[hg] galaxy 1725: Adding modified hyphy functional test output f... - galaxy-dev

28 Jan 2009

details:   http://www.bx.psu.edu/hg/galaxy/rev/7411b119a3c9
changeset: 1725:7411b119a3c9
user:      guru
date:      Tue Jan 27 16:17:22 2009 -0500
description:
Adding modified hyphy functional test output files, which have changed as the new version of HYPHY is installed on Galaxy. Also changing version numbers for all the affected tools.
8 file(s) affected in this change:
test-data/branchlength_out.dat
test-data/dnds_out.tabular
test-data/nj_tree_newick_out.dat
tools/hyphy/hyphy_branch_lengths_wrapper.xml
tools/hyphy/hyphy_dnds_wrapper.xml
tools/hyphy/hyphy_nj_tree_wrapper.xml
tools/regVariation/microsats_mutability.xml
tools/stats/grouping.xml
diffs (140 lines):
diff -r 546e2d835e16 -r 7411b119a3c9 test-data/branchlength_out.dat

--- a/test-data/branchlength_out.dat	Tue Jan 27 14:48:51 2009 -0500
+++ b/test-data/branchlength_out.dat	Tue Jan 27 16:17:22 2009 -0500
@@ -9,25 +9,25 @@
 1	Total Tree	3.45679e-30	2.60643e-34	2.54701e-20
 2	hg17.chr7(+):26907310-26907326|hg17_1	1.48148e-31	0	0.0915385
 2	panTro1.chr6(+):28037328-28037344|panTro1_1	1.48148e-31	0	0.0915385
-2	Node1	1.48148e-31	0	0.0915385
-2	mm5.chr6(+):52104031-52104047|mm5_1	1.48148e-31	0	0.0915385
-2	rn3.chr4(+):80734404-80734420|rn3_1	0.0435496	0.00241411	0.219651
+2	Node1	6.69055e-19	0	0.0915385
+2	mm5.chr6(+):52104031-52104047|mm5_1	5.00368e-19	0	0.0915385
+2	rn3.chr4(+):80734404-80734420|rn3_1	0.0435526	0.00241411	0.219651
 2	Node4	1.48148e-31	0	0.0915385
-2	canFam1.chr14(+):42826418-42826434|canFam1_1	1.48148e-31	0	0.0915385
-2	Total Tree	0.0435496	0.00241411	0.219655
+2	canFam1.chr14(+):42826418-42826434|canFam1_1	1.76058e-19	0	0.0915385
+2	Total Tree	0.0435526	0.00241411	0.219651
 3	hg17.chr7(+):26907326-26907338|hg17_2	1.70011e-31	0	0.143452
 3	panTro1.chr6(+):28037344-28037356|panTro1_2	1.70011e-31	0	0.143452
-3	Node1	1.70011e-31	0	0.143452
+3	Node1	1.27931e-17	0	0.143452
 3	mm5.chr6(+):52104047-52104059|mm5_2	1.70011e-31	0	0.143452
 3	rn3.chr4(+):80734420-80734432|rn3_2	0	0	0.143452
-3	Node4	1.70011e-31	0	0.143452
+3	Node4	0	0	0.143452
 3	canFam1.chr14(+):42826434-42826446|canFam1_2	1.70011e-31	0	0.143452
-3	Total Tree	1.02006e-30	7.69131e-35	7.51597e-21
-4	hg17.chr7(+):26907338-26907654|hg17_3	1.98983e-31	0	0.0066257
-4	panTro1.chr6(+):28037356-28037672|panTro1_3	1.98983e-31	0	0.0066257
-4	Node1	0.0148072	0.00246575	0.0381554
-4	mm5.chr6(+):52104059-52104375|mm5_3	0.0275943	0.0109457	0.0548099
-4	rn3.chr4(+):80734432-80734748|rn3_3	0.0217662	0.00736615	0.0466518
-4	Node4	0.045162	0.0224707	0.0792981
-4	canFam1.chr14(+):42826446-42826762|canFam1_3	0.0320463	0.0139406	0.0605161
-4	Total Tree	0.141376	0.100446	0.192464
+3	Total Tree	1.27931e-17	9.64599e-22	9.4261e-08
