Mercurial > repos > iuc > hyphy_fade
diff test-data/params.json @ 0:6164d9298db9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
| author | iuc |
|---|---|
| date | Wed, 21 Aug 2019 12:25:26 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/params.json Wed Aug 21 12:25:26 2019 -0400 @@ -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" +}