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

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