+4	hg17.chr7(+):26907338-26907654|hg17_3	1.98974e-31	0	0.00662576
+4	panTro1.chr6(+):28037356-28037672|panTro1_3	1.98974e-31	0	0.00662576
+4	Node1	0.014806	0.00246541	0.0381554
+4	mm5.chr6(+):52104059-52104375|mm5_3	0.0275935	0.0109456	0.0548103
+4	rn3.chr4(+):80734432-80734748|rn3_3	0.0217688	0.00736645	0.0466551
+4	Node4	0.0451597	0.0224663	0.0792997
+4	canFam1.chr14(+):42826446-42826762|canFam1_3	0.0320496	0.013941	0.0605175
+4	Total Tree	0.141378	0.100447	0.192467
diff -r 546e2d835e16 -r 7411b119a3c9 test-data/dnds_out.tabular
--- a/test-data/dnds_out.tabular	Tue Jan 27 14:48:51 2009 -0500
+++ b/test-data/dnds_out.tabular	Tue Jan 27 16:17:22 2009 -0500
@@ -1,12 +1,12 @@
 BLOCK	BP	S_sites	NS_sites	Stop_codons	LogL	omega	omega_range	AC	AT	CG	CT	GT	Tree
-1	1554	355.669	1129.12	1	-2747.41	0.101159	0.0765061-0.130636	1	1	1	1	1	(human:0,chimp:0.00240762,mouse:0.146649)
-2	3795	924.935	2749.35	1	-5781.01	0.0179485	0.0119925-0.02562	1	1	1	1	1	(human:0.0004305,chimp:0.00147714,mouse:0.144943)
-3	1194	272.323	881.914	1	-2043.72	0.0578339	0.0372207-0.0849736	1	1	1	1	1	(human:0.00285309,chimp:0.00410455,mouse:0.11988)
-4	1146	248.261	850.364	1	-1871.67	0.012771	0.00548036-0.0247371	1	1	1	1	1	(human:0,chimp:0.00093192,mouse:0.147209)
-5	1500	366.374	1086.09	2	-2522.97	0.0331894	0.0203743-0.0505255	1	1	1	1	1	(human:0,chimp:0.00225976,mouse:0.156089)
-6	3444	824.107	2475.54	1	-5459.18	0.0439755	0.0326426-0.0576899	1	1	1	1	1	(human:0.000512784,chimp:0.00203485,mouse:0.126653)
-7	2175	505.186	1587.7	0	-3307.52	0.0712367	0.0564019-0.088443	1	1	1	1	1	(human:0.00229486,chimp:0.00236745,mouse:0.226418)
-8	3519	792.702	2601.36	0	-6219.39	0.0669992	0.0568977-0.078214	1	1	1	1	1	(human:0.00103092,chimp:0.00431199,mouse:0.251293)
-9	501	100.22	376.039	1	-834.329	0.13041	0.0835498-0.192248	1	1	1	1	1	(human:0,chimp:0,mouse:0.150462)
-10	633	160.252	453.228	1	-618.997	0.0150887	0.00250412-0.0467112	1	1	1	1	1	(human:0,chimp:0.00611143,mouse:0.104315)
-11	915	229.705	658.82	0	-1664.02	0.299737	0.227826-0.385548	1	1	1	1	1	(human:0.0045721,chimp:0,mouse:0.145563)
+1	1554	355.669	1129.12	1	-2747.41	0.101087	0.0764772-0.130598	1	1	1	1	1	(human:0,chimp:0.0024086,mouse:0.146678)
+2	3795	924.935	2749.35	1	-5781.01	0.0179487	0.0119926-0.0256204	1	1	1	1	1	(human:0.000420365,chimp:0.00148429,mouse:0.144946)
+3	1194	272.323	881.914	1	-2043.72	0.057806	0.0372158-0.0849625	1	1	1	1	1	(human:0.00284622,chimp:0.0041096,mouse:0.119889)
+4	1146	248.261	850.364	1	-1871.67	0.0127683	0.00548023-0.0247365	1	1	1	1	1	(human:1.64845e-31,chimp:0.000931909,mouse:0.147211)
+5	1500	366.374	1086.09	2	-2522.97	0.0331759	0.0203729-0.0505178	1	1	1	1	1	(human:0,chimp:0.00225973,mouse:0.156094)
