openapi: 3.2.0 info: title: Seven Bridges Platform Apps API version: unknown servers: - url: https://api.sbgenomics.com/v2 security: - {} tags: - name: Apps paths: /apps: get: summary: List all apps available to you description: This call lists all the apps available to you. operationId: list-all-apps-available-to-you parameters: - name: X-SBG-Auth-Token in: header description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). required: true schema: type: string - name: fields in: query description: Selector specifying a subset of fields to include in the response. schema: type: array items: type: string - name: project in: query description: Enter a project, in the form `{project_owner}/{project_short_name}` to restrict the results to apps from that project only. schema: type: string - name: visibility in: query description: Set this to `public` to see all public apps on the Seven Bridges Platform. schema: type: string - name: q in: query description: Enter one or more search terms to query apps using the `q` parameter. Learn more about querying above. schema: type: string - name: id in: query description: Use this parameter to query apps based on their ID. schema: type: string - name: limit in: query description: The maximum number of collection items to return for a single request. Minimum value is 1. The maximum value is 100 and the default value is 50. This is a pagination-specific attribute. schema: type: integer format: int32 default: 50 - name: offset in: query description: The zero-based starting index in the entire collection of the first item to return. The default value is 0. This is a pagination-specific attribute. schema: type: integer format: int32 default: 0 responses: '200': description: '200' content: application/json: examples: Result: value: "{\n \"href\": \"https://api.sbgenomics.com/v2/apps/\",\n \"items\": [\n {\n \"href\": \"https://api.sbgenomics.com/v2/apps/RFranklin/my-project/workflow-9\",\n \"id\": \"RFranklin/my-project/workflow-9\",\n \"name\": \"workflow\"\n },\n {\n \"href\": \"https://api.sbgenomics.com/v2/apps/RFranklin/my-project/fusion-transcript-detection-chimeras\",\n \"id\": \"RFranklin/my-project/fusion-transcript-detection-chimeras\",\n \"name\": \"fusion-transcript-detection-chimerascan\"\n },\n {\n \"href\": \"https://api.sbgenomics.com/v2/apps/RFranklin/my-project/somatic-filters\",\n \"id\": \"RFranklin/my-project/somatic-filters\",\n \"name\": \"somaticsniper-filters\"\n },\n {\n \"href\": \"https://api.sbgenomics.com/v2/apps/RFranklin/my-project/command-line-tool-3\",\n \"id\": \"RFranklin/my-project/command-line-tool-3\",\n \"name\": \"command-line-tool\"\n },\n {\n \"href\": \"https://api.sbgenomics.com/v2/apps/RFranklin/my-project/delly2-workflow-test\",\n \"id\": \"RFranklin/my-project/delly2-workflow-test\",\n \"name\": \"delly2-workflow\"\n }\n ]\n}" schema: type: object properties: href: type: string example: https://api.sbgenomics.com/v2/apps/ items: type: array items: type: object properties: href: type: string example: https://api.sbgenomics.com/v2/apps/RFranklin/my-project/workflow-9 id: type: string example: RFranklin/my-project/workflow-9 name: type: string example: workflow deprecated: false x-readme: code-samples: - language: python code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='3210a98c1db9318fa9d9273156740f74')\n\n# send GET request to SB API\napps = api.apps.query()\n\nfor app in apps:\n print(app.name, app.id)" samples-languages: - python tags: - Apps /apps/{project_owner}/{project}/{app_short_name}: get: summary: Get details of an app description: 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 Seven Bridges Platform by a project member, or a publicly available app that has been copied to the project. operationId: get-details-of-an-app parameters: - name: project_owner in: path description: If you are using [Enterprise](doc:about-the-enterprise-feature), use the name of the Division that owns the project in which the app is located; otherwise, enter the Platform username of the project owner. schema: type: string required: true - name: project in: path description: The name of the project in which the app is located. schema: type: string required: true - name: app_short_name in: path description: The short name of the app you are querying. Optionally, to get details of a specific revision of the app, use the `{app_short_name}/{revision_number}` format, for example `bamtools-index-2-4-0/1` schema: type: string required: true - name: fields in: query description: Selector specifying a subset of fields to include in the response. schema: type: array items: type: string - name: X-SBG-Auth-Token in: header description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). required: true schema: type: string responses: '200': description: '200' content: application/json: examples: Result: value: "{\n \"href\": \"https://api.sbgenomics.com/v2/apps/rfranklin/my-project/bamtools-index-2/0\",\n \"id\": \"rfranklin/my-project/bamtools-index-2/0\",\n \"project\": \"rfranklin/my-project\",\n \"name\": \"BamTools Index\",\n \"revision\": 0,\n \"raw\": {\n \"sbg:categories\": [\n \"SAM/BAM-Processing\",\n \"Indexing\"\n ],\n \"sbg:image_url\": null,\n \"requirements\": [\n {\n \"class\": \"ExpressionEngineRequirement\",\n \"id\": \"#cwl-js-engine\",\n \"requirements\": [\n {\n \"class\": \"DockerRequirement\",\n \"dockerPull\": \"rabix/js-engine\"\n }\n ]\n }\n ],\n \"baseCommand\": [\n {\n \"class\": \"Expression\",\n \"script\": \"{\\n if ($job.inputs.input_bai_file){\\n \\treturn\\\"echo Skipping index step because BAI file is provided on the input.\\\"\\n }\\n else{\\n return \\\"/opt/bamtools/bin/bamtools index\\\"\\n }\\n}\",\n \"engine\": \"#cwl-js-engine\"\n }\n ],\n \"class\": \"CommandLineTool\",\n \"sbg:cmdPreview\": \"/opt/bamtools/bin/bamtools index -in input_bam.bam\",\n \"sbg:homepage\": \"https://github.com/pezmaster31/bamtools/wiki\",\n \"label\": \"BamTools Index\",\n \"outputs\": [\n {\n \"description\": \"Output BAM file with index (BAI or BTI) file as a secondary file (not visible in the output list of the task).\",\n \"type\": [\n \"null\",\n \"File\"\n ],\n \"id\": \"#output_bam_file\",\n \"label\": \"Output BAM file\",\n \"outputBinding\": {\n \"glob\": {\n \"class\": \"Expression\",\n \"script\": \"{\\n if ($job.inputs.indexed_data === true){\\n\\treturn ''\\n } else {\\n return $job.inputs.input_bam_file.path.split(\\\"/\\\").pop()\\n }\\n}\\n\\n\\n\",\n \"engine\": \"#cwl-js-engine\"\n },\n \"secondaryFiles\": [\n \".bai\",\n \".bti\"\n ],\n \"sbg:inheritMetadataFrom\": \"#input_bam_file\"\n },\n \"sbg:fileTypes\": \"BAM\"\n },\n {\n \"description\": \"Generated index file (without the indexed data).\",\n \"type\": [\n \"null\",\n \"File\"\n ],\n \"id\": \"#generated_index\",\n \"label\": \"Generated index file\",\n \"outputBinding\": {\n \"glob\": \"{*.bai,*.bti}\",\n \"sbg:inheritMetadataFrom\": \"#input_bam_file\"\n },\n \"sbg:fileTypes\": \"BAI,BTI\"\n }\n ],\n \"cwlVersion\": \"sbg:draft-2\",\n \"temporaryFailCodes\": [],\n \"sbg:job\": {\n \"inputs\": {\n \"bti_format\": false,\n \"indexed_data\": false,\n \"input_bam_file\": {\n \"class\": \"File\",\n \"path\": \"input/input_bam.bam\",\n \"size\": 0,\n \"secondaryFiles\": []\n }\n },\n \"allocatedResources\": {\n \"mem\": 1000,\n \"cpu\": 1\n }\n },\n \"sbg:toolkitVersion\": \"2.4.0\",\n \"arguments\": [\n {\n \"position\": 0,\n \"separate\": true,\n \"valueFrom\": {\n \"class\": \"Expression\",\n \"script\": \"{\\n if (!(typeof $job.inputs.input_bai_file !== \\\"undefined\\\")){\\n return \\\"-in \\\" + $job.inputs.input_bam_file.path.split('/').pop() \\n }\\n}\",\n \"engine\": \"#cwl-js-engine\"\n }\n },\n {\n \"position\": 1,\n \"separate\": true,\n \"valueFrom\": {\n \"class\": \"Expression\",\n \"script\": \"{\\n if (!(typeof $job.inputs.input_bai_file !== \\\"undefined\\\"))\\n if ((typeof $job.inputs.bti_format !