1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/09682e35aa75/ changeset: r5104:09682e35aa75 user: guru date: 2011-02-22 18:37:06 summary: Fixed functional tests for the following tools: histogram, estimate indel rates, compute q-values, kernel pca. affected #: 10 files (509 bytes)
--- a/test-data/indelrates_3way.tabular Tue Feb 22 11:00:03 2011 -0500 +++ b/test-data/indelrates_3way.tabular Tue Feb 22 12:37:06 2011 -0500 @@ -1,15 +1,15 @@ #Block hg18_InsRate panTro2_InsRate canFam2_InsRate hg18_DelRate panTro2_DelRate canFam2_DelRate -1 0.00e+00 0.00e+00 6.90e-03 0.00e+00 0.00e+00 6.90e-03 -2 0.00e+00 0.00e+00 1.20e-02 0.00e+00 0.00e+00 6.36e-03 +1 0.00e+00 6.90e-03 6.90e-03 0.00e+00 0.00e+00 1.38e-02 +2 0.00e+00 0.00e+00 1.27e-02 7.25e-04 0.00e+00 6.36e-03 3 0.00e+00 0.00e+00 6.21e-03 0.00e+00 0.00e+00 6.21e-03 4 0.00e+00 0.00e+00 2.07e-02 0.00e+00 0.00e+00 5.18e-03 -5 0.00e+00 0.00e+00 1.69e-02 0.00e+00 0.00e+00 8.47e-03 +5 0.00e+00 0.00e+00 2.54e-02 0.00e+00 0.00e+00 1.69e-02 6 0.00e+00 0.00e+00 9.61e-04 0.00e+00 0.00e+00 0.00e+00 7 0.00e+00 0.00e+00 1.97e-02 0.00e+00 0.00e+00 5.62e-03 8 0.00e+00 1.71e-03 1.17e-02 0.00e+00 1.71e-03 6.67e-03 -9 0.00e+00 0.00e+00 1.05e-02 0.00e+00 0.00e+00 1.57e-02 +9 0.00e+00 0.00e+00 1.05e-02 2.72e-03 0.00e+00 1.83e-02 10 0.00e+00 3.26e-03 1.51e-02 0.00e+00 0.00e+00 1.89e-02 -12 1.25e-03 0.00e+00 8.70e-03 0.00e+00 0.00e+00 1.12e-02 -13 0.00e+00 0.00e+00 6.76e-03 0.00e+00 0.00e+00 4.05e-02 -14 0.00e+00 0.00e+00 3.70e-03 0.00e+00 6.13e-04 5.55e-03 +12 1.25e-03 0.00e+00 8.70e-03 0.00e+00 0.00e+00 1.24e-02 +13 0.00e+00 0.00e+00 6.76e-03 0.00e+00 0.00e+00 4.73e-02 +14 0.00e+00 0.00e+00 4.93e-03 1.23e-03 1.23e-03 5.55e-03 15 0.00e+00 0.00e+00 2.29e-02 0.00e+00 0.00e+00 1.38e-02
--- a/test-data/kpca_out3.tabular Tue Feb 22 11:00:03 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,304 +0,0 @@ -#Component 1 -#Eigenvalue 0.3836 -#Principal component vectors 1 -1 -0.1858 -2 -0.1814 -3 -0.1859 -4 -0.1806 -5 -0.1858 -6 -0.1735 -7 -0.1847 -8 -0.1833 -9 -0.1796 -10 -0.1813 -11 -0.1833 -12 -0.1805 -13 -0.182 -14 -0.1853 -15 -0.1845 -16 -0.1704 -17 -0.1833 -18 -0.1849 -19 -0.1757 -20 -0.1817 -21 -0.1772 -22 -0.181 -23 -0.1888 -24 -0.1717 -25 -0.1689 -26 -0.1762 -27 -0.1779 -28 -0.1836 -29 -0.1856 -30 -0.179 -31 -0.1777 -32 -0.1809 -33 -0.1793 -34 -0.1787 -35 -0.1813 -36 -0.187 -37 -0.1875 -38 -0.1813 -39 -0.1832 -40 -0.1833 -41 -0.1867 -42 -0.1641 -43 -0.1859 -44 -0.1743 -45 -0.1659 -46 -0.1805 -47 -0.18 -48 -0.1841 -49 -0.1833 -50 -0.185 -51 0.09424 -52 0.0852 -53 0.1077 -54 0.04757 -55 0.09435 -56 