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
planDisplayedName Unicode string data. Ex: “Hello World” n/a true false false false string
autoAnalyze Boolean data. Ex: True n/a false false false false boolean
endBarcodeKitName Unicode string data. Ex: “Hello World”   true false true false string
templatingKitBarcode Unicode string data. Ex: “Hello World” n/a true false false false string
preAnalysis Boolean data. Ex: True true false false true false boolean
applicationGroup A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related
mixedTypeRNA_hotSpotRegionBedFile Unicode string data. Ex: “Hello World”   false false true false string
mixedTypeRNA_targetRegionBedFile 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
categories Unicode string data. Ex: “Hello World”   true false false false string
planPGM Unicode string data. Ex: “Hello World” n/a true false false false string
libkit Unicode string data. Ex: “Hello World” n/a true false false 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
notes Unicode string data. Ex: “Hello World”   true false true false string
sequencekitname 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
storageHost Unicode string data. Ex: “Hello World” n/a true false false false string
expName Unicode string data. Ex: “Hello World”   false false true false string
cycles Integer data. Ex: 2673 n/a true false false false integer
isReverseRun Boolean data. Ex: True false false false true false boolean
storage_options Unicode string data. Ex: “Hello World” A false false false false string
chipType Unicode string data. Ex: “Hello World”   false false false false string
library Unicode string data. Ex: “Hello World”   true false true false string
reverselibrarykey Unicode string data. Ex: “Hello World”   false true false false string
sampleTubeLabel Unicode string data. Ex: “Hello World” n/a true false false false string
seqKitBarcode 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
isPlanGroup Boolean data. Ex: True false false false true false boolean
realign Boolean data. Ex: True n/a false false false false boolean
sampleGroupingName Unicode string data. Ex: “Hello World” n/a true true 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
bedfile Unicode string data. Ex: “Hello World”   false false true false string
applicationCategoryDisplayedName Unicode string data. Ex: “Hello World” n/a true true true false string
isReusable Boolean data. Ex: True false false false true false boolean
isDuplicateReads Boolean data. Ex: True n/a false false false false boolean
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
librarykitname Unicode string data. Ex: “Hello World”   true false true false string
sseBedFile Unicode string data. Ex: “Hello World”   false false true false string
adapter Unicode string data. Ex: “Hello World” n/a true false false false string
earlyDatFileDeletion Boolean data. Ex: True false false true false false boolean
parentPlan Unicode string data. Ex: “Hello World” None false false true false string
origin Unicode string data. Ex: “Hello World”   true false false false string
forward3primeadapter Unicode string data. Ex: “Hello World”   true false true false string
isCustom_kitSettings Boolean data. Ex: True false false false true false boolean
samplePrepKitName Unicode string data. Ex: “Hello World” n/a true false false false string
applicationGroupDisplayedName Unicode string data. Ex: “Hello World” n/a true true true false string
metaData Unicode string data. Ex: “Hello World” {} false false true false string
isFavorite Boolean data. Ex: True false false false true false boolean
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
planStatus Unicode string data. Ex: “Hello World”   false false true false string
templatingKitName Unicode string data. Ex: “Hello World” n/a true false false false string
runType Unicode string data. Ex: “Hello World” GENS false false false false string
username 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
sampleDisplayedName Unicode string data. Ex: “Hello World”   true false true false string
controlSequencekitname 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
mixedTypeRNA_reference Unicode string data. Ex: “Hello World”   true false true false string
childPlans A list of data. Ex: [‘abc’, 26.73, 8] [] false false false false list
pairedEndLibraryAdapterName Unicode string data. Ex: “Hello World” n/a true false false false string
runMode Unicode string data. Ex: “Hello World”   false false true false string
irworkflow Unicode string data. Ex: “Hello World”   false false true false string
planExecuted Boolean data. Ex: True false false false true false boolean
project Unicode string data. Ex: “Hello World” n/a false true true false string
usePostBeadfind Boolean data. Ex: True true false false true false boolean
libraryReadLength Integer data. Ex: 2673 0 false false false false integer
runname Unicode string data. Ex: “Hello World” n/a true false false false string
chefInfo A dictionary of data. Ex: {‘price’: 26.73, ‘name’: ‘Daniel’} {} false false false false dict
planGUID 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
planShortID 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
planExecutedDate A date & time as a string. Ex: “2010-11-10T03:07:43” n/a true false false false datetime