== \\\"undefined\\\") && ($job.inputs.bti_format))\\n \\treturn \\\"-bti\\\" \\n}\",\n \"engine\": \"#cwl-js-engine\"\n }\n }\n ],\n \"sbg:license\": \"The MIT License\",\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:links\": [\n {\n \"label\": \"Homepage\",\n \"id\": \"https://github.com/pezmaster31/bamtools\"\n },\n {\n \"label\": \"Wiki\",\n \"id\": \"https://github.com/pezmaster31/bamtools/wiki\"\n }\n ],\n \"stdout\": \"\",\n \"description\": \"BamTools Index creates an index file (BAI or BTI) for a BAM file. If BAI file is present on the input the tool will skip indexing step and output BAM with provided BAI file.\\n\\n**Common issues:** Providing a BAI file on input will result in a pass-through without execution, even if a different index format is requested on the output (BTI instead of BAI).\",\n \"sbg:toolkit\": \"BamTools\",\n \"successCodes\": [],\n \"inputs\": [\n {\n \"description\": \"The input BAM file.\",\n \"type\": [\n \"File\"\n ],\n \"id\": \"#input_bam_file\",\n \"sbg:stageInput\": \"link\",\n \"label\": \"Input BAM file\",\n \"sbg:category\": \"Input & Output\",\n \"sbg:fileTypes\": \"BAM\"\n },\n {\n \"type\": [\n \"null\",\n \"boolean\"\n ],\n \"label\": \"BTI format\",\n \"id\": \"#bti_format\",\n \"sbg:category\": \"Input & Output\",\n \"description\": \"Create (non-standard) BamTools index file (*.BTI). Default behavior is to create standard BAM index (*.BAI).\"\n },\n {\n \"description\": \"Input BAI(BAM index) file.\",\n \"type\": [\n \"null\",\n \"File\"\n ],\n \"id\": \"#input_bai_file\",\n \"sbg:stageInput\": \"link\",\n \"label\": \"Input BAI(BAM index) file\",\n \"sbg:category\": \"File input\",\n \"sbg:fileTypes\": \"BAI\"\n },\n {\n \"type\": [\n \"null\",\n \"boolean\"\n ],\n \"label\": \"Don't output indexed data file\",\n \"id\": \"#indexed_data\",\n \"sbg:category\": \"Input & Output\",\n \"description\": \"Don't output indexed data file. The default value is [FALSE].\"\n }\n ],\n \"stdin\": \"\",\n \"sbg:toolAuthor\": \"Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg\",\n \"$namespaces\": {\n \"sbg\": \"https://sevenbridges.com\"\n },\n \"sbg:appVersion\": [\n \"sbg:draft-2\"\n ],\n \"id\": \"https://api.sbgenomics.com/v2/apps/rfranklin/my-project/bamtools-index-2-4-0/0/raw/\",\n \"sbg:id\": \"rfranklin/my-project/bamtools-index-2-4-0/0\",\n \"sbg:revision\": 0,\n \"sbg:revisionNotes\": \"Copy of admin/sbg-public-data/bamtools-index-2-4-0/30\",\n \"sbg:modifiedOn\": 1584016152,\n \"sbg:modifiedBy\": \"rfranklin\",\n \"sbg:createdOn\": 1584016152,\n \"sbg:createdBy\": \"rfranklin\",\n \"sbg:project\": \"rfranklin/my-project\",\n \"sbg:projectName\": \"My project\",\n \"sbg:sbgMaintained\": false,\n \"sbg:validationErrors\": [],\n \"sbg:contributors\": [\n \"rfranklin\"\n ],\n \"sbg:latestRevision\": 0,\n \"sbg:revisionsInfo\": [\n {\n \"sbg:revision\": 0,\n \"sbg:modifiedBy\": \"rfranklin\",\n \"sbg:modifiedOn\": 1584016152,\n \"sbg:revisionNotes\": \"Copy of admin/sbg-public-data/bamtools-index-2-4-0/30\"\n }\n ],\n \"sbg:publisher\": \"sbg\",\n \"sbg:content_hash\": null,\n \"sbg:copyOf\": \"admin/sbg-public-data/bamtools-index-2-4-0/30\"\n }\n}" schema: type: object properties: href: type: string example: https://api.sbgenomics.com/v2/apps/rfranklin/my-project/bamtools-index-2/0 id: type: string example: rfranklin/my-project/bamtools-index-2/0 project: type: string example: rfranklin/my-project name: type: string example: BamTools Index revision: type: integer example: 0 default: 0 raw: type: object properties: sbg:categories: type: array items: type: string example: SAM/BAM-Processing sbg:image_url: {} requirements: type: array items: type: object properties: class: type: string example: ExpressionEngineRequirement id: type: string example: '#cwl-js-engine' requirements: type: array items: type: object properties: class: type: string example: DockerRequirement dockerPull: type: string example: rabix/js-engine baseCommand: type: array items: type: object properties: class: type: string example: Expression script: type: string example: "{\n if ($job.inputs.input_bai_file){\n \treturn\"echo Skipping index step because BAI file is provided on the input.\"\n }\n else{\n return \"/opt/bamtools/bin/bamtools index\"\n }\n}" engine: type: string example: '#cwl-js-engine' class: type: string example: CommandLineTool sbg:cmdPreview: type: string example: /opt/bamtools/bin/bamtools index -in input_bam.bam sbg:homepage: type: string example: https://github.com/pezmaster31/bamtools/wiki label: type: string example: BamTools Index outputs: type: array items: type: object properties: description: type: string example: Output BAM file with index (BAI or BTI) file as a secondary file (not visible in the output list of the task). type: type: array items: type: string example: 'null' id: type: string example: '#output_bam_file' label: type: string example: Output BAM file outputBinding: type: object properties: glob: type: object properties: class: type: string example: Expression script: type: string example: "{\n if ($job.inputs.indexed_data === true){\n\treturn ''\n } else {\n return $job.inputs.input_bam_file.path.split(\"/\").pop()\n }\n}\n\n\n" engine: type: string example: '#cwl-js-engine' secondaryFiles: type: array items: type: string example: .bai sbg:inheritMetadataFrom: type: string example: '#input_bam_file' sbg:fileTypes: type: string example: BAM cwlVersion: type: string example: sbg:draft-2 temporaryFailCodes: type: array sbg:job: type: object properties: inputs: type: object properties: bti_format: type: boolean example: false default: true indexed_data: type: boolean example: false default: true input_bam_file: type: object properties: class: type: string example: File path: type: string example: input/input_bam.bam size: type: integer example: 0 default: 0 secondaryFiles: type: array allocatedResources: type: object properties: mem: type: integer example: 1000 default: 0 cpu: type: integer example: 1 default: 0 sbg:toolkitVersion: type: string example: 2.4.0 arguments: type: array items: type: object properties: position: type: integer example: 0 default: 0 separate: type: boolean example: true default: true valueFrom: type: object properties: class: type: string example: Expression script: type: string example: "{\n if (!(typeof $job.inputs.input_bai_file !== \"undefined\")){\n return \"-in \" + $job.inputs.input_bam_file.path.split('/').pop() \n }\n}" engine: type: string example: '#cwl-js-engine' sbg:license: type: string example: The MIT License hints: type: array items: type: object properties: dockerImageId: type: string example: f808163d4cd3 class: type: string example: DockerRequirement dockerPull: type: string example: images.sbgenomics.com/markop/bamtools:2.4.0 sbg:links: type: array items: type: object properties: label: type: string example: Homepage id: type: string example: https://github.com/pezmaster31/bamtools stdout: type: string example: '' description: type: string example: 'BamTools Index creates an index file (BAI or BTI) for a BAM file. If BAI file is present on the input the tool will skip indexing step and output BAM with provided BAI file. **Common issues:** Providing a BAI file on input will result in a pass-through without execution, even if a different index format is requested on the output (BTI instead of BAI).' sbg:toolkit: type: string example: BamTools successCodes: type: array inputs: type: array items: type: object properties: description: type: string example: The input BAM file. type: type: array items: type: string example: File id: type: string example: '#input_bam_file' sbg:stageInput: type: string example: link label: type: string example: Input BAM file sbg:category: type: string example: Input & Output sbg:fileTypes: type: string example: BAM stdin: type: string example: '' sbg:toolAuthor: type: string example: Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg $namespaces: type: object properties: sbg: type: string example: https://sevenbridges.com sbg:appVersion: type: array items: type: string example: sbg:draft-2 id: type: string example: https://api.sbgenomics.com/v2/apps/rfranklin/my-project/bamtools-index-2-4-0/0/raw/ sbg:id: type: string example: rfranklin/my-project/bamtools-index-2-4-0/0 sbg:revision: