Onetouch Plan Template Resource¶
Resource URL
http://mytorrentserver/rundb/api/v1/onetouchplantemplate/Schema URL
http://mytorrentserver/rundb/api/v1/onetouchplantemplate/schema/Resource Fields¶
| field | help text | default | nullable | readonly | blank | unique | type |
|---|---|---|---|---|---|---|---|
| adapter | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| applicationCategoryDisplayedName | Unicode string data. Ex: “Hello World” | n/a | true | true | true | false | string |
| applicationGroup | A single related resource. Can be either a URI or set of nested resource data. | n/a | true | false | true | false | related |
| applicationGroupDisplayedName | Unicode string data. Ex: “Hello World” | n/a | true | true | true | false | string |
| autoAnalyze | Boolean data. Ex: True | n/a | false | false | false | false | boolean |
| autoName | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| barcodeId | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| barcodedSamples | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| base_recalibration_mode | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| bedfile | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| categories | Unicode string data. Ex: “Hello World” | true | false | false | false | string | |
| chefInfo | A dictionary of data. Ex: {‘price’: 26.73, ‘name’: ‘Daniel’} | {} | false | false | false | false | dict |
| childPlans | A list of data. Ex: [‘abc’, 26.73, 8] | [] | false | false | false | false | list |
| chipBarcode | Unicode string data. Ex: “Hello World” | false | false | false | false | string | |
| chipType | Unicode string data. Ex: “Hello World” | false | false | false | false | string | |
| controlSequencekitname | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| cycles | Integer data. Ex: 2673 | n/a | true | false | false | false | integer |
| date | A date & time as a string. Ex: “2010-11-10T03:07:43” | n/a | true | false | false | false | datetime |
| earlyDatFileDeletion | Boolean data. Ex: True | false | false | true | false | false | boolean |
| endBarcodeKitName | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| expName | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| experiment | A single related resource. Can be either a URI or set of nested resource data. | n/a | true | false | true | false | related |
| flows | Integer data. Ex: 2673 | 0 | false | false | false | false | integer |
| flowsInOrder | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| forward3primeadapter | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| id | Integer data. Ex: 2673 | false | false | true | true | integer | |
| irworkflow | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| isCustom_kitSettings | Boolean data. Ex: True | false | false | false | true | false | boolean |
| isDuplicateReads | Boolean data. Ex: True | n/a | false | false | false | false | boolean |
| isFavorite | Boolean data. Ex: True | false | false | false | true | false | boolean |
| isPlanGroup | Boolean data. Ex: True | false | false | false | true | false | boolean |
| isReusable | Boolean data. Ex: True | false | false | false | true | false | boolean |
| isReverseRun | Boolean data. Ex: True | false | false | false | true | false | boolean |
| isSystem | Boolean data. Ex: True | false | false | false | true | false | boolean |
| isSystemDefault | Boolean data. Ex: True | false | false | false | true | false | boolean |
| libkit | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| library | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| libraryKey | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| libraryPrepType | Unicode string data. Ex: “Hello World” | true | true | true | false | string | |
| libraryPrepTypeDisplayedName | Unicode string data. Ex: “Hello World” | true | true | true | false | string | |
| libraryReadLength | Integer data. Ex: 2673 | 0 | false | false | false | false | integer |
| librarykitname | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| metaData | Unicode string data. Ex: “Hello World” | {} | false | false | true | false | string |