reverse_primer Unicode string data. Ex: “Hello World” n/a true false false false string
id Integer data. Ex: 2673   false false true true integer
barcodedSamples Unicode string data. Ex: “Hello World”   true false true false string
regionfile Unicode string data. Ex: “Hello World”   false false true false string
selectedPlugins Unicode string data. Ex: “Hello World”   true false true false string
isSystemDefault Boolean data. Ex: True false false false true false boolean
autoName Unicode string data. Ex: “Hello World” n/a true false false false string
libraryKey Unicode string data. Ex: “Hello World”   false false true false string
flows Integer data. Ex: 2673 0 false false false false integer
date A date & time as a string. Ex: “2010-11-10T03:07:43” n/a true false false false datetime
isSystem Boolean data. Ex: True false false false true false boolean
variantfrequency Unicode string data. Ex: “Hello World”   false true false false string
sampleSetDisplayedName Unicode string data. Ex: “Hello World” n/a true true true false string
flowsInOrder Unicode string data. Ex: “Hello World”   true false true false string
libraryPrepType Unicode string data. Ex: “Hello World”   true true 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
chipBarcode Unicode string data. Ex: “Hello World”   false false false false string
usePreBeadfind Boolean data. Ex: True true false false true false boolean
resource_uri Unicode string data. Ex: “Hello World” n/a false true false false string
libraryPrepTypeDisplayedName Unicode string data. Ex: “Hello World”   true true true false string
reverse3primeadapter Unicode string data. Ex: “Hello World”   false true false false string

Example Response

{
    "meta": {
        "previous": null,
        "total_count": 37,
        "offset": 0,
        "limit": 1,
        "next": "/rundb/api/v1/onetouchplantemplate/?offset=1&limit=1&format=json"
    },
    "objects": [
        {
            "planDisplayedName": "PGx Research Panel",
            "autoAnalyze": true,
            "endBarcodeKitName": "",
            "templatingKitBarcode": null,
            "preAnalysis": true,
            "thumbnailanalysisargs": "",
            "applicationGroup": "/rundb/api/v1/applicationgroup/6/",
            "mixedTypeRNA_hotSpotRegionBedFile": null,
            "mixedTypeRNA_targetRegionBedFile": null,
            "platform": "PGM",
            "categories": "",
            "planPGM": null,
            "prebasecallerargs": "",
            "alignmentargs": "",
            "thumbnailbasecallerargs": "",
            "libkit": null,
            "projects": [],
            "notes": "",
            "sequencekitname": "IonPGMHiQ",
            "base_recalibration_mode": "standard_recal",
            "storageHost": null,
            "expName": "",
            "thumbnailionstatsargs": "",
            "cycles": null,
            "isReverseRun": false,
            "storage_options": "A",
            "thumbnailalignmentargs": "",
            "chipType": "",
            "library": "hg19",
            "runMode": "",
            "sampleTubeLabel": null,
            "seqKitBarcode": null,
            "barcodeId": "IonXpress",
            "isPlanGroup": false,
            "realign": false,
            "sampleGroupingName": "",
            "experiment": "/rundb/api/v1/experiment/122/",
            "bedfile": "/results/uploads/BED/5/hg19/unmerged/detail/PGx.20150728.designed.bed",
            "applicationCategoryDisplayedName": "",
            "isReusable": true,
            "isDuplicateReads": false,
            "sampleSets": [],
            "thumbnailbeadfindargs": "",
            "librarykitname": "Ion AmpliSeq 2.0 Library Kit",
            "sseBedFile": "",
            "adapter": null,
            "basecallerargs": "",
            "earlyDatFileDeletion": false,
            "parentPlan": null,
            "origin": "ampliseq.com|5.8.0",
            "forward3primeadapter": "ATCACCGACTGCCCATAGAGAGGCTGAGAC",
            "planStatus": "planned",
            "isCustom_kitSettings": false,
            "samplePrepKitName": null,
            "applicationGroupDisplayedName": "Pharmacogenomics",
            "metaData": {},
            "isFavorite": false,
            "qcValues": [],
            "analysisargs": "",
            "thumbnailcalibrateargs": "",
            "templatingKitName": "Ion PGM Hi-Q OT2 Kit - 200",
            "runType": "AMPS",
            "username": "ionuser",
            "planShortID": "OO9C5",
            "sampleDisplayedName": "",
            "prethumbnailbasecallerargs": "",
            "controlSequencekitname": "",
            "tfKey": "ATCG",
            "mixedTypeRNA_reference": null,
            "childPlans": [],
            "pairedEndLibraryAdapterName": "",
            "reverselibrarykey": "",
            "irworkflow": "",
            "planExecuted": false,
            "project": "",
            "usePostBeadfind": true,
            "libraryReadLength": 0,
            "runname": null,
            "chefInfo": {},
            "planGUID": "7489c32d-d3ed-4cc1-a7a2-e59b819ea395",
            "ionstatsargs": "",
            "samplePrepProtocol": "",
            "sample": "",
            "planExecutedDate": null,
            "reverse_primer": null,
            "id": 130,
            "barcodedSamples": {},