type: integer example: 0 default: 0 sbg:revisionNotes: type: string example: Copy of admin/sbg-public-data/bamtools-index-2-4-0/30 sbg:modifiedOn: type: integer example: 1584016152 default: 0 sbg:modifiedBy: type: string example: rfranklin sbg:createdOn: type: integer example: 1584016152 default: 0 sbg:createdBy: type: string example: rfranklin sbg:project: type: string example: rfranklin/my-project sbg:projectName: type: string example: My project sbg:sbgMaintained: type: boolean example: false default: true sbg:validationErrors: type: array sbg:contributors: type: array items: type: string example: rfranklin sbg:latestRevision: type: integer example: 0 default: 0 sbg:revisionsInfo: type: array items: type: object properties: sbg:revision: type: integer example: 0 default: 0 sbg:modifiedBy: type: string example: rfranklin sbg:modifiedOn: type: integer example: 1584016152 default: 0 sbg:revisionNotes: type: string example: Copy of admin/sbg-public-data/bamtools-index-2-4-0/30 sbg:publisher: type: string example: sbg sbg:content_hash: {} sbg:copyOf: type: string example: admin/sbg-public-data/bamtools-index-2-4-0/30 deprecated: false x-readme: code-samples: - language: python code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='3210a98c1db9318fa9d9273156740f74')\n\n# send GET request to SB API\napp = api.apps.get(id='rfranklin/my-project/bamtools-index-2')\n\nprint(app.name, app.revision)" samples-languages: - python tags: - Apps /apps/{app_id}/actions/sync: post: summary: Synchronize a copied app with its parent app description: This call synchronizes a copied app with the source app from which it has been copied. For example, when **FASTQC** is copied from public apps to a project and updates are made to **FASTQC** in the public apps gallery (there are new revisions), this action fetches all revisions and revision notes from the updated parent app and applies them to your copied app. Once this has been done, the copied app is updated to the latest revision and includes the complete revision history of its parent app, following the logic of the `git pull` command. operationId: synchronize-a-copied-app-with-its-parent-app parameters: - name: X-SBG-Auth-Token in: header description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). required: true schema: type: string - name: fields in: query description: Selector specifying a subset of fields to include in the response. schema: type: array items: type: string - name: app_id in: path description: The ID of the app you want to update. It should reference the project owner, the project that your app is copied to, and the app's short name (containing no non-alphanumeric characters or spaces). schema: type: string required: true responses: '200': description: '200' content: application/json: examples: Result: value: "{\n \"href\": \"https://api.sbgenomics.com/v2/apps/rfranklin/test-project/bamtools-index-2/1\",\n \"id\": \"rfranklin/test-project/bamtools-index-2/1\",\n \"project\": \"rfranklin/test-project\",\n \"name\": \"BamTools Index\",\n \"revision\": 1,\n \"raw\": {\n \"sbg:sbgMaintained\": false,\n \"requirements\": [\n {\n \"class\": \"ExpressionEngineRequirement\",\n \"id\": \"#cwl-js-engine\",\n \"requirements\": [\n {\n \"class\": \"DockerRequirement\",\n \"dockerPull\": \"rabix/js-engine\"\n }\n ]\n }\n ],\n \"sbg:modifiedOn\": 1494849814,\n \"outputs\": [\n {\n \"label\": \"Output BAM file\",\n \"sbg:fileTypes\": \"BAM\",\n \"description\": \"Output BAM file with index (BAI or BTI) file as a secondary file (not visible in the output list of the task).\",\n \"id\": \"#output_bam_file\",\n \"type\": [\n \"null\",\n \"File\"\n ],\n \"outputBinding\": {\n \"glob\": {\n \"class\": \"Expression\",\n \"engine\": \"#cwl-js-engine\",\n \"script\": \"{\\n if ($job.inputs.indexed_data === true){\\n\\treturn ''\\n } else {\\n return $job.inputs.input_bam_file.path.split(\\\"/\\\").pop()\\n }\\n}\\n\\n\\n\"\n },\n \"secondaryFiles\": [\n \".bai\",\n \".bti\"\n ],\n \"sbg:inheritMetadataFrom\": \"#input_bam_file\"\n }\n },\n {\n \"label\": \"Generated Index File\",\n \"sbg:fileTypes\": \"BAI,BTI\",\n \"description\": \"Generated index file (without the indexed data).\",\n \"id\": \"#generated_index\",\n \"type\": [\n \"null\",\n \"File\"\n ],\n \"outputBinding\": {\n \"glob\": \"{*.bai,*.bti}\",\n \"sbg:inheritMetadataFrom\": \"#input_bam_file\"\n }\n }\n ],\n \"sbg:toolAuthor\": \"Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg\",\n \"sbg:revisionsInfo\": [\n {\n \"sbg:modifiedOn\": 1494849680,\n \"sbg:modifiedBy\": \"rfranklin\",\n \"sbg:revision\": 0,\n \"sbg:revisionNotes\": \"Copy of rfranklin/bam-test/bamtools-index-2/0\"\n },\n {\n \"sbg:modifiedOn\": 1494849814,\n \"sbg:modifiedBy\": \"rfranklin\",\n \"sbg:revision\": 1,\n \"sbg:revisionNotes\": \"Modified output description.\"\n }\n ],\n \"sbg:categories\": [\n \"SAM/BAM-Processing\",\n \"Indexing\"\n ],\n \"sbg:modifiedBy\": \"rfranklin\",\n \"sbg:image_url\": null,\n \"sbg:appVersion\": [\n \"sbg:draft-2\"\n ],\n \"sbg:createdBy\": \"rfranklin\",\n \"sbg:copyOf\": \"rfranklin/bam-test/bamtools-index-2/1\",\n \"stdout\": \"\",\n \"sbg:latestRevision\": 1,\n \"temporaryFailCodes\": [],\n \"sbg:job\": {\n \"inputs\": {\n \"bti_format\": false,\n \"input_bam_file\": {\n \"class\": \"File\",\n \"size\": 0,\n \"secondaryFiles\": [],\n \"path\": \"input/input_bam.bam\"\n },\n \"indexed_data\": false\n },\n \"allocatedResources\": {\n \"cpu\": 1,\n \"mem\": 1000\n }\n },\n \"successCodes\": [],\n \"sbg:links\": [\n {\n \"label\": \"Homepage\",\n \"id\": \"https://github.com/pezmaster31/bamtools\"\n },\n {\n \"label\": \"Wiki\",\n \"id\": \"https://github.com/pezmaster31/bamtools/wiki\"\n }\n ],\n \"sbg:revisionNotes\": \"Modified output description.\",\n \"label\": \"BamTools Index\",\n \"cwlVersion\": \"sbg:draft-2\",\n \"sbg:homepage\": \"https://github.com/pezmaster31/bamtools/wiki\",\n \"sbg:cmdPreview\": \"/opt/bamtools/bin/bamtools index -in input_bam.bam\",\n \"stdin\": \"\",\n \"sbg:id\": \"rfranklin/test-project/bamtools-index-2/1\",\n \"hints\": [\n {\n \"class\": \"DockerRequirement\",\n \"dockerPull\": \"images.sbgenomics.com/rfranklin/bamtools:2.4.0\",\n \"dockerImageId\": \"f808163d4cd3\"\n },\n {\n \"class\": \"sbg:CPURequirement\",\n \"value\": 1\n },\n {\n \"class\": \"sbg:MemRequirement\",\n \"value\": 1000\n }\n ],\n \"sbg:toolkitVersion\": \"2.4.0\",\n \"sbg:license\": \"The MIT License\",\n \"sbg:toolkit\": \"BamTools\",\n \"sbg:validationErrors\": [],\n \"class\": \"CommandLineTool\",\n \"inputs\": [\n {\n \"sbg:category\": \"Input & Output\",\n \"label\": \"Input BAM file\",\n \"sbg:fileTypes\": \"BAM\",\n \"id\": \"#input_bam_file\",\n \"description\": \"The input BAM file.\",\n \"type\": [\n \"File\"\n ],\n \"sbg:stageInput\": \"link\"\n },\n {\n \"sbg:category\": \"Input & Output\",\n \"description\": \"Create (non-standard) BamTools index file (*.BTI). Default behavior is to create standard BAM index (*.BAI).\",\n \"type\": [\n \"null\",\n \"boolean\"\n ],\n \"label\": \"BTI format\",\n \"id\": \"#bti_format\"\n },\n {\n \"sbg:category\": \"File input\",\n \"label\": \"Input BAI(BAM index) file\",\n \"sbg:fileTypes\": \"BAI\",\n \"id\": \"#input_bai_file\",\n \"description\": \"Input BAI(BAM index) file.\",\n \"type\": [\n \"null\",\n \"File\"\n ],\n \"sbg:stageInput\": \"link\"\n },\n {\n \"sbg:category\": \"Input & Output\",\n \"description\": \"Don't output indexed data file. The default value is [FALSE].\",\n \"type\": [\n \"null\",\n \"boolean\"\n ],\n \"label\": \"Don't output indexed data file\",\n \"id\": \"#indexed_data\"\n }\n ],\n \"sbg:createdOn\": 1494849680,\n \"arguments\": [\n {\n \"valueFrom\": {\n \"class\": \"Expression\",\n \"engine\": \"#cwl-js-engine\",\n \"script\": \"{\\n if (!(typeof $job.inputs.input_bai_file !== \\\"undefined\\\")){\\n return \\\"-in \\\" + $job.inputs.input_bam_file.path.split('/').pop() \\n }\\n}\"\n },\n \"position\": 0,\n \"separate\": true\n },\n {\n \"valueFrom\": {\n \"class\": \"Expression\",\n \"engine\": \"#cwl-js-engine\",\n \"script\": \"{\\n if (!