March 2010 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3478: Added a new tool set for performing multivaria...
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/11dcd9d18663 changeset: 3478:11dcd9d18663 user: gua110 date: Thu Mar 04 11:48:10 2010 -0500 description: Added a new tool set for performing multivariate statistical analyses diffstat: test-data/cca_out1.tabular | 22 + test-data/cca_out2.pdf | 858 +++++++++++++++++++++ test-data/iris.tabular | 151 +++ test-data/kcca_out1.tabular | 304 +++++++ test-data/kcca_out2.tabular | 304 +++++++ test-data/kpca_out1.tabular | 304 +++++++ test-data/kpca_out2.pdf | 1190 ++++++++++++++++++++++++++++++ test-data/kpca_out3.tabular | 304 +++++++ test-data/kpca_out4.pdf | 624 +++++++++++++++ test-data/pca_out1.tabular | 159 ++++ test-data/pca_out2.pdf | 705 +++++++++++++++++ test-data/pca_out3.tabular | 159 ++++ test-data/pca_out4.pdf | 705 +++++++++++++++++ tool_conf.xml.sample | 6 + tools/multivariate_stats/cca.py | 159 ++++ tools/multivariate_stats/cca.xml | 95 ++ tools/multivariate_stats/kcca.py | 146 +++ tools/multivariate_stats/kcca.xml | 150 +++ tools/multivariate_stats/kpca.py | 134 +++ tools/multivariate_stats/kpca.xml | 151 +++ tools/multivariate_stats/pca.py | 98 ++ tools/multivariate_stats/pca.xml | 76 + tools/regVariation/linear_regression.xml | 8 +- 23 files changed, 6809 insertions(+), 3 deletions(-) diffs (truncated from 6932 to 3000 lines): diff -r d9afcaa386f6 -r 11dcd9d18663 test-data/cca_out1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cca_out1.tabular Thu Mar 04 11:48:10 2010 -0500 @@ -0,0 +1,22 @@ +#Component 1 2 +#Correlation 0.940897180432 0.131074795925 +#F-statistic 144.410560578 2.5696974623 +#p-value 6.21285598619e-68 0.111075110551 +#X-Coefficients 1 2 +c3 1.50661351834 -3.37790409332 +c4 -0.537226204038 3.65944099051 +#Y-Coefficients 1 2 +c1 6.35046749378 3.37940792566 +c2 -2.6597206473 6.66976562808 +#X-Loadings 1 2 +c3 0.989395177676 0.145248691528 +c4 0.913276653253 0.407339851504 +#Y-Loadings 1 2 +c1 0.928869265104 0.370407732566 +c2 -0.469775462051 0.882785939656 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(l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 343.19 350.47 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 346.02 347.75 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 372.35 359.47 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 353.36 393.10 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 352.91 369.12 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 408.79 382.78 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 428.99 398.47 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 365.36 377.95 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 373.69 362.43 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 342.70 356.45 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 341.43 364.38 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 390.35 383.17 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 364.81 361.11 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 323.46 332.43 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 354.88 363.16 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 378.35 365.44 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 371.47 365.80 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 397.48 376.83 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 341.88 329.96 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 367.72 363.23 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 372.30 434.31 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 339.00 391.90 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 409.11 443.63 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 367.29 414.42 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 374.30 428.48 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 420.93 475.72 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 299.97 359.69 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 408.20 455.63 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 359.82 425.71 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 445.99 459.92 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 407.45 409.66 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 366.64 408.76 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 401.25 426.13 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 323.72 387.44 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 338.35 396.98 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 392.56 415.56 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 387.57 416.69 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 482.63 488.15 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 386.43 486.67 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 328.36 387.15 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 412.65 436.99 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 337.62 384.87 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 411.68 478.64 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 371.84 396.06 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 409.91 431.08 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 431.01 446.81 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 374.57 392.27 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 378.79 393.76 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 362.59 418.87 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 425.45 437.89 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 411.65 452.74 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 509.16 481.64 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 361.20 419.85 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 377.17 398.64 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 343.58 404.69 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 438.91 465.67 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 390.61 423.35 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 388.08 