| mixedTypeRNA_hotSpotRegionBedFile | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| mixedTypeRNA_reference | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| mixedTypeRNA_targetRegionBedFile | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| notes | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| origin | Unicode string data. Ex: “Hello World” | true | false | false | false | string | |
| pairedEndLibraryAdapterName | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| parentPlan | Unicode string data. Ex: “Hello World” | None | false | false | true | false | string |
| planDisplayedName | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| planExecuted | Boolean data. Ex: True | false | false | false | true | false | boolean |
| planExecutedDate | A date & time as a string. Ex: “2010-11-10T03:07:43” | n/a | true | false | false | false | datetime |
| planGUID | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| planName | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| planPGM | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| planShortID | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| planStatus | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| platform | Unicode string data. Ex: “Hello World” | n/a | true | false | true | false | string |
| preAnalysis | Boolean data. Ex: True | true | false | false | true | false | boolean |
| project | Unicode string data. Ex: “Hello World” | n/a | false | true | true | false | string |
| projects | Many related resources. Can be either a list of URIs or list of individually nested resource data. | n/a | true | false | true | false | related |
| qcValues | Many related resources. Can be either a list of URIs or list of individually nested resource data. | n/a | true | false | true | false | related |
| realign | Boolean data. Ex: True | n/a | false | false | false | false | boolean |
| regionfile | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| resource_uri | Unicode string data. Ex: “Hello World” | n/a | false | true | false | false | string |
| reverse3primeadapter | Unicode string data. Ex: “Hello World” | false | true | false | false | string | |
| reverse_primer | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| reverselibrarykey | Unicode string data. Ex: “Hello World” | false | true | false | false | string | |
| runMode | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| runType | Unicode string data. Ex: “Hello World” | GENS | false | false | false | false | string |
| runname | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| sample | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| sampleDisplayedName | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| sampleGrouping | A single related resource. Can be either a URI or set of nested resource data. | n/a | true | false | true | false | related |
| sampleGroupingName | Unicode string data. Ex: “Hello World” | n/a | true | true | true | false | string |
| samplePrepKitName | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| samplePrepProtocol | Unicode string data. Ex: “Hello World” | true | false | false | false | string | |
| sampleSetDisplayedName | Unicode string data. Ex: “Hello World” | n/a | true | true | true | false | string |
| sampleSets | Many related resources. Can be either a list of URIs or list of individually nested resource data. | n/a | true | false | true | false | related |
| sampleTubeLabel | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| selectedPlugins | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| seqKitBarcode | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| sequencekitname | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| sseBedFile | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| storageHost | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| storage_options | Unicode string data. Ex: “Hello World” | A | false | false | false | false | string |
| templatingKitBarcode | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| templatingKitName | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| tfKey | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| usePostBeadfind | Boolean data. Ex: True | true | false | false | true | false | boolean |