(typeof $job.inputs.input_bai_file !== \\\"undefined\\\"))\\n if ((typeof $job.inputs.bti_format !== \\\"undefined\\\") && ($job.inputs.bti_format))\\n \\treturn \\\"-bti\\\" \\n}\"\n },\n \"position\": 1,\n \"separate\": true\n }\n ],\n \"description\": \"BamTools Index creates an index file (BAI or BTI) for a BAM file. If BAI file is present on the input the tool will skip indexing step and output BAM with provided BAI file.\\n\\n**Common issues:** Providing a BAI file on input will result in a pass-through without execution, even if a different index format is requested on the output (BTI instead of BAI).\",\n \"sbg:contributors\": [\n \"rfranklin\"\n ],\n \"id\": \"https://api.sbgenomics.com/v2/apps/rfranklin/test-project/bamtools-index-2/1/raw/\",\n \"baseCommand\": [\n {\n \"class\": \"Expression\",\n \"engine\": \"#cwl-js-engine\",\n \"script\": \"{\\n if ($job.inputs.input_bai_file){\\n \\treturn\\\"echo Skipping index step because BAI file is provided on the input.\\\"\\n }\\n else{\\n return \\\"/opt/bamtools/bin/bamtools index\\\"\\n }\\n}\"\n }\n ],\n \"sbg:projectName\": \"Test Project\",\n \"sbg:project\": \"rfranklin/test-project\",\n \"sbg:revision\": 1\n }\n}" schema: type: object properties: href: type: string example: https://api.sbgenomics.com/v2/apps/rfranklin/test-project/bamtools-index-2/1 id: type: string example: rfranklin/test-project/bamtools-index-2/1 project: type: string example: rfranklin/test-project name: type: string example: BamTools Index revision: type: integer example: 1 default: 0 raw: type: object properties: sbg:sbgMaintained: type: boolean example: false default: true requirements: type: array items: type: object properties: class: type: string example: ExpressionEngineRequirement id: type: string example: '#cwl-js-engine' requirements: type: array items: type: object properties: class: type: string example: DockerRequirement dockerPull: type: string example: rabix/js-engine sbg:modifiedOn: type: integer example: 1494849814 default: 0 outputs: type: array items: type: object properties: label: type: string example: Output BAM file sbg:fileTypes: type: string example: BAM description: type: string example: Output BAM file with index (BAI or BTI) file as a secondary file (not visible in the output list of the task). id: type: string example: '#output_bam_file' type: type: array items: type: string example: 'null' outputBinding: type: object properties: glob: type: object properties: class: type: string example: Expression engine: type: string example: '#cwl-js-engine' script: type: string example: "{\n if ($job.inputs.indexed_data === true){\n\treturn ''\n } else {\n return $job.inputs.input_bam_file.path.split(\"/\").pop()\n }\n}\n\n\n" secondaryFiles: type: array items: type: string example: .bai sbg:inheritMetadataFrom: type: string example: '#input_bam_file' sbg:toolAuthor: type: string example: Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg sbg:revisionsInfo: type: array items: type: object properties: sbg:modifiedOn: type: integer example: 1494849680 default: 0 sbg:modifiedBy: type: string example: rfranklin sbg:revision: type: integer example: 0 default: 0 sbg:revisionNotes: type: string example: Copy of rfranklin/bam-test/bamtools-index-2/0 sbg:categories: type: array items: type: string example: SAM/BAM-Processing sbg:modifiedBy: type: string example: rfranklin sbg:image_url: {} sbg:appVersion: type: array items: type: string example: sbg:draft-2 sbg:createdBy: type: string example: rfranklin sbg:copyOf: type: string example: rfranklin/bam-test/bamtools-index-2/1 stdout: type: string example: '' sbg:latestRevision: type: integer example: 1 default: 0 temporaryFailCodes: type: array sbg:job: type: object properties: inputs: type: object properties: bti_format: type: boolean example: false default: true input_bam_file: type: object properties: class: type: string example: File size: type: integer example: 0 default: 0 secondaryFiles: type: array path: type: string example: input/input_bam.bam indexed_data: type: boolean example: false default: true allocatedResources: type: object properties: cpu: type: integer example: 1 default: 0 mem: type: integer example: 1000 default: 0 successCodes: type: array sbg:links: type: array items: type: object properties: label: type: string example: Homepage id: type: string example: https://github.com/pezmaster31/bamtools sbg:revisionNotes: type: string example: Modified output description. label: type: string example: BamTools Index cwlVersion: type: string example: sbg:draft-2 sbg:homepage: type: string example: https://github.com/pezmaster31/bamtools/wiki sbg:cmdPreview: type: string example: /opt/bamtools/bin/bamtools index -in input_bam.bam stdin: type: string example: '' sbg:id: type: string example: rfranklin/test-project/bamtools-index-2/1 hints: type: array items: type: object properties: class: type: string example: DockerRequirement dockerPull: type: string example: images.sbgenomics.com/rfranklin/bamtools:2.4.0 dockerImageId: type: string example: f808163d4cd3 sbg:toolkitVersion: type: string example: 2.4.0 sbg:license: type: string example: The MIT License sbg:toolkit: type: string example: BamTools sbg:validationErrors: type: array class: type: string example: CommandLineTool inputs: type: array items: type: object properties: sbg:category: type: string example: Input & Output label: type: string example: Input BAM file sbg:fileTypes: type: string example: BAM id: type: string example: '#input_bam_file' description: type: string example: The input BAM file. type: type: array items: type: string example: File sbg:stageInput: type: string example: link sbg:createdOn: type: integer example: 1494849680 default: 0 arguments: type: array items: type: object properties: valueFrom: type: object properties: class: type: string example: Expression engine: type: string example: '#cwl-js-engine' script: type: string example: "{\n if (!(typeof $job.inputs.input_bai_file !== \"undefined\")){\n return \"-in \" + $job.inputs.input_bam_file.path.split('/').pop() \n }\n}" position: type: integer example: 0 default: 0 separate: type: boolean example: true default: true description: type: string example: 'BamTools Index creates an index file (BAI or BTI) for a BAM file. If BAI file is present on the input the tool will skip indexing step and output BAM with provided BAI file. **Common issues:** Providing a BAI file on input will result in a pass-through without execution, even if a different index format is requested on the output (BTI instead of BAI).' sbg:contributors: type: array items: type: string example: rfranklin id: type: string example: https://api.sbgenomics.com/v2/apps/rfranklin/test-project/bamtools-index-2/1/raw/ baseCommand: type: array items: type: object properties: class: type: string example: Expression engine: type: string example: '#cwl-js-engine' script: type: string example: "{\n if ($job.inputs.input_bai_file){\n \treturn\"echo Skipping index step because BAI file is provided on the input.