annotate test-data/params.json @ 24:efdd06f7f857 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e22821f51ae326b3696a9456cbc44f9982512a52"

{
    "filepath": "/home/sweaver/datamonkey/datamonkey-js-dev/app/models/../../uploads/msa/5446bc0d355080301f18a8c6.fasta",
    "msa": [
        {
            "rawsites": 1698,
            "nj": "(((((((TREESPARROW_HENAN_1_2004:0.0111333782927653,TREESPARROW_HENAN_3_2004:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.009062780987312381):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-0.001089936320307174,(GOOSE_HONGKONG_W355_97:-0.002798420018760263,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97:-8.034074555865944e-05):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452)",
            "goodtree": 0,
            "sequences": 21,
            "sites": 566,
            "partitions": 1,
            "analysis_type": "1",
            "gencodeid": 0,
            "datatype": 0,
            "_id": "5446bc0d355080301f18a8c7",
            "created": "2014-10-21T20:03:25.803Z",
            "sequence_info": [
                {
                    "seqindex": 0,
                    "name": "TREESPARROW_HENAN_1_2004",
                    "_id": "5446bc0d355080301f18a8c8"
                },
                {
                    "seqindex": 1,
                    "name": "HUMAN_VIETNAM_CL105_2005",
                    "_id": "5446bc0d355080301f18a8c9"
                },
                {
                    "seqindex": 2,
                    "name": "TREESPARROW_HENAN_4_2004",
                    "_id": "5446bc0d355080301f18a8ca"
                },
                {
                    "seqindex": 3,
                    "name": "CHICKEN_HEBEI_326_2005",
                    "_id": "5446bc0d355080301f18a8cb"
                },
                {
                    "seqindex": 4,
                    "name": "CHICKEN_HONGKONG_915_97",
                    "_id": "5446bc0d355080301f18a8cc"
                },
                {
                    "seqindex": 5,
                    "name": "HUMAN_VIETNAM_3062_2004",
                    "_id": "5446bc0d355080301f18a8cd"
                },
                {
                    "seqindex": 6,
                    "name": "GOOSE_HONGKONG_W355_97",
                    "_id": "5446bc0d355080301f18a8ce"
                },
                {
                    "seqindex": 7,
                    "name": "DUCK_HONGKONG_Y283_97",
                    "_id": "5446bc0d355080301f18a8cf"
                },
                {
                    "seqindex": 8,
                    "name": "DUCK_VIETNAM_376_2005",
                    "_id": "5446bc0d355080301f18a8d0"
                },
                {
                    "seqindex": 9,
                    "name": "MALLARD_VIETNAM_16_2003",
                    "_id": "5446bc0d355080301f18a8d1"
                },
                {
                    "seqindex": 10,
                    "name": "CHICKEN_CK_160_2005",
                    "_id": "5446bc0d355080301f18a8d2"
                },
                {
                    "seqindex": 11,
                    "name": "DUCK_GUANGZHOU_20_2005",
                    "_id": "5446bc0d355080301f18a8d3"
                },
                {
                    "seqindex": 12,
                    "name": "CK_HK_WF157_2003",
                    "_id": "5446bc0d355080301f18a8d4"
                },
                {
                    "seqindex": 13,
                    "name": "SWINE_ANHUI_1_2004",
                    "_id": "5446bc0d355080301f18a8d5"
                },
                {
                    "seqindex": 14,
                    "name": "DUCK_VIETNAM_272_2005",
                    "_id": "5446bc0d355080301f18a8d6"
                },
                {
                    "seqindex": 15,
                    "name": "HONGKONG_1_97_98",
                    "_id": "5446bc0d355080301f18a8d7"
                },
                {
                    "seqindex": 16,
                    "name": "GOOSE_SHANTOU_2216_2005",
                    "_id": "5446bc0d355080301f18a8d8"
                },
                {
                    "seqindex": 17,
                    "name": "TREESPARROW_HENAN_3_2004",
                    "_id": "5446bc0d355080301f18a8d9"
                },
                {
                    "seqindex": 18,
                    "name": "PEREGRINEFALCON_HK_D0028_2004",
                    "_id": "5446bc0d355080301f18a8da"
                },
                {
                    "seqindex": 19,
                    "name": "TREESPARROW_HENAN_2_2004",
                    "_id": "5446bc0d355080301f18a8db"
                },
                {
                    "seqindex": 20,
                    "name": "HONGKONG_1_538_97",
                    "_id": "5446bc0d355080301f18a8dc"
                }
            ],
            "partition_info": [
                {
                    "partition": 1,
                    "startcodon": 0,
                    "endcodon": 1697,
                    "span": 1698,
                    "_id": "5446bc0d355080301f18a8dd"
                }
            ]
        }
    ],
    "analysis": {
        "status": "In Queue",
        "tagged_nwk_tree": "(((((((TREESPARROW_HENAN_1_2004{FG}:0.0111333782927653,TREESPARROW_HENAN_3_2004{FG}:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.00906278098731238):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97,(GOOSE_HONGKONG_W355_97,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452)",
        "_id": "5446bc0d355080301f18a8c6",
        "__t": "Busted",