| usePreBeadfind | Boolean data. Ex: True | true | false | false | true | false | boolean |
| username | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| variantfrequency | Unicode string data. Ex: “Hello World” | false | true | false | false | string |
Example Response¶
{
"meta": {
"limit": 1,
"next": "/rundb/api/v1/onetouchplantemplate/?offset=1&limit=1&format=json",
"offset": 0,
"previous": null,
"total_count": 36
},
"objects": [
{
"adapter": null,
"alignmentargs": "",
"analysisargs": "",
"applicationCategoryDisplayedName": "",
"applicationGroup": "/rundb/api/v1/applicationgroup/6/",
"applicationGroupDisplayedName": "Pharmacogenomics",
"autoAnalyze": true,
"autoName": null,
"barcodeId": "IonXpress",
"barcodedSamples": {},
"base_recalibration_mode": "standard_recal",
"basecallerargs": "",
"beadfindargs": "",
"bedfile": "/results/uploads/BED/5/hg19/unmerged/detail/PGx.20150728.designed.bed",
"calibrateargs": "",
"categories": "",
"chefInfo": {},
"childPlans": [],
"chipBarcode": "",
"chipType": "",
"controlSequencekitname": "",
"custom_args": false,
"cycles": null,
"date": "2018-02-08T19:41:44.000698+00:00",
"earlyDatFileDeletion": false,
"endBarcodeKitName": "",
"expName": "",
"experiment": "/rundb/api/v1/experiment/122/",
"flows": 500,
"flowsInOrder": "",
"forward3primeadapter": "ATCACCGACTGCCCATAGAGAGGCTGAGAC",
"id": 130,
"ionstatsargs": "",
"irworkflow": "",
"isCustom_kitSettings": false,
"isDuplicateReads": false,
"isFavorite": false,
"isPlanGroup": false,
"isReusable": true,
"isReverseRun": false,
"isSystem": false,
"isSystemDefault": false,
"libkit": null,
"library": "hg19",
"libraryKey": "TCAG",
"libraryPrepType": "",
"libraryPrepTypeDisplayedName": "",
"libraryReadLength": 0,
"librarykitname": "Ion AmpliSeq 2.0 Library Kit",
"metaData": {},
"mixedTypeRNA_hotSpotRegionBedFile": null,
"mixedTypeRNA_reference": null,
"mixedTypeRNA_targetRegionBedFile": null,
"notes": "",
"origin": "ampliseq.com|5.8.0",
"pairedEndLibraryAdapterName": "",
"parentPlan": null,
"planDisplayedName": "PGx Research Panel",
"planExecuted": false,
"planExecutedDate": null,
"planGUID": "7489c32d-d3ed-4cc1-a7a2-e59b819ea395",
"planName": "PGx_Research_Panel",
"planPGM": null,
"planShortID": "OO9C5",
"planStatus": "planned",
"platform": "PGM",
"preAnalysis": true,
"prebasecallerargs": "",
"prethumbnailbasecallerargs": "",
"project": "",
"projects": [],
"qcValues": [],
"realign": false,
"regionfile": "/results/uploads/BED/15/hg19/unmerged/detail/PGx.20180131.hotspots.bed",
"resource_uri": "/rundb/api/v1/onetouchplantemplate/130/",
"reverse3primeadapter": "",
"reverse_primer": null,
"reverselibrarykey": "",
"runMode": "",
"runType": "AMPS",
"runname": null,
"sample": "",
"sampleDisplayedName": "",
"sampleGrouping": null,
"sampleGroupingName": "",
"samplePrepKitName": null,
"samplePrepProtocol": "",
"sampleSetDisplayedName": "",
"sampleSets": [],
"sampleTubeLabel": null,
"selectedPlugins": {
"variantCaller": {
"ampliSeqVariantCallerConfig": {
"freebayes": {
"allow_complex": 0,
"allow_indels": 1,
"allow_mnps": 1,
"allow_snps": 1,
"gen_min_alt_allele_freq": "0.15",
"gen_min_coverage": 10,
"gen_min_indel_alt_allele_freq": "0.15",
"min_mapping_qv": 4,
"read_max_mismatch_fraction": 1,
"read_snp_limit": 10
},
"long_indel_assembler": {
"kmer_len": 19,
"max_hp_length": 8,
"min_indel_size": 4,
"min_var_count": 5,
"min_var_freq": "0.15",
"output_mnv": 0,
"relative_strand_bias": "0.8",
"short_suffix_match": 5
},
"meta": {
"built_in": true,
"compatibility": {
"panel": "/rundb/api/v1/contentupload/15/"
},
"configuration": "PGx_germline_low_stringency",
"name": "PGx - Germ Line - Customized parameters",
"repository_id": "",
"tooltip": "Panel-optimized parameters from AmpliSeq.com",
"ts_version": "5.0",
"tvcargs": "tvc --use-input-allele-only",
"user_selections": {
"chip": "pgm",
"frequency": "germline",
"library": "ampliseq",
"panel": "/rundb/api/v1/contentupload/15/"
}
},
"torrent_variant_caller": {
"data_quality_stringency": "6.5",
"do_mnp_realignment": 1,
"do_snp_realignment": 1,
