\t\t\t\t\"description\": \"If this is set, RSEM will not look for “ZW” tag and each alignment appeared in the BAM file has weight 1. Set this if your BAM file is not generated by RSEM.\",\n\t\t\t\t\"label\": \"No fractional weight\",\n\t\t\t\t\"sbg:category\": \"Options\",\n\t\t\t\t\"type\": [\n\t\t\t\t\t\"null\",\n\t\t\t\t\t\"boolean\"\n\t\t\t\t],\n\t\t\t\t\"id\": \"#no_fractional_weight\",\n\t\t\t\t\"inputBinding\":\n\t\t\t\t\t{ \"prefix\": \"--no-fractional-weight\", \"position\": 3, \"separate\": true, \"sbg:cmdInclude\": true },\n\t\t\t\t\"sbg:toolDefaultValue\": \"off\"\n\t\t\t}\n\t\t],\n\t\t\"sbg:cmdPreview\": \"rsem-bam2wig /path/to/aligned_file.bam aligned_file.wiggle_plot.wig aligned_file.wiggle_plot\",\n\t\t\"sbg:latestRevision\": 4,\n\t\t\"sbg:revisionsInfo\": [\n{ \"sbg:revisionNotes\": null, \"sbg:revision\": 0, \"sbg:modifiedOn\": 1476979693, \"sbg:modifiedBy\": \"admin\" }\n,\n{ \"sbg:revisionNotes\": null, \"sbg:revision\": 1, \"sbg:modifiedOn\": 1476979693, \"sbg:modifiedBy\": \"admin\" }\n,\n{ \"sbg:revisionNotes\": null, \"sbg:revision\": 2, \"sbg:modifiedOn\": 1476979693, \"sbg:modifiedBy\": \"admin\" }\n,\n{ \"sbg:revisionNotes\": \"Updated description.\", \"sbg:revision\": 3, \"sbg:modifiedOn\": 1476979693, \"sbg:modifiedBy\": \"admin\" }\n,\n{ \"sbg:revisionNotes\": null, \"sbg:revision\": 4, \"sbg:modifiedOn\": 1476979693, \"sbg:modifiedBy\": \"admin\" }\n],\n\"hints\": [\n{ \"value\": 1, \"class\": \"sbg:CPURequirement\" }\n,\n{ \"value\": 1000, \"class\": \"sbg:MemRequirement\" }\n,\n{ \"dockerImageId\": \"67d3a6c01e92210f43c8ef809c2a245a75bf7d5a52762823cdc3b2e784de576c\", \"class\": \"DockerRequirement\", \"dockerPull\": \"images.sbgenomics.com/uros_sipetic/rsem:1.2.31\" }\n],\n\"stdin\": \"\",\n\"sbg:links\": [\n{ \"label\": \"RSEM Homepage\", \"id\": \"http://deweylab.github.io/RSEM/\" }\n,\n{ \"label\": \"RSEM Source Code\", \"id\": \"https://github.com/deweylab/RSEM\" }\n,\n{ \"label\": \"RSEM Download\", \"id\": \"https://github.com/deweylab/RSEM/archive/v1.2.31.tar.gz\" }\n,\n{ \"label\": \"RSEM Publications\", \"id\": \"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323\" }\n,\n{ \"label\": \"RSEM Documentation\", \"id\": \"http://deweylab.github.io/RSEM/README.html\" }\n],\n\"stdout\": \"\",\n\"description\": \"RSEM BAM2WIG generates a wiggle plot representing the expected number of reads overlapping each position in the genome/transcript from the sorted genome/transcript BAM file output.\\n\\n###Common issues###\\nNone\",\n\"sbg:validationErrors\": [],\n\"sbg:image_url\": null,\n\"sbg:toolkitVersion\": \"1.2.31\",\n\"sbg:toolkit\": \"RSEM\",\n\"requirements\": [\n{\n\"id\": \"#cwl-js-engine\",\n\"class\": \"ExpressionEngineRequirement\",\n\"requirements\": [\n{ \"class\": \"DockerRequirement\", \"dockerPull\": \"rabix/js-engine\" }\n]\n}\n],\n\"sbg:id\": \"admin/sbg-public-data/rsem-bam2wig-1-2-31/4\",\n\"sbg:categories\": [\n\"Converters\",\n\"Plotting-and-Rendering\",\n\"RNA\"\n],\n\"sbg:toolAuthor\": \"Bo Li, Colin Dewey\",\n\"temporaryFailCodes\": [],\n\"label\": \"RSEM BAM2WIG\",\n\"sbg:createdBy\": \"admin\",\n\"class\": \"CommandLineTool\",\n\"sbg:project\": \"admin/sbg-public-data\",\n\"sbg:sbgMaintained\": false,\n\"sbg:revision\": 4,\n\"baseCommand\": [\n\"rsem-bam2wig\"\n],\n\"sbg:contributors\": [\n\"admin\"\n],\n\"sbg:createdOn\": 1476979693,\n\"successCodes\": [],\n\"sbg:modifiedBy\": \"admin\",\n\"sbg:license\": \"GNU General Public License v3.0 only\",\n\"arguments\": [\n{\n\"position\": 1,\n\"valueFrom\": {\n\"engine\": \"#cwl-js-engine\",\n\"script\": \"{\\n var str = $job.inputs.sorted_alignment_file.path.split('/').pop().split('.')\\n x = \\\"\\\"\\n for (i=0; i<str.length-1; i++) {\\n if (i<str.length-2)\n{\\n x = x + str[i] + '.'\\n } else {\\n x = x + str[i]\\n }\\n }\\n return x + \\\".wiggle_plot.wig\\\"\\n}\",\n\"class\": \"Expression\"\n},\n\"separate\": true\n},\n{\n\"position\": 2,\n\"valueFrom\": {\n\"engine\": \"#cwl-js-engine\",\n\"script\": \"{\\n var str = $job.inputs.sorted_alignment_file.path.split('/').pop().split('.')\\n x = \\\"\\\"\\n for (i=0; i<str.length-1; i++) {\\n if (i<str.length-2) {n x = x + str[i] + '.'n }\nelse\n{\\n x = x + str[i]\\n }\n\\n }\\n return x + \\\".wiggle_plot\\\"\\n}\",\n\"class\": \"Expression\"\n},\n\"separate\": true\n}\n],\n\"outputs\": [\n{\n\"description\": \"Output wiggle file.\",\n\"label\": \"Output wiggle file\",\n\"type\": [\n\"null\",\n\"File\"\n],\n\"sbg:fileTypes\": \"WIG\",\n\"outputBinding\":\n{ \"glob\": \"*.wig\", \"sbg:inheritMetadataFrom\": \"#sorted_alignment_file\" }\n,\n\"id\": \"#rsem_bam_to_wiggle_plot_file\"\n}\n],\n\"sbg:job\": {\n\"allocatedResources\":\n{ \"mem\": 1000, \"cpu\": 1 }\n,\n\"inputs\": {\n\"no_fractional_weight\": false,\n\"sorted_alignment_file\":\n{ \"size\": 0, \"path\": \"/path/to/aligned_file.bam\", \"secondaryFiles\": [], \"class\": \"File\" }\n}\n}\n}\n}", "language": "json" } ], "sidebar": true } [/block]