+6	3444	824.107	2475.54	1	-5459.18	0.0439729	0.032642-0.0576888	1	1	1	1	1	(human:0.000513623,chimp:0.00203456,mouse:0.126654)
+7	2175	505.186	1587.7	0	-3307.52	0.0711481	0.0563562-0.0883841	1	1	1	1	1	(human:0.0022939,chimp:0.00236854,mouse:0.226516)
+8	3519	792.702	2601.36	0	-6219.39	0.0669805	0.0568888-0.0782017	1	1	1	1	1	(human:0.00102641,chimp:0.00431646,mouse:0.25132)
+9	501	100.22	376.039	1	-834.329	0.130019	0.0833975-0.191896	1	1	1	1	1	(human:0,chimp:2.19778e-31,mouse:0.150592)
+10	633	160.252	453.228	1	-618.997	0.0150806	0.00250396-0.0467057	1	1	1	1	1	(human:0,chimp:0.00611203,mouse:0.104319)
+11	915	229.705	658.82	0	-1664.02	0.299406	0.227634-0.385273	1	1	1	1	1	(human:0.00457505,chimp:3.44909e-31,mouse:0.145589)
diff -r 546e2d835e16 -r 7411b119a3c9 test-data/nj_tree_newick_out.dat
--- a/test-data/nj_tree_newick_out.dat	Tue Jan 27 14:48:51 2009 -0500
+++ b/test-data/nj_tree_newick_out.dat	Tue Jan 27 16:17:22 2009 -0500
@@ -1,10 +1,10 @@
-0	((hg17,panTro1),rheMac2,(rn3,mm7))	((hg17.chr7(+):127471195-127471526|hg17_0:0.00346971,panTro1.chr6(+):129885076-129885407|panTro1_0:0.00260712):0.0126114,rheMac2.chr3(+):165787989-165788319|rheMac2_0:0.028188,(rn3.chr4(+):56178191-56178473|rn3_0:0.0617996,mm7.chr6(+):28984529-28984886|mm7_0:0.0662353):0.305784)
+0	(hg17,panTro1,(rheMac2,(rn3,mm7)))	(hg17.chr7(+):127471195-127471526|hg17_0:0.00283776,panTro1.chr6(+):129885076-129885407|panTro1_0:0.00323907,(rheMac2.chr3(+):165787989-165788319|rheMac2_0:0.0324438,(rn3.chr4(+):56178191-56178473|rn3_0:0.0264183,mm7.chr6(+):28984529-28984886|mm7_0:0.148227):0.457076):0.00849339)
 1	((hg17,panTro1),mm7,rheMac2)	((hg17.chr7(+):127471526-127471584|hg17_1:0.00446699,panTro1.chr6(+):129885407-129885465|panTro1_1:0.013401):0.00483543,mm7.chr6(+):28984886-28984940|mm7_1:999.986,rheMac2.chr3(+):165788319-165788377|rheMac2_1:0.0137694)
-2	(((hg17,panTro1),rheMac2),(canFam2,dasNov1),(bosTau2,rn3))	(((hg17.chr7(+):127471584-127471688|hg17_2:0.00234609,panTro1.chr6(+):129885465-129885569|panTro1_2:0.0173725):0.0101799,rheMac2.chr3(+):165788377-165788482|rheMac2_2:0.063065):0.106752,(canFam2.chr14(-):11090703-11090811|canFam2_2:0.187046,dasNov1.scaffold_256527(+):298-392|dasNov1_2:0.0930379):0.0263477,(bosTau2.chr4(-):50243931-50244034|bosTau2_2:0.154553,rn3.chr4(+):56182200-56182295|rn3_2:0.21476):0.0231563)
-3	((hg17,panTro1),rheMac2,(rn3,((bosTau2,dasNov1),canFam2)))	((hg17.chr7(+):127471688-127471871|hg17_3:0.0186952,panTro1.chr6(+):129885569-129885752|panTro1_3:0.00389261):0.024721,rheMac2.chr3(+):165788482-165788684|rheMac2_3:0.0326957,(rn3.chr4(+):56182295-56182489|rn3_3:0.151674,((bosTau2.chr4(-):50243792-50243930|bosTau2_3:0.0510929,dasNov1.scaffold_256527(+):393-625|dasNov1_3:0.119004):0.0284421,canFam2.chr14(-):11090345-11090505|canFam2_3:0.0489193):0.0426697):0.0457765)
