diff test-data/params.json @ 0:7c86ceaf523c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author iuc
date Tue, 20 Apr 2021 10:27:46 +0000
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/params.json	Tue Apr 20 10:27:46 2021 +0000
@@ -0,0 +1,280 @@
+{
+    "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": "sweaver@ucsd.edu",
+        "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"
+}