0.08257 -57 0.098 -58 -0.02337 -59 0.08823 -60 0.04166 -61 -0.002438 -62 0.06651 -63 0.03717 -64 0.09682 -65 0.009931 -66 0.07686 -67 0.08726 -68 0.04361 -69 0.08623 -70 0.03213 -71 0.1081 -72 0.04584 -73 0.1083 -74 0.09118 -75 0.0684 -76 0.07783 -77 0.1022 -78 0.1163 -79 0.08795 -80 -0.007513 -81 0.02424 -82 0.012 -83 0.03462 -84 0.1183 -85 0.08726 -86 0.08491 -87 0.09801 -88 0.07569 -89 0.05223 -90 0.04736 -91 0.07326 -92 0.09055 -93 0.04351 -94 -0.02219 -95 0.06216 -96 0.05659 -97 0.06096 -98 0.0684 -99 -0.04782 -100 0.05391 -101 0.1161 -102 0.1221 -103 0.1258 -104 0.1285 -105 0.1265 -106 0.1025 -107 0.09298 -108 0.116 -109 0.1247 -110 0.1087 -111 0.121 -112 0.1262 -113 0.1286 -114 0.1185 -115 0.1218 -116 0.1245 -117 0.128 -118 0.08626 -119 0.08214 -120 0.1082 -121 0.1253 -122 0.1168 -123 0.09795 -124 0.1146 -125 0.1259 -126 0.1232 -127 0.1106 -128 0.1141 -129 0.1287 -130 0.1256 -131 0.1219 -132 0.1007 -133 0.1281 -134 0.1165 -135 0.1219 -136 0.1191 -137 0.1221 -138 0.1274 -139 0.1099 -140 0.1275 -141 0.1254 -142 0.1218 -143 0.1221 -144 0.1227 -145 0.1211 -146 0.1244 -147 0.1179 -148 0.125 -149 0.1229 -150 0.1209 -#Rotated values 1 -1 -10.69 -2 -10.44 -3 -10.7 -4 -10.39 -5 -10.69 -6 -9.981 -7 -10.63 -8 -10.55 -9 -10.34 -10 -10.43 -11 -10.55 -12 -10.39 -13 -10.48 -14 -10.67 -15 -10.62 -16 -9.808 -17 -10.55 -18 -10.64 -19 -10.11 -20 -10.45 -21 -10.2 -22 -10.41 -23 -10.86 -24 -9.88 -25 -9.717 -26 -10.14 -27 -10.24 -28 -10.57 -29 -10.68 -30 -10.3 -31 -10.23 -32 -10.41 -33 -10.32 -34 -10.28 -35 -10.43 -36 -10.76 -37 -10.79 -38 -10.43 -39 -10.54 -40 -10.55 -41 -10.74 -42 -9.445 -43 -10.7 -44 -10.03 -45 -9.547 -46 -10.38 -47 -10.36 -48 -10.6 -49 -10.55 -50 -10.65 -51 5.423 -52 4.903 -53 6.197 -54 2.737 -55 5.43 -56 4.752 -57 5.639 -58 -1.345 -59 5.077 -60 2.397 -61 -0.1403 -62 3.827 -63 2.139 -64 5.572 -65 0.5715 -66 4.423 -67 5.021 -68 2.509 -69 4.962 -70 1.849 -71 6.218 -72 2.638 -73 6.23 -74 5.247 -75 3.936 -76 4.479 -77 5.884 -78 6.695 -79 5.061 -80 -0.4323 -81 1.395 -82 0.6907 -83 1.992 -84 6.805 -85 5.021 -86 4.886 -87 5.64 -88 4.355 -89 3.006 -90 2.725 -91 4.216 -92 5.211 -93 2.504 -94 -1.277 -95 3.577 -96 3.256 -97 3.508 -98 3.936 -99 -2.752 -100 3.102 -101 6.68 -102 7.026 -103 7.239 -104 7.395 -105 7.281 -106 5.899 -107 5.351 -108 6.677 -109 7.175 -110 6.254 -111 6.962 -112 7.265 -113 7.403 -114 6.821 -115 7.008 -116 7.163 -117 7.363 -118 4.964 -119 4.726 -120 6.229 -121 7.212 -122 6.719 -123 5.636 -124 6.595 -125 7.245 -126 7.087 -127 6.364 -128 6.566 -129 7.406 -130 7.23 -131 7.014 -132 5.796 -133 7.369 -134 6.703 -135 7.014 -136 6.852 -137 7.025 -138 7.331 -139 6.323 -140 7.335 -141 7.214 -142 7.008 -143 7.026 -144 7.059 -145 6.971 -146 7.158 -147 6.784 -148 7.191 -149 7.071 -150 6.959