-4	((hg17,rheMac2),panTro1,((bosTau2,canFam2),dasNov1))	((hg17.chr7(+):127471871-127471910|hg17_4:0,rheMac2.chr3(+):165788684-165788723|rheMac2_4:0.0586327):0.0163653,panTro1.chr6(+):129885752-129885791|panTro1_4:0,((bosTau2.chr4(-):50243734-50243773|bosTau2_4:0.462227,canFam2.chr14(-):11090081-11090120|canFam2_4:0.199596):0.112898,dasNov1.scaffold_256527(+):625-665|dasNov1_4:0.160286):0.163376)
-5	(((hg17,panTro1),rheMac2),((mm7,rn3),dasNov1),(bosTau2,canFam2))	(((hg17.chr7(+):127471910-127472074|hg17_5:0,panTro1.chr6(+):129885791-129885955|panTro1_5:0.0185501):0.0510514,rheMac2.chr3(+):165788723-165788885|rheMac2_5:0.0284199):0.105274,((mm7.chr6(+):28990714-28990875|mm7_5:0.110927,rn3.chr4(+):56183448-56183705|rn3_5:0):0.18866,dasNov1.scaffold_256527(+):665-786|dasNov1_5:0.1964):0.0403849,(bosTau2.chr4(-):50243566-50243734|bosTau2_5:0.169804,canFam2.chr14(-):11089913-11090081|canFam2_5:0.135334):0.0416476)
-6	(hg17,panTro1,(rheMac2,((mm7,rn3),(canFam2,dasNov1))))	(hg17.chr7(+):127472074-127472258|hg17_6:0.00678011,panTro1.chr6(+):129885955-129886139|panTro1_6:0,(rheMac2.chr3(+):165788885-165789069|rheMac2_6:0.0438345,((mm7.chr6(+):28990875-28991025|mm7_6:0.0290692,rn3.chr4(+):56183705-56183879|rn3_6:0.13263):0.168495,(canFam2.chr14(-):11089743-11089913|canFam2_6:0.138698,dasNov1.scaffold_256527(+):786-964|dasNov1_6:0.1994):0.0351372):0.128281):0.0237393)
-7	(((hg17,(canFam2,dasNov1)),panTro1),rheMac2,(mm7,rn3))	(((hg17.chr7(+):127472258-127472280|hg17_7:0,(canFam2.chr14(-):11089526-11089548|canFam2_7:0.513656,dasNov1.scaffold_256527(+):964-987|dasNov1_7:0.205512):0.34336):0,panTro1.chr6(+):129886139-129886161|panTro1_7:0):0,rheMac2.chr3(+):165789069-165789091|rheMac2_7:0,(mm7.chr6(+):28991025-28991048|mm7_7:0.0744383,rn3.chr4(+):56183879-56183902|rn3_7:0.0195258):125.2)
-8	(((hg17,panTro1),rheMac2),(rn3,canFam2),dasNov1)	(((hg17.chr7(+):127472280-127472681|hg17_8:0.00751116,panTro1.chr6(+):129886161-129886562|panTro1_8:2.84007e-05):0.0348269,rheMac2.chr3(+):165789091-165789492|rheMac2_8:0.0280716):0.115196,(rn3.chr4(+):56183902-56184219|rn3_8:0.16879,canFam2.chr14(-):11089143-11089523|canFam2_8:0.158484):0.0249651,dasNov1.scaffold_256527(+):987-1401|dasNov1_8:0.21816)
-9	(((hg17,panTro1),canFam2),rheMac2,dasNov1)	(((hg17.chr7(+):127472681-127472715|hg17_9:0.0115551,panTro1.chr6(+):129886562-129886596|panTro1_9:0.0221032):0.044958,canFam2.chr14(-):11089108-11089143|canFam2_9:0.218642):0.030703,rheMac2.chr3(+):165789492-165789526|rheMac2_9:0.00773783,dasNov1.scaffold_256527(+):1401-1433|dasNov1_9:0.113241)