\"\n }\n else{\n return \"/opt/bamtools/bin/bamtools index\"\n }\n}" sbg:projectName: type: string example: Test Project sbg:project: type: string example: rfranklin/test-project sbg:revision: type: integer example: 1 default: 0 deprecated: false x-readme: code-samples: - language: python code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='3210a98c1db9318fa9d9273156740f74')\n\napp = api.apps.get(id='rfranklin/test-project/bamtools-index-2')\n\n# send POST request to SB API\napp.sync()\n\nprint(app.revision)" samples-languages: - python tags: - Apps /apps/{app_id}/{revision_number}: get: summary: Get details of an app revision description: This call allows you to obtain a particular revision of a tool, which is not necessarily the most recent version. operationId: get-details-of-an-app-revision parameters: - name: X-SBG-Auth-Token in: header description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). required: true schema: type: string - name: fields in: query description: Selector specifying a subset of fields to include in the response. schema: type: array items: type: string - name: app_id in: path description: The ID for the app you are querying. It can be obtained by making the call to [list all apps available to you](ref:list-all-apps-available-to-you). schema: type: string required: true - name: revision_number in: path description: The integer denoting the revision of the app. schema: type: string required: true responses: '200': description: '200' content: application/json: examples: Result: value: "{\n \"href\": \"https://api.sbgenomics.com/v2/apps/rfranklin/my-project/bamtools-index-2/0\",\n \"id\": \"rfranklin/my-project/bamtools-index-2/0\",\n \"project\": \"rfranklin/my-project\",\n \"name\": \"BamTools Index\",\n \"revision\": 0,\n \"raw\": {\n \"sbg:categories\": [\n \"SAM/BAM-Processing\",\n \"Indexing\"\n ],\n \"sbg:image_url\": null,\n \"requirements\": [\n {\n \"class\": \"ExpressionEngineRequirement\",\n \"id\": \"#cwl-js-engine\",\n \"requirements\": [\n {\n \"class\": \"DockerRequirement\",\n \"dockerPull\": \"rabix/js-engine\"\n }\n ]\n }\n ],\n \"baseCommand\": [\n {\n \"class\": \"Expression\",\n \"script\": \"{\\n if ($job.inputs.input_bai_file){\\n \\treturn\\\"echo Skipping index step because BAI file is provided on the input.\\\"\\n }\\n else{\\n return \\\"/opt/bamtools/bin/bamtools index\\\"\\n }\\n}\",\n \"engine\": \"#cwl-js-engine\"\n }\n ],\n \"class\": \"CommandLineTool\",\n \"sbg:cmdPreview\": \"/opt/bamtools/bin/bamtools index -in input_bam.bam\",\n \"sbg:homepage\": \"https://github.com/pezmaster31/bamtools/wiki\",\n \"label\": \"BamTools Index\",\n \"outputs\": [\n {\n \"description\": \"Output BAM file with index (BAI or BTI) file as a secondary file (not visible in the output list of the task).\",\n \"type\": [\n \"null\",\n \"File\"\n ],\n \"id\": \"#output_bam_file\",\n \"label\": \"Output BAM file\",\n \"outputBinding\": {\n \"glob\": {\n \"class\": \"Expression\",\n \"script\": \"{\\n if ($job.inputs.indexed_data === true){\\n\\treturn ''\\n } else {\\n return $job.inputs.input_bam_file.path.split(\\\"/\\\").pop()\\n }\\n}\\n\\n\\n\",\n \"engine\": \"#cwl-js-engine\"\n },\n \"secondaryFiles\": [\n \".bai\",\n \".bti\"\n ],\n \"sbg:inheritMetadataFrom\": \"#input_bam_file\"\n },\n \"sbg:fileTypes\": \"BAM\"\n },\n {\n \"description\": \"Generated index file (without the indexed data).\",\n \"type\": [\n \"null\",\n \"File\"\n ],\n \"id\": \"#generated_index\",\n \"label\": \"Generated index file\",\n \"outputBinding\": {\n \"glob\": \"{*.bai,*.bti}\",\n \"sbg:inheritMetadataFrom\": \"#input_bam_file\"\n },\n \"sbg:fileTypes\": \"BAI,BTI\"\n }\n ],\n \"cwlVersion\": \"sbg:draft-2\",\n \"temporaryFailCodes\": [],\n \"sbg:job\": {\n \"inputs\": {\n \"bti_format\": false,\n \"indexed_data\": false,\n \"input_bam_file\": {\n \"class\": \"File\",\n \"path\": \"input/input_bam.bam\",\n \"size\": 0,\n \"secondaryFiles\": []\n }\n },\n \"allocatedResources\": {\n \"mem\": 1000,\n \"cpu\": 1\n }\n },\n \"sbg:toolkitVersion\": \"2.4.0\",\n \"arguments\": [\n {\n \"position\": 0,\n \"separate\": true,\n \"valueFrom\": {\n \"class\": \"Expression\",\n \"script\": \"{\\n if (!(typeof $job.inputs.input_bai_file !== \\\"undefined\\\")){\\n return \\\"-in \\\" + $job.inputs.input_bam_file.path.split('/').pop() \\n }\\n}\",\n \"engine\": \"#cwl-js-engine\"\n }\n },\n {\n \"position\": 1,\n \"separate\": true,\n \"valueFrom\": {\n \"class\": \"Expression\",\n \"script\": \"{\\n if (!(typeof $job.inputs.input_bai_file !== \\\"undefined\\\"))\\n if ((typeof $job.inputs.bti_format !== \\\"undefined\\\") && ($job.inputs.bti_format))\\n \\treturn \\\"-bti\\\" \\n}\",\n \"engine\": \"#cwl-js-engine\"\n }\n }\n ],\n \"sbg:license\": \"The MIT License\",\n \"hints\": [\n {\n \"dockerImageId\": \"f808163d4cd3\",\n \"class\": \"DockerRequirement\",\n \"dockerPull\": \"images.sbgenomics.com/rfranklin/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:links\": [\n {\n \"label\": \"Homepage\",\n \"id\": \"https://github.com/pezmaster31/bamtools\"\n },\n {\n \"label\": \"Wiki\",\n \"id\": \"https://github.com/pezmaster31/bamtools/wiki\"\n }\n ],\n \"stdout\": \"\",\n \"description\": \"BamTools Index creates an index file (BAI or BTI) for a BAM file. If BAI file is present on the input the tool will skip indexing step and output BAM with provided BAI file.\\n\\n**Common issues:** Providing a BAI file on input will result in a pass-through without execution, even if a different index format is requested on the output (BTI instead of BAI).\",\n \"sbg:toolkit\": \"BamTools\",\n \"successCodes\": [],\n \"inputs\": [\n {\n \"description\": \"The input BAM file.\",\n \"type\": [\n \"File\"\n ],\n \"id\": \"#input_bam_file\",\n \"sbg:stageInput\": \"link\",\n \"label\": \"Input BAM file\",\n \"sbg:category\": \"Input & Output\",\n \"sbg:fileTypes\": \"BAM\"\n },\n {\n \"type\": [\n \"null\",\n \"boolean\"\n ],\n \"label\": \"BTI format\",\n \"id\": \"#bti_format\",\n \"sbg:category\": \"Input & Output\",\n \"description\": \"Create (non-standard) BamTools index file (*.BTI). Default behavior is to create standard BAM index (*.BAI).\"\n },\n {\n \"description\": \"Input BAI(BAM index) file.\",\n \"type\": [\n \"null\",\n \"File\"\n ],\n \"id\": \"#input_bai_file\",\n \"sbg:stageInput\": \"link\",\n \"label\": \"Input BAI(BAM index) file\",\n \"sbg:category\": \"File input\",\n \"sbg:fileTypes\": \"BAI\"\n },\n {\n \"type\": [\n \"null\",\n \"boolean\"\n ],\n \"label\": \"Don't output indexed data file\",\n \"id\": \"#indexed_data\",\n \"sbg:category\": \"Input & Output\",\n \"description\": \"Don't output indexed data file. The default value is [FALSE].\"\n }\n ],\n \"stdin\": \"\",\n \"sbg:toolAuthor\": \"Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg\",\n \"$namespaces\": {\n \"sbg\": \"https://sevenbridges.com\"\n },\n \"sbg:appVersion\": [\n \"sbg:draft-2\"\n ],\n \"id\": \"https://api.sbgenomics.com/v2/apps/rfranklin/my-project/bamtools-index-2/0/raw/\",\n \"sbg:id\": \"rfranklin/my-project/bamtools-index-2/0\",\n \"sbg:revision\": 0,\n \"sbg:revisionNotes\": \"Copy of admin/sbg-public-data/bamtools-index-2/30\",\n \"sbg:modifiedOn\": 1584016152,\n \"sbg:modifiedBy\": \"rfranklin\",\n \"sbg:createdOn\": 1584016152,\n \"sbg:createdBy\": \"rfranklin\",\n \"sbg:project\": \"rfranklin/my-project\",\n \"sbg:projectName\": \"My project\",\n \"sbg:sbgMaintained\": false,\n \"sbg:validationErrors\": [],\n \"sbg:contributors\": [\n \"rfranklin\"\n ],\n \"sbg:latestRevision\": 0,\n \"sbg:revisionsInfo\": [\n {\n \"sbg:revision\": 0,\n \"sbg:modifiedBy\": \"rfranklin\",\n \"sbg:modifiedOn\": 1584016152,\n \"sbg:revisionNotes\": \"Copy of admin/sbg-public-data/bamtools-index-2/30\"\n }\n ],\n \"sbg:publisher\": \"sbg\",\n \"sbg:content_hash\": null,\n \"sbg:copyOf\": \"admin/sbg-public-data/bamtools-index-2/30\"\n }\n}" schema: type: object properties: href: type: string example: https://api.sbgenomics.com/v2/apps/rfranklin/my-project/bamtools-index-2/0 id: type: string example: rfranklin/my-project/bamtools-index-2/0 project: type: string example: rfranklin/my-project name: type: string example: BamTools Index revision: type: integer example: 0 default: 0 raw: type: object properties: sbg:categories: type: array items: type: string example: SAM/BAM-Processing sbg:image_url: {} requirements: type: array items: type: object properties: class: type: string example: ExpressionEngineRequirement id: type: string example: '#cwl-js-engine' requirements: type: array items: type: object properties: class: type: string example: DockerRequirement dockerPull: type: string example: rabix/js-engine baseCommand: type: array items: type: object properties: class: type: string example: Expression script: type: string example: "{\n if ($job.inputs.input_bai_file){\n \treturn\"echo Skipping index step because BAI file is provided on the input.