            "custom_args": false,
            "regionfile": "/results/uploads/BED/15/hg19/unmerged/detail/PGx.20180131.hotspots.bed",
            "selectedPlugins": {
                "variantCaller": {
                    "features": [],
                    "ampliSeqVariantCallerConfig": {
                        "torrent_variant_caller": {
                            "snp_min_allele_freq": "0.1",
                            "snp_strand_bias": "0.95",
                            "hotspot_min_coverage": 6,
                            "hotspot_min_cov_each_strand": 3,
                            "position_bias": "0.75",
                            "hotspot_min_allele_freq": "0.1",
                            "snp_min_variant_score": 10,
                            "mnp_min_variant_score": 10,
                            "hotspot_strand_bias": "0.98",
                            "hp_max_length": 10,
                            "filter_insertion_predictions": "0.4",
                            "indel_min_variant_score": 10,
                            "indel_min_coverage": 15,
                            "heavy_tailed": 3,
                            "outlier_probability": "0.01",
                            "position_bias_ref_fraction": "0.05",
                            "indel_strand_bias_pval": 1,
                            "data_quality_stringency": "6.5",
                            "snp_min_cov_each_strand": 0,
                            "indel_as_hpindel": 0,
                            "snp_strand_bias_pval": 1,
                            "mnp_strand_bias": "0.95",
                            "mnp_strand_bias_pval": 1,
                            "process_input_positions_only": 1,
                            "hotspot_strand_bias_pval": "0.01",
                            "hotspot_min_variant_score": 4,
                            "do_mnp_realignment": 1,
                            "indel_strand_bias": "0.85",
                            "downsample_to_coverage": 4000,
                            "filter_unusual_predictions": "0.7",
                            "indel_min_allele_freq": "0.1",
                            "mnp_min_allele_freq": "0.1",
                            "mnp_min_coverage": 6,
                            "do_snp_realignment": 1,
                            "mnp_min_cov_each_strand": 0,
                            "snp_min_coverage": 6,
                            "prediction_precision": 1,
                            "indel_min_cov_each_strand": 5,
                            "filter_deletion_predictions": "0.2",
                            "realignment_threshold": 1,
                            "suppress_recalibration": 0,
                            "position_bias_pval": "0.05",
                            "use_position_bias": 0
                        },
                        "meta": {
                            "repository_id": "",
                            "ts_version": "5.0",
                            "name": "PGx - Germ Line - Customized parameters",
                            "user_selections": {
                                "chip": "pgm",
                                "frequency": "germline",
                                "library": "ampliseq",
                                "panel": "/rundb/api/v1/contentupload/15/"
                            },
                            "tooltip": "Panel-optimized parameters from AmpliSeq.com",
                            "tvcargs": "tvc --use-input-allele-only",
                            "built_in": true,
                            "configuration": "PGx_germline_low_stringency",
                            "compatibility": {
                                "panel": "/rundb/api/v1/contentupload/15/"
                            }
                        },
                        "long_indel_assembler": {
                            "min_indel_size": 4,
                            "short_suffix_match": 5,
                            "output_mnv": 0,
                            "min_var_count": 5,
                            "min_var_freq": "0.15",
                            "kmer_len": 19,
                            "max_hp_length": 8,
                            "relative_strand_bias": "0.8"
                        },
                        "freebayes": {
                            "gen_min_coverage": 10,
                            "allow_mnps": 1,
                            "allow_complex": 0,
                            "read_snp_limit": 10,
                            "read_max_mismatch_fraction": 1,
                            "allow_indels": 1,
                            "min_mapping_qv": 4,
                            "gen_min_alt_allele_freq": "0.15",
                            "allow_snps": 1,
                            "gen_min_indel_alt_allele_freq": "0.15"
                        }
                    },
                    "userInput": {
                        "torrent_variant_caller": {
                            "snp_min_allele_freq": "0.1",
                            "snp_strand_bias": "0.95",
                            "hotspot_min_coverage": 6,
                            "hotspot_min_cov_each_strand": 3,
                            "position_bias": "0.75",