        "mail": "[e-mail]",
        "analysis_type": 1,
        "__v": 0,
        "msa": [
            {
                "partition_info": [
                    {
                        "_id": "5446bc0d355080301f18a8dd",
                        "span": 1698,
                        "endcodon": 1697,
                        "startcodon": 0,
                        "partition": 1
                    }
                ],
                "sequence_info": [
                    {
                        "_id": "5446bc0d355080301f18a8c8",
                        "name": "TREESPARROW_HENAN_1_2004",
                        "seqindex": 0
                    },
                    {
                        "_id": "5446bc0d355080301f18a8c9",
                        "name": "HUMAN_VIETNAM_CL105_2005",
                        "seqindex": 1
                    },
                    {
                        "_id": "5446bc0d355080301f18a8ca",
                        "name": "TREESPARROW_HENAN_4_2004",
                        "seqindex": 2
                    },
                    {
                        "_id": "5446bc0d355080301f18a8cb",
                        "name": "CHICKEN_HEBEI_326_2005",
                        "seqindex": 3
                    },
                    {
                        "_id": "5446bc0d355080301f18a8cc",
                        "name": "CHICKEN_HONGKONG_915_97",
                        "seqindex": 4
                    },
                    {
                        "_id": "5446bc0d355080301f18a8cd",
                        "name": "HUMAN_VIETNAM_3062_2004",
                        "seqindex": 5
                    },
                    {
                        "_id": "5446bc0d355080301f18a8ce",
                        "name": "GOOSE_HONGKONG_W355_97",
                        "seqindex": 6
                    },
                    {
                        "_id": "5446bc0d355080301f18a8cf",
                        "name": "DUCK_HONGKONG_Y283_97",
                        "seqindex": 7
                    },
                    {
                        "_id": "5446bc0d355080301f18a8d0",
                        "name": "DUCK_VIETNAM_376_2005",
                        "seqindex": 8
                    },
                    {
                        "_id": "5446bc0d355080301f18a8d1",
                        "name": "MALLARD_VIETNAM_16_2003",
                        "seqindex": 9
                    },
                    {
                        "_id": "5446bc0d355080301f18a8d2",
                        "name": "CHICKEN_CK_160_2005",
                        "seqindex": 10
                    },
                    {
                        "_id": "5446bc0d355080301f18a8d3",
                        "name": "DUCK_GUANGZHOU_20_2005",
                        "seqindex": 11
                    },
                    {
                        "_id": "5446bc0d355080301f18a8d4",
                        "name": "CK_HK_WF157_2003",
                        "seqindex": 12
                    },
                    {
                        "_id": "5446bc0d355080301f18a8d5",
                        "name": "SWINE_ANHUI_1_2004",
                        "seqindex": 13
                    },
                    {
                        "_id": "5446bc0d355080301f18a8d6",
                        "name": "DUCK_VIETNAM_272_2005",
                        "seqindex": 14
                    },
                    {
                        "_id": "5446bc0d355080301f18a8d7",
                        "name": "HONGKONG_1_97_98",
                        "seqindex": 15
                    },
                    {
                        "_id": "5446bc0d355080301f18a8d8",
                        "name": "GOOSE_SHANTOU_2216_2005",
                        "seqindex": 16
                    },
                    {
                        "_id": "5446bc0d355080301f18a8d9",
                        "name": "TREESPARROW_HENAN_3_2004",
                        "seqindex": 17
                    },
                    {
                        "_id": "5446bc0d355080301f18a8da",
                        "name": "PEREGRINEFALCON_HK_D0028_2004",
                        "seqindex": 18
                    },
                    {
                        "_id": "5446bc0d355080301f18a8db",
                        "name": "TREESPARROW_HENAN_2_2004",
                        "seqindex": 19
                    },
                    {
                        "_id": "5446bc0d355080301f18a8dc",
                        "name": "HONGKONG_1_538_97",
                        "seqindex": 20
                    }
                ],
                "created": "2014-10-21T20:03:25.803Z",
                "_id": "5446bc0d355080301f18a8c7",
                "datatype": 0,
                "gencodeid": 0,
                "partitions": 1,
                "sites": 566,
                "sequences": 21,
                "goodtree": 0,
                "nj": "(((((((TREESPARROW_HENAN_1_2004:0.0111333782927653,TREESPARROW_HENAN_3_2004:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.009062780987312381):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-0.001089936320307174,(GOOSE_HONGKONG_W355_97:-0.002798420018760263,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97:-8.034074555865944e-05):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452)",
                "rawsites": 1698
            }
        ],
        "created": "2014-10-21T20:03:25.798Z"
    },
    "status_stack": [
        "In Queue",
        "Running",
        "Completed"
    ],
    "type": "relax"
}