\"\n }\n else{\n return \"/opt/bamtools/bin/bamtools index\"\n }\n}" engine: type: string example: '#cwl-js-engine' class: type: string example: CommandLineTool sbg:cmdPreview: type: string example: /opt/bamtools/bin/bamtools index -in input_bam.bam sbg:homepage: type: string example: https://github.com/pezmaster31/bamtools/wiki label: type: string example: BamTools Index outputs: type: array items: type: object properties: description: type: string example: Output BAM file with index (BAI or BTI) file as a secondary file (not visible in the output list of the task). type: type: array items: type: string example: 'null' id: type: string example: '#output_bam_file' label: type: string example: Output BAM file outputBinding: type: object properties: glob: type: object properties: class: type: string example: Expression script: type: string example: "{\n if ($job.inputs.indexed_data === true){\n\treturn ''\n } else {\n return $job.inputs.input_bam_file.path.split(\"/\").pop()\n }\n}\n\n\n" engine: type: string example: '#cwl-js-engine' secondaryFiles: type: array items: type: string example: .bai sbg:inheritMetadataFrom: type: string example: '#input_bam_file' sbg:fileTypes: type: string example: BAM cwlVersion: type: string example: sbg:draft-2 temporaryFailCodes: type: array sbg:job: type: object properties: inputs: type: object properties: bti_format: type: boolean example: false default: true indexed_data: type: boolean example: false default: true input_bam_file: type: object properties: class: type: string example: File path: type: string example: input/input_bam.bam size: type: integer example: 0 default: 0 secondaryFiles: type: array allocatedResources: type: object properties: mem: type: integer example: 1000 default: 0 cpu: type: integer example: 1 default: 0 sbg:toolkitVersion: type: string example: 2.4.0 arguments: type: array items: type: object properties: position: type: integer example: 0 default: 0 separate: type: boolean example: true default: true valueFrom: type: object properties: class: type: string example: Expression script: type: string example: "{\n if (!(typeof $job.inputs.input_bai_file !== \"undefined\")){\n return \"-in \" + $job.inputs.input_bam_file.path.split('/').pop() \n }\n}" engine: type: string example: '#cwl-js-engine' sbg:license: type: string example: The MIT License hints: type: array items: type: object properties: dockerImageId: type: string example: f808163d4cd3 class: type: string example: DockerRequirement dockerPull: type: string example: images.sbgenomics.com/rfranklin/bamtools:2.4.0 sbg:links: type: array items: type: object properties: label: type: string example: Homepage id: type: string example: https://github.com/pezmaster31/bamtools stdout: type: string example: '' description: type: string example: 'BamTools Index creates an index file (BAI or BTI) for a BAM file. If BAI file is present on the input the tool will skip indexing step and output BAM with provided BAI file. **Common issues:** Providing a BAI file on input will result in a pass-through without execution, even if a different index format is requested on the output (BTI instead of BAI).' sbg:toolkit: type: string example: BamTools successCodes: type: array inputs: type: array items: type: object properties: description: type: string example: The input BAM file. type: type: array items: type: string example: File id: type: string example: '#input_bam_file' sbg:stageInput: type: string example: link label: type: string example: Input BAM file sbg:category: type: string example: Input & Output sbg:fileTypes: type: string example: BAM stdin: type: string example: '' sbg:toolAuthor: type: string example: Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg $namespaces: type: object properties: sbg: type: string example: https://sevenbridges.com sbg:appVersion: type: array items: type: string example: sbg:draft-2 id: type: string example: https://api.sbgenomics.com/v2/apps/rfranklin/my-project/bamtools-index-2/0/raw/ sbg:id: type: string example: rfranklin/my-project/bamtools-index-2/0 sbg:revision: type: integer example: 0 default: 0 sbg:revisionNotes: type: string example: Copy of admin/sbg-public-data/bamtools-index-2/30 sbg:modifiedOn: type: integer example: 1584016152 default: 0 sbg:modifiedBy: type: string example: rfranklin sbg:createdOn: type: integer example: 1584016152 default: 0 sbg:createdBy: type: string example: rfranklin sbg:project: type: string example: rfranklin/my-project sbg:projectName: type: string example: My project sbg:sbgMaintained: type: boolean example: false default: true sbg:validationErrors: type: array sbg:contributors: type: array items: type: string example: rfranklin sbg:latestRevision: type: integer example: 0 default: 0 sbg:revisionsInfo: type: array items: type: object properties: sbg:revision: type: integer example: 0 default: 0 sbg:modifiedBy: type: string example: rfranklin sbg:modifiedOn: type: integer example: 1584016152 default: 0 sbg:revisionNotes: type: string example: Copy of admin/sbg-public-data/bamtools-index-2/30 sbg:publisher: type: string example: sbg sbg:content_hash: {} sbg:copyOf: type: string example: admin/sbg-public-data/bamtools-index-2/30 deprecated: false x-readme: code-samples: - language: python code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='3210a98c1db9318fa9d9273156740f74')\n\n# send GET request to SB API\napp = api.apps.get_revision(\n id='rfranklin/my-project/bamtools-index-2',\n revision=0\n)\n\nprint(app.name)" samples-languages: - python tags: - Apps /apps/{project_owner}/{project}/{app_short_name}/{revision_number}/raw: post: summary: Add an app using raw CWL description: This call allows you to add an app using raw CWL. operationId: add-an-app-using-raw-cwl parameters: - name: X-SBG-Auth-Token in: header description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). required: true schema: type: string - name: fields in: query description: Selector specifying a subset of fields to include in the response. schema: type: array items: type: string - name: project_owner in: path description: If you are using [Enterprise](doc:about-the-enterprise-feature), use the name of the Division that owns the project in which you want to store the app; otherwise, enter the Platform username of the project owner. schema: type: string required: true - name: Content-Type in: header description: 'Depending on the type of file you are uploading: * `application/json` for a JSON file * `application/yaml` for a YAML file' schema: type: string - name: project in: path description: The name of the project in which you want to store the app. schema: type: string required: true - name: app_short_name in: path description: A short name for the app (without any non-alphanumeric characters or spaces) schema: type: string required: true - name: revision_number in: path description: The app [revision (version)](doc:app-versions) number. schema: type: integer format: int32 required: true requestBody: content: application/json: schema: type: object properties: RAW_BODY: type: string description: The body of the request should be a CWL app description saved as a JSON or YAML file. For a template of this description, try making the call to [get raw CWL for an app](ref:get-raw-cwl-for-an-app) about an app already in one of your projects. format: json deprecated: false x-readme: code-samples: - language: python code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='3210a98c1db9318fa9d9273156740f74')\n\n# send POST request to SB API\nnew_app = api.apps.install_app(\n id='RFranklin/my-project/my-app',\n raw='... CWL JSON/YAML HERE ...'