+2	((((hg17,panTro1),rheMac2),(canFam2,dasNov1)),bosTau2,rn3)	((((hg17.chr7(+):127471584-127471688|hg17_2:0.00103752,panTro1.chr6(+):129885465-129885569|panTro1_2:0.018681):0.00493709,rheMac2.chr3(+):165788377-165788482|rheMac2_2:0.0691856):0.106183,(canFam2.chr14(-):11090703-11090811|canFam2_2:0.213381,dasNov1.scaffold_256527(+):298-392|dasNov1_2:0.123834):0.0305914):0.028679,bosTau2.chr4(-):50243931-50244034|bosTau2_2:0.170682,rn3.chr4(+):56182200-56182295|rn3_2:0.285956)
+3	((hg17,panTro1),rheMac2,(rn3,(bosTau2,(canFam2,dasNov1))))	((hg17.chr7(+):127471688-127471871|hg17_3:0.0225878,panTro1.chr6(+):129885569-129885752|panTro1_3:0):0.0221216,rheMac2.chr3(+):165788482-165788684|rheMac2_3:0.0429855,(rn3.chr4(+):56182295-56182489|rn3_3:0.286513,(bosTau2.chr4(-):50243792-50243930|bosTau2_3:0.135108,(canFam2.chr14(-):11090345-11090505|canFam2_3:0.0418005,dasNov1.scaffold_256527(+):393-625|dasNov1_3:0.198071):0.0128256):0.0852898):0.0472209)
+4	((hg17,rheMac2),panTro1,((bosTau2,canFam2),dasNov1))	((hg17.chr7(+):127471871-127471910|hg17_4:0,rheMac2.chr3(+):165788684-165788723|rheMac2_4:0.0586327):0.0166268,panTro1.chr6(+):129885752-129885791|panTro1_4:0,((bosTau2.chr4(-):50243734-50243773|bosTau2_4:0.462377,canFam2.chr14(-):11090081-11090120|canFam2_4:0.199446):0.119837,dasNov1.scaffold_256527(+):625-665|dasNov1_4:0.17977):0.172715)
+5	(((hg17,panTro1),rheMac2),(mm7,rn3),((bosTau2,dasNov1),canFam2))	(((hg17.chr7(+):127471910-127472074|hg17_5:0.000139728,panTro1.chr6(+):129885791-129885955|panTro1_5:0.0184104):0.05206,rheMac2.chr3(+):165788723-165788885|rheMac2_5:0.0285966):0.0250925,(mm7.chr6(+):28990714-28990875|mm7_5:0.123289,rn3.chr4(+):56183448-56183705|rn3_5:0.0718529):0.38361,((bosTau2.chr4(-):50243566-50243734|bosTau2_5:0.181878,dasNov1.scaffold_256527(+):665-786|dasNov1_5:0.429124):0.0618692,canFam2.chr14(-):11089913-11090081|canFam2_5:0.133548):0.11305)
+6	((hg17,panTro1),rheMac2,((mm7,rn3),(canFam2,dasNov1)))	((hg17.chr7(+):127472074-127472258|hg17_6:0.00549431,panTro1.chr6(+):129885955-129886139|panTro1_6:0):0.0241181,rheMac2.chr3(+):165788885-165789069|rheMac2_6:0.0447415,((mm7.chr6(+):28990875-28991025|mm7_6:0.0851965,rn3.chr4(+):56183705-56183879|rn3_6:0.109546):0.319094,(canFam2.chr14(-):11089743-11089913|canFam2_6:0.186816,dasNov1.scaffold_256527(+):786-964|dasNov1_6:0.219003):0.0699235):0.0966238)
+7	(((hg17,(canFam2,dasNov1)),panTro1),rheMac2,(mm7,rn3))	(((hg17.chr7(+):127472258-127472280|hg17_7:0,(canFam2.chr14(-):11089526-11089548|canFam2_7:0.572157,dasNov1.scaffold_256527(+):964-987|dasNov1_7:0.212507):0.327632):0,panTro1.chr6(+):129886139-129886161|panTro1_7:0):0,rheMac2.chr3(+):165789069-165789091|rheMac2_7:0,(mm7.chr6(+):28991025-28991048|mm7_7:0.0708909,rn3.chr4(+):56183879-56183902|rn3_7:0.0230732):125.221)