                            "hotspot_min_allele_freq": "0.1",
                            "snp_min_variant_score": 10,
                            "mnp_min_variant_score": 10,
                            "hotspot_strand_bias": "0.98",
                            "hp_max_length": 10,
                            "filter_insertion_predictions": "0.4",
                            "indel_min_variant_score": 10,
                            "indel_min_coverage": 15,
                            "heavy_tailed": 3,
                            "outlier_probability": "0.01",
                            "position_bias_ref_fraction": "0.05",
                            "indel_strand_bias_pval": 1,
                            "data_quality_stringency": "6.5",
                            "snp_min_cov_each_strand": 0,
                            "indel_as_hpindel": 0,
                            "snp_strand_bias_pval": 1,
                            "mnp_strand_bias": "0.95",
                            "mnp_strand_bias_pval": 1,
                            "process_input_positions_only": 1,
                            "hotspot_strand_bias_pval": "0.01",
                            "hotspot_min_variant_score": 4,
                            "do_mnp_realignment": 1,
                            "indel_strand_bias": "0.85",
                            "downsample_to_coverage": 4000,
                            "filter_unusual_predictions": "0.7",
                            "indel_min_allele_freq": "0.1",
                            "mnp_min_allele_freq": "0.1",
                            "mnp_min_coverage": 6,
                            "do_snp_realignment": 1,
                            "mnp_min_cov_each_strand": 0,
                            "snp_min_coverage": 6,
                            "prediction_precision": 1,
                            "indel_min_cov_each_strand": 5,
                            "filter_deletion_predictions": "0.2",
                            "realignment_threshold": 1,
                            "suppress_recalibration": 0,
                            "position_bias_pval": "0.05",
                            "use_position_bias": 0
                        },
                        "meta": {
                            "repository_id": "",
                            "ts_version": "5.0",
                            "name": "PGx - Germ Line - Customized parameters",
                            "user_selections": {
                                "chip": "pgm",
                                "frequency": "germline",
                                "library": "ampliseq",
                                "panel": "/rundb/api/v1/contentupload/15/"
                            },
                            "tooltip": "Panel-optimized parameters from AmpliSeq.com",
                            "tvcargs": "tvc --use-input-allele-only",
                            "built_in": true,
                            "configuration": "PGx_germline_low_stringency",
                            "compatibility": {
                                "panel": "/rundb/api/v1/contentupload/15/"
                            }
                        },
                        "long_indel_assembler": {
                            "min_indel_size": 4,
                            "short_suffix_match": 5,
                            "output_mnv": 0,
                            "min_var_count": 5,
                            "min_var_freq": "0.15",
                            "kmer_len": 19,
                            "max_hp_length": 8,
                            "relative_strand_bias": "0.8"
                        },
                        "freebayes": {
                            "gen_min_coverage": 10,
                            "allow_mnps": 1,
                            "allow_complex": 0,
                            "read_snp_limit": 10,
                            "read_max_mismatch_fraction": 1,
                            "allow_indels": 1,
                            "min_mapping_qv": 4,
                            "gen_min_alt_allele_freq": "0.15",
                            "allow_snps": 1,
                            "gen_min_indel_alt_allele_freq": "0.15"
                        }
                    },
                    "version": "5.8.0.19",
                    "id": 36,
                    "name": "variantCaller"
                }
            },
            "beadfindargs": "",
            "isSystemDefault": false,
            "autoName": null,
            "libraryKey": "TCAG",
            "flows": 500,
            "date": "2018-02-08T19:41:44.000698+00:00",
            "isSystem": false,
            "variantfrequency": "",
            "planName": "PGx_Research_Panel",
            "calibrateargs": "",
            "flowsInOrder": "",
            "libraryPrepType": "",
            "sampleGrouping": null,
            "chipBarcode": "",
            "sampleSetDisplayedName": "",
            "usePreBeadfind": true,
            "resource_uri": "/rundb/api/v1/onetouchplantemplate/130/",
            "libraryPrepTypeDisplayedName": "",
            "reverse3primeadapter": ""
        }
    ]
}

Allowed list HTTP methods

  • GET
  • POST
  • PUT
  • DELETE
  • PATCH

Allowed detail HTTP methods

  • GET
  • POST
  • PUT
  • DELETE
  • PATCH