\n)\n\nprint(new_app.name, new_app.id)" samples-languages: - python tags: - Apps /apps/{project_owner}/{project}/{app_short_name}/raw: get: summary: Get raw CWL for an app description: "This call returns information about the specified app, as raw CWL. The call differs from the call to [ get details of an app](ref: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 the Seven Bridges Platform by a project member, or a publicly available app that has been copied to the project." operationId: get-raw-cwl-for-an-app parameters: - name: project_owner in: path description: If you are using [Enterprise](doc:about-the-enterprise-feature), use the name of the Division that owns the project in which the app is located; otherwise, enter the Platform username of the project owner. schema: type: string required: true - name: fields in: query description: Selector specifying a subset of fields to include in the response. schema: type: array items: type: string - name: X-SBG-Auth-Token in: header description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). required: true schema: type: string - name: project in: path description: The name of the project in which the app is located. schema: type: string required: true - name: app_short_name in: path description: The short name of the app you are querying. Optionally, to get raw CWL of a specific revision of the app, use the `{app_short_name}/{revision_number}` format, for example `bamtools-index-2-4-0/1` schema: type: string required: true responses: '200': description: '200' content: application/json: examples: Result: value: "{\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://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}" schema: type: object properties: successCodes: type: array sbg:homepage: type: string example: https://github.com/pezmaster31/bamtools/wiki sbg:validationErrors: type: array sbg:sbgMaintained: type: boolean example: false default: true temporaryFailCodes: type: array requirements: type: array sbg:latestRevision: type: integer example: 0 default: 0 description: type: string example: BamTools Merge merges multiple BAM files into a single file. sbg:job: type: object properties: inputs: type: object properties: region: type: string example: chr1 input_bam_files: type: array items: type: object properties: path: type: string example: 1.bam allocatedResources: type: object properties: cpu: type: integer example: 1 default: 0 mem: type: integer example: 1000 default: 0 sbg:toolAuthor: type: string example: Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg hints: type: array items: type: object properties: dockerImageId: type: string example: f808163d4cd3 class: type: string example: DockerRequirement dockerPull: type: string example: images.sbgenomics.com/markop/bamtools:2.4.0 sbg:copyOf: type: string example: djordje_klisic/public-apps-by-seven-bridges/bamtools-merge-2-4-0/0 sbg:createdOn: type: integer example: 1452181866 default: 0 arguments: type: array items: type: object properties: position: type: integer example: 1 default: 0 prefix: type: string example: -out separate: type: boolean example: true default: true valueFrom: type: string example: merged.bam outputs: type: array items: type: object properties: sbg:fileTypes: type: string example: BAM id: type: string example: '#output_bam_file' outputBinding: type: object properties: glob: type: string example: merged.bam sbg:metadata: type: object properties: {} sbg:inheritMetadataFrom: type: string example: '#input_bams' description: type: string example: Output BAM file. type: type: array items: type: string example: File label: type: string example: Output BAM file sbg:categories: type: array items: type: string example: SAM/BAM-Processing sbg:contributors: type: array items: type: string example: RFranklin sbg:links: type: array items: type: object properties: id: type: string example: https://github.com/pezmaster31/bamtools label: type: string example: Homepage stdout: type: string example: '' stdin: type: string example: '' sbg:project: type: string example: RFranklin/my-project inputs: type: array items: type: object properties: sbg:fileTypes: type: string example: BAM id: type: string example: '#input_bam_files' inputBinding: type: object properties: sbg:cmdInclude: type: boolean example: true default: true prefix: type: string example: -in separate: type: boolean example: true default: true itemSeparator: {} position: type: integer example: 0 default: 0 description: type: string example: The input BAM files. label: type: string example: Input BAM files type: type: array items: type: object properties: type: type: string example: array items: type: string example: File sbg:category: type: string example: Input & Output label: type: string example: BamTools Merge sbg:createdBy: type: string example: RFranklin baseCommand: type: array items: type: string example: /opt/bamtools/bin/bamtools sbg:toolkitVersion: type: string example: 2.4.0 sbg:id: type: string example: RFranklin/my-project/bamtools-merge-2-4-0/0 sbg:license: type: string example: The MIT License sbg:revision: type: integer example: 0 default: 0 sbg:cmdPreview: type: string example: /opt/bamtools/bin/bamtools merge -in 1.bam -in 2.bam -out merged.bam -region chr1 sbg:modifiedOn: type: integer example: 1452181866 default: 0 id: type: string example: https://api.sbgenomics.com/RFranklin/my-project/bamtools-merge-2-4-0/0/raw/ class: type: string example: CommandLineTool sbg:modifiedBy: type: string example: RFranklin sbg:revisionsInfo: type: array items: type: object properties: sbg:modifiedBy: type: string example: RFranklin sbg:modifiedOn: type: integer example: 1452181866 default: 0 sbg:revision: type: integer example: 0 default: 0 sbg:toolkit: type: string example: BamTools deprecated: false x-readme: code-samples: - language: python code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='1e43fEXampLEa5523dfd14exAMPle3e5')\n\n# send GET request to SB API\napp = api.apps.get(id='RFranklin/my-project/bamtools-merge-2-4-0')\n\nprint(app.raw)" samples-languages: - python tags: - Apps /apps/{project_owner}/{project}/{app_short_name}/actions/copy: post: summary: Copy an app description: This call copies the specified app to the specified project. The app should be one in a project that you can access; this could be an app that has been uploaded to the Seven Bridges Platform by a project member, or a publicly available app that has been copied to the project. operationId: copy-an-app parameters: - name: X-SBG-Auth-Token in: header description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). required: true schema: type: string - name: fields in: query description: Selector specifying a subset of fields to include in the response. schema: type: array items: type: string - name: project_owner in: path description: If you are using [Enterprise](doc:about-the-enterprise-feature), use the name of the Division that owns the project in which the app is located; otherwise, enter the Platform username of the project owner. schema: type: string required: true - name: project in: path description: The name of the project in which the app is located. schema: type: string required: true - name: app_short_name in: path description: The short name of the app you are copying. Optionally, to copy a specific revision of the app, use the `{app_short_name}/{revision_number}` format, for example `rfranklin/my-project/bamtools-index-2-4-0/1` schema: type: string required: true requestBody: content: application/json: schema: type: object required: - project properties: project: type: string description: The name of the project you want to copy the app to. name: type: string description: The new name the app will have in the target project. If its name will not change, omit this key. strategy: type: string description: 'The method for copying the app `clone` : copy all revisions; get updates from the same app as the copied app (default) `direct`: copy latest revision; get updates from the copied app `clone_direct`: copy all revisions; get updates from the copied app `transient`: copy latest revision; get updates from the same app as the copied app' default: clone deprecated: false x-readme: code-samples: - language: python code: "from sevenbridges import Api, AppCopyStrategy\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='3210a98c1db9318fa9d9273156740f74')\n\napp = api.apps.get(id='RFranklin/my-project/bamtools-merge-2-4/0')\n\n# send POST request to SB API\nnew_app = app.copy(\n project='rfranklin/my-project',\n name='new app name',\n strategy=AppCopyStrategy.DIRECT\n)\n\nprint(new_app.name, new_app.id)" samples-languages: - python tags: - Apps /apps/{app_id}/{revision_number}/raw: post: summary: Add an app revision using raw CWL description: This call