+8	(((hg17,panTro1),rheMac2),(rn3,canFam2),dasNov1)	(((hg17.chr7(+):127472280-127472681|hg17_8:0.00753956,panTro1.chr6(+):129886161-129886562|panTro1_8:0):0.0353922,rheMac2.chr3(+):165789091-165789492|rheMac2_8:0.0278572):0.0967916,(rn3.chr4(+):56183902-56184219|rn3_8:0.379264,canFam2.chr14(-):11089143-11089523|canFam2_8:0.207268):0.0346594,dasNov1.scaffold_256527(+):987-1401|dasNov1_8:0.268281)
+9	(hg17,((rheMac2,dasNov1),canFam2),panTro1)	(hg17.chr7(+):127472681-127472715|hg17_9:0.0183718,((rheMac2.chr3(+):165789492-165789526|rheMac2_9:0,dasNov1.scaffold_256527(+):1401-1433|dasNov1_9:0.160078):0.0595979,canFam2.chr14(-):11089108-11089143|canFam2_9:0.237132):0.0383088,panTro1.chr6(+):129886562-129886596|panTro1_9:0.0152865)
diff -r 546e2d835e16 -r 7411b119a3c9 tools/hyphy/hyphy_branch_lengths_wrapper.xml
--- a/tools/hyphy/hyphy_branch_lengths_wrapper.xml	Tue Jan 27 14:48:51 2009 -0500
+++ b/tools/hyphy/hyphy_branch_lengths_wrapper.xml	Tue Jan 27 16:17:22 2009 -0500
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.1.0"?>
 <tool name="Branch Lengths" id="hyphy_branch_lengths_wrapper1">
    
    <description>Estimation</description>
diff -r 546e2d835e16 -r 7411b119a3c9 tools/hyphy/hyphy_dnds_wrapper.xml
--- a/tools/hyphy/hyphy_dnds_wrapper.xml	Tue Jan 27 14:48:51 2009 -0500
+++ b/tools/hyphy/hyphy_dnds_wrapper.xml	Tue Jan 27 16:17:22 2009 -0500
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.1.0"?>
 <tool name="dN/dS Ratio" id="hyphy_dnds_wrapper1">
    
    <description>Estimation</description>
diff -r 546e2d835e16 -r 7411b119a3c9 tools/hyphy/hyphy_nj_tree_wrapper.xml
--- a/tools/hyphy/hyphy_nj_tree_wrapper.xml	Tue Jan 27 14:48:51 2009 -0500
+++ b/tools/hyphy/hyphy_nj_tree_wrapper.xml	Tue Jan 27 16:17:22 2009 -0500
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.1.0"?>
 <tool name="Neighbor Joining Tree" id="hyphy_nj_tree_wrapper1">
<description>Builder</description>
diff -r 546e2d835e16 -r 7411b119a3c9 tools/regVariation/microsats_mutability.xml
--- a/tools/regVariation/microsats_mutability.xml	Tue Jan 27 14:48:51 2009 -0500
+++ b/tools/regVariation/microsats_mutability.xml	Tue Jan 27 16:17:22 2009 -0500
@@ -1,4 +1,4 @@
-<tool id="microsats_mutability1" name="Estimate microsatellite mutability" version="1.0.0">
+<tool id="microsats_mutability1" name="Estimate microsatellite mutability" version="1.1.0">
   <description>by specified attributes</description>
   <command interpreter="python">
    microsats_mutability.py 
diff -r 546e2d835e16 -r 7411b119a3c9 tools/stats/grouping.xml
--- a/tools/stats/grouping.xml	Tue Jan 27 14:48:51 2009 -0500
+++ b/tools/stats/grouping.xml	Tue Jan 27 16:17:22 2009 -0500
@@ -1,4 +1,4 @@
-<tool id="Grouping1" name="Group" version="1.4.0">
+<tool id="Grouping1" name="Group" version="1.5.0">
   <description>data by a column and perform aggregate operation on other columns.</description>
   <command interpreter="python">
     grouping.py

    