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Reference"},"githubsync":"","parentDoc":null,"user":"554340dfb7f4540d00fcef1d","updates":["56a6177fb28bc217005039bf"],"next":{"pages":[],"description":""},"createdAt":"2015-10-29T21:25:47.935Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","examples":{"codes":[]},"method":"get","auth":"required","params":[],"url":""},"isReference":true,"order":65,"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]","excerpt":"/apps/{app_id}/{revision_number}","slug":"get-a-specific-revision-of-an-app","type":"endpoint","title":"Get details of an app revision"}

GET STARTED

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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]