creates a new revision for an existing app. It adds a new CWL app description, and stores it as the named revision for the specified app. The revision number must not already exist and should follow the sequence of previously created revisions. operationId: add-an-app-revision-using-raw-cwl parameters: - name: X-SBG-Auth-Token in: header description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). required: true schema: type: string - name: fields in: query description: Selector specifying a subset of fields to include in the response. schema: type: array items: type: string - name: app_id in: path description: The ID for the app you are you want to upload. It should reference the project that you want the app to be added to, a short name for the app (containing no non-alphanumeric characters or spaces), and a revision number. schema: type: string required: true - name: Content-Type in: header description: 'Depending on the type of file you are uploading: * `application/json` for a JSON file * `application/yaml` for a YAML file' schema: type: string - name: revision_number in: path description: The number of the app revision you want to addd. schema: type: integer format: int32 required: true requestBody: content: application/json: schema: type: object properties: RAW_BODY: type: string description: The body of the request should be a CWL app description, saved as a JSON file. For a template of this description, try making the call to [get raw app information](ref:get-raw-cwl-for-an-app) about an app already in one of your projects. format: json deprecated: false x-readme: code-samples: - language: python code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='3210a98c1db9318fa9d9273156740f74')\n\n# send POST request to SB API\nnew_app_revision = api.apps.create_revision(\n id='RFranklin/my-project/my-app',\n revision=4,\n raw='... CWL JSON/YAML HERE ...'\n)\n\nprint(new_app_revision.name, new_app_revision.id, new_app_revision.revision)" samples-languages: - python tags: - Apps get: summary: Get raw CWL for an app revision description: 'This call returns information about the specified app revision, as raw CWL. The call differs from the call to [get details of an app revision](ref:get-details-of-an-app-revision) by returning a JSON object that is the CWL description of the app revision. The app should be in a project that you can access. This could be an app that has been uploaded to the Seven Bridges Platform by a project member, or a publicly available app that has been copied to the project.' operationId: get-raw-cwl-for-an-app-revision parameters: - name: app_id in: path description: The ID for the app you are querying. It can be obtained by making the call to [list all apps available to you](ref:list-all-apps-available-to-you). schema: type: string required: true - name: fields in: query description: Selector specifying a subset of fields to include in the response. schema: type: array items: type: string - name: X-SBG-Auth-Token in: header description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). required: true schema: type: string - name: revision_number in: path description: The integer that is the revision number of the app schema: type: integer format: int32 required: true responses: '200': description: '200' content: application/json: examples: Result: value: "{\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/rfranklin/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-2/0\",\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://api.sbgenomics.com/RFranklin/my-project/bamtools-merge-2/0/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}" schema: type: object properties: successCodes: type: array sbg:homepage: type: string example: https://github.com/pezmaster31/bamtools/wiki sbg:validationErrors: type: array sbg:sbgMaintained: type: boolean example: false default: true temporaryFailCodes: type: array requirements: type: array sbg:latestRevision: type: integer example: 0 default: 0 description: type: string example: BamTools Merge merges multiple BAM files into a single file. sbg:job: type: object properties: inputs: type: object properties: region: type: string example: chr1 input_bam_files: type: array items: type: object properties: path: type: string example: 1.bam allocatedResources: type: object properties: cpu: type: integer example: 1 default: 0 mem: type: integer example: 1000 default: 0 sbg:toolAuthor: type: string example: Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg hints: type: array items: type: object properties: dockerImageId: type: string example: f808163d4cd3 class: type: string example: DockerRequirement dockerPull: type: string example: images.sbgenomics.com/rfranklin/bamtools:2.4.0 sbg:copyOf: type: string example: djordje_klisic/public-apps-by-seven-bridges/bamtools-merge-2-4-0/0 sbg:createdOn: type: integer example: 1452181866 default: 0 arguments: type: array items: type: object properties: position: type: integer example: 1 default: 0 prefix: type: string example: -out separate: type: boolean example: true default: true valueFrom: type: string example: merged.bam outputs: type: array items: type: object properties: sbg:fileTypes: type: string example: BAM id: type: string example: '#output_bam_file' outputBinding: type: object properties: glob: type: string example: merged.bam sbg:metadata: type: object properties: {} sbg:inheritMetadataFrom: type: string example: '#input_bams' description: type: string example: Output BAM file. type: type: array items: type: string example: File label: type: string example: Output BAM file sbg:categories: type: array items: type: string example: SAM/BAM-Processing sbg:contributors: type: array items: type: string example: RFranklin sbg:links: type: array items: type: object properties: id: type: string example: https://github.com/pezmaster31/bamtools label: type: string example: Homepage stdout: type: string example: '' stdin: type: string example: '' sbg:project: type: string example: RFranklin/my-project inputs: type: array items: type: object properties: sbg:fileTypes: type: string example: BAM id: type: string example: '#input_bam_files' inputBinding: type: object properties: sbg:cmdInclude: type: boolean example: true default: true prefix: type: string example: -in separate: type: boolean example: true default: true itemSeparator: {} position: type: integer example: 0 default: 0 description: type: string example: The input BAM files. label: type: string example: Input BAM files type: type: array items: type: object properties: type: type: string example: array items: type: string example: File sbg:category: type: string example: Input & Output label: type: string example: BamTools Merge sbg:createdBy: type: string example: RFranklin baseCommand: type: array items: type: string example: /opt/bamtools/bin/bamtools sbg:toolkitVersion: type: string example: 2.4.0 sbg:id: type: string example: RFranklin/my-project/bamtools-merge-2/0 sbg:license: type: string example: The MIT License sbg:revision: type: integer example: 0 default: 0 sbg:cmdPreview: type: string example: /opt/bamtools/bin/bamtools merge -in 1.bam -in 2.bam -out merged.bam -region chr1 sbg:modifiedOn: type: integer example: 1452181866 default: 0 id: type: string example: https://api.sbgenomics.com/RFranklin/my-project/bamtools-merge-2/0/raw/ class: type: string example: CommandLineTool sbg:modifiedBy: type: string example: RFranklin sbg:revisionsInfo: type: array items: type: object properties: sbg:modifiedBy: type: string example: RFranklin sbg:modifiedOn: type: integer example: 1452181866 default: 0 sbg:revision: type: integer example: 0 default: 0 sbg:toolkit: type: string example: BamTools deprecated: false x-readme: code-samples: - language: python code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='3210a98c1db9318fa9d9273156740f74')\n\n# send GET request to SB API\napp = api.apps.get(id='RFranklin/my-project/bamtools-merge-2/0')\n\nprint(app.raw)" samples-languages: - python tags: - Apps x-readme: headers: - key: X-SBG-Auth-Token value: x-readme-fauxas: true