"downsample_to_coverage": 4000,
"filter_deletion_predictions": "0.2",
"filter_insertion_predictions": "0.4",
"filter_unusual_predictions": "0.7",
"heavy_tailed": 3,
"hotspot_min_allele_freq": "0.1",
"hotspot_min_cov_each_strand": 3,
"hotspot_min_coverage": 6,
"hotspot_min_variant_score": 4,
"hotspot_strand_bias": "0.98",
"hotspot_strand_bias_pval": "0.01",
"hp_max_length": 10,
"indel_as_hpindel": 0,
"indel_min_allele_freq": "0.1",
"indel_min_cov_each_strand": 5,
"indel_min_coverage": 15,
"indel_min_variant_score": 10,
"indel_strand_bias": "0.85",
"indel_strand_bias_pval": 1,
"mnp_min_allele_freq": "0.1",
"mnp_min_cov_each_strand": 0,
"mnp_min_coverage": 6,
"mnp_min_variant_score": 10,
"mnp_strand_bias": "0.95",
"mnp_strand_bias_pval": 1,
"outlier_probability": "0.01",
"position_bias": "0.75",
"position_bias_pval": "0.05",
"position_bias_ref_fraction": "0.05",
"prediction_precision": 1,
"process_input_positions_only": 1,
"realignment_threshold": 1,
"snp_min_allele_freq": "0.1",
"snp_min_cov_each_strand": 0,
"snp_min_coverage": 6,
"snp_min_variant_score": 10,
"snp_strand_bias": "0.95",
"snp_strand_bias_pval": 1,
"suppress_recalibration": 0,
"use_position_bias": 0
}
},
"features": [],
"id": 36,
"name": "variantCaller",
"userInput": {
"freebayes": {
"allow_complex": 0,
"allow_indels": 1,
"allow_mnps": 1,
"allow_snps": 1,
"gen_min_alt_allele_freq": "0.15",
"gen_min_coverage": 10,
"gen_min_indel_alt_allele_freq": "0.15",
"min_mapping_qv": 4,
"read_max_mismatch_fraction": 1,
"read_snp_limit": 10
},
"long_indel_assembler": {
"kmer_len": 19,
"max_hp_length": 8,
"min_indel_size": 4,
"min_var_count": 5,
"min_var_freq": "0.15",
"output_mnv": 0,
"relative_strand_bias": "0.8",
"short_suffix_match": 5
},
"meta": {
"built_in": true,
"compatibility": {
"panel": "/rundb/api/v1/contentupload/15/"
},
"configuration": "PGx_germline_low_stringency",
"name": "PGx - Germ Line - Customized parameters",
"repository_id": "",
"tooltip": "Panel-optimized parameters from AmpliSeq.com",
"ts_version": "5.0",
"tvcargs": "tvc --use-input-allele-only",
"user_selections": {
"chip": "pgm",
"frequency": "germline",
"library": "ampliseq",
"panel": "/rundb/api/v1/contentupload/15/"
}
},
"torrent_variant_caller": {
"data_quality_stringency": "6.5",
"do_mnp_realignment": 1,
"do_snp_realignment": 1,
"downsample_to_coverage": 4000,
"filter_deletion_predictions": "0.2",
"filter_insertion_predictions": "0.4",
"filter_unusual_predictions": "0.7",
"heavy_tailed": 3,
"hotspot_min_allele_freq": "0.1",
"hotspot_min_cov_each_strand": 3,
"hotspot_min_coverage": 6,
"hotspot_min_variant_score": 4,
"hotspot_strand_bias": "0.98",
"hotspot_strand_bias_pval": "0.01",
"hp_max_length": 10,
"indel_as_hpindel": 0,
"indel_min_allele_freq": "0.1",
"indel_min_cov_each_strand": 5,
"indel_min_coverage": 15,
"indel_min_variant_score": 10,
"indel_strand_bias": "0.85",
"indel_strand_bias_pval": 1,
"mnp_min_allele_freq": "0.1",
"mnp_min_cov_each_strand": 0,
"mnp_min_coverage": 6,
"mnp_min_variant_score": 10,
"mnp_strand_bias": "0.95",
"mnp_strand_bias_pval": 1,
"outlier_probability": "0.01",
"position_bias": "0.75",
"position_bias_pval": "0.05",
"position_bias_ref_fraction": "0.05",
"prediction_precision": 1,
"process_input_positions_only": 1,
"realignment_threshold": 1,
"snp_min_allele_freq": "0.1",
"snp_min_cov_each_strand": 0,
"snp_min_coverage": 6,
"snp_min_variant_score": 10,
"snp_strand_bias": "0.95",
"snp_strand_bias_pval": 1,
"suppress_recalibration": 0,
"use_position_bias": 0
}
},
"version": "5.8.0.19"
}
},
"seqKitBarcode": null,
"sequencekitname": "IonPGMHiQ",
"sseBedFile": "",
"storageHost": null,
"storage_options": "A",
"templatingKitBarcode": null,
"templatingKitName": "Ion PGM Hi-Q OT2 Kit - 200",
"tfKey": "ATCG",
"thumbnailalignmentargs": "",
"thumbnailanalysisargs": "",
"thumbnailbasecallerargs": "",
"thumbnailbeadfindargs": "",
"thumbnailcalibrateargs": "",
"thumbnailionstatsargs": "",
"usePostBeadfind": true,
"usePreBeadfind": true,
"username": "ionuser",
"variantfrequency": ""
}
]
}
Allowed list HTTP methods¶
- GET
- POST
- PUT
- DELETE
- PATCH
Allowed detail HTTP methods¶
- GET
- POST
- PUT
- DELETE
- PATCH