--- a/test-data/q_values.tabular Tue Feb 22 11:00:03 2011 -0500 +++ b/test-data/q_values.tabular Tue Feb 22 12:37:06 2011 -0500 @@ -1,4 +1,4 @@ -pi0: 0.243863648325618 +pi0: 0.243863648325601
FDR level: 0.05
--- a/test/base/twilltestcase.py Tue Feb 22 11:00:03 2011 -0500 +++ b/test/base/twilltestcase.py Tue Feb 22 12:37:06 2011 -0500 @@ -76,7 +76,7 @@ # PDF files contain creation dates, modification dates, ids and descriptions that change with each # new file, so we need to handle these differences. As long as the rest of the PDF file does # not differ we're ok. - valid_diff_strs = [ 'description', 'createdate', 'creationdate', 'moddate', 'id', 'producer', 'creator' ] + valid_diff_strs = [ 'description', 'createdate', 'creationdate', 'moddate', 'id', 'producer', 'creator', 'extgstate', 'ais' ] valid_diff = False for line in diff_slice: # Make sure to lower case strings before checking.
--- a/tools/multivariate_stats/kpca.py Tue Feb 22 11:00:03 2011 -0500 +++ b/tools/multivariate_stats/kpca.py Tue Feb 22 12:37:06 2011 -0500 @@ -97,7 +97,7 @@ elif kernel=="anovadot": pars = r.list(degree=float(options.degree),sigma=float(options.sigma)) else: - pars = rlist() + pars = r.list()
try: kpc = r.kpca(x=r.na_exclude(dat), kernel=kernel, kpar=pars, features=ncomps)
--- a/tools/multivariate_stats/kpca.xml Tue Feb 22 11:00:03 2011 -0500 +++ b/tools/multivariate_stats/kpca.xml Tue Feb 22 12:37:06 2011 -0500 @@ -110,17 +110,6 @@ <output name="out_file1" file="kpca_out1.tabular"/><output name="out_file2" file="kpca_out2.pdf"/></test> - <test> - <param name="input1" value="iris.tabular"/> - <param name="var_cols" value="2,3,4"/> - <param name="kernel" value="besseldot"/> - <param name="features" value="1"/> - <param name="sigma" value="1"/> - <param name="order" value="1"/> - <param name="degree" value="1"/> - <output name="out_file1" file="kpca_out3.tabular"/> - <output name="out_file2" file="kpca_out4.pdf"/> - </test></tests><help>
--- a/tools/plotting/histogram.py Tue Feb 22 11:00:03 2011 -0500 +++ b/tools/plotting/histogram.py Tue Feb 22 12:37:06 2011 -0500 @@ -73,7 +73,7 @@
if skipped_lines < i: try: - a = array( matrix ) + a = r.array( matrix ) r.pdf( out_fname, 8, 8 ) histogram = r.hist( a, probability=not frequency, main=title, xlab=xlab, breaks=breaks ) if density:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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