415.17 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 375.41 389.47 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 416.57 426.28 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 394.94 430.25 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 421.28 420.43 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 339.00 391.90 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 401.15 440.18 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 404.12 435.21 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 400.00 418.17 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 356.25 398.26 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 392.21 411.03 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 391.09 415.07 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 363.10 394.60 Tm (l) Tj 0 Tr +ET +Q q 53.78 53.78 228.24 216.29 re W n +Q q 47.81 47.81 240.19 228.24 re W n +Q q +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +53.78 53.78 m +282.02 53.78 l +282.02 270.07 l +53.78 270.07 l +53.78 53.78 l +S +75.97 53.78 m 280.25 53.78 l S +75.97 53.78 m 75.97 47.81 l S +110.01 53.78 m 110.01 47.81 l S +144.06 53.78 m 144.06 47.81 l S +178.11 53.78 m 178.11 47.81 l S +212.15 53.78 m 212.15 47.81 l S +246.20 53.78 m 246.20 47.81 l S +280.25 53.78 m 280.25 47.81 l S +BT +0.000 0.000 0.000 rg +/F2 1 Tf 10.00 0.00 -0.00 10.00 64.71 32.27 Tm (-400) Tj +ET +BT +/F2 1 Tf 10.00 0.00 -0.00 10.00 98.75 32.27 Tm (-200) Tj +ET +BT +/F2 1 Tf 10.00 0.00 -0.00 10.00 141.28 32.27 Tm (0) Tj +ET +BT +/F2 1 Tf 10.00 0.00 -0.00 10.00 169.77 32.27 Tm (200) Tj +ET +BT +/F2 1 Tf 10.00 0.00 -0.00 10.00 203.81 32.27 Tm (400) Tj +ET +BT +/F2 1 Tf 10.00 0.00 -0.00 10.00 237.86 32.27 Tm (600) Tj +ET +BT +/F2 1 Tf 10.00 0.00 -0.00 10.00 271.91 32.27 Tm (800) Tj +ET +53.78 95.29 m 53.78 257.05 l S +53.78 95.29 m 47.81 95.29 l S +53.78 149.21 m 47.81 149.21 l S +53.78 203.13 m 47.81 203.13 l S +53.78 257.05 m 47.81 257.05 l S +BT +/F2 1 Tf 0.00 10.00 -10.00 0.00 39.44 84.03 Tm (-100) Tj +ET +BT +/F2 1 Tf 0.00 10.00 -10.00 0.00 39.44 146.43 Tm (0) Tj +ET +BT +/F2 1 Tf 0.00 10.00 -10.00 0.00 39.44 194.79 Tm (100) Tj +ET +BT +/F2 1 Tf 0.00 10.00 -10.00 0.00 39.44 248.71 Tm (200) Tj +ET +Q q 53.78 53.78 228.24 216.29 re W n +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 73.69 174.79 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 70.46 138.86 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 67.31 139.19 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 68.98 127.77 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 72.79 174.50 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 84.35 209.76 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 68.70 142.36 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 73.93 163.25 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 65.11 109.76 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 71.59 143.54 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 79.16 201.86 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 73.26 151.72 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 68.83 134.44 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 59.78 112.33 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 79.46 246.29 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 85.75 259.91 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 77.59 213.44 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 74.31 174.12 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 87.18 222.87 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 76.55 189.27 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 81.80 183.51 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 76.97 183.18 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 62.77 155.80 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 79.92 159.55 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 77.97 148.96 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 74.59 142.20 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 76.75 160.99 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 76.40 179.50 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 74.59 175.08 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 71.74 136.70 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 72.60 136.90 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 79.78 183.98 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 77.05 213.14 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 79.74 237.48 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 71.59 143.54 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 68.95 155.59 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 76.59 198.41 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 71.59 143.54 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 63.93 115.05 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 75.05 168.69 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 71.65 169.45 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 64.07 88.41 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 64.30 124.22 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 78.24 164.76 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 83.84 184.79 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 69.98 133.17 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 77.53 189.08 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 67.73 133.34 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 77.99 196.03 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 72.17 159.00 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 182.34 207.51 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 165.84 174.72 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 185.94 189.45 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 131.19 90.09 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 168.19 154.41 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 148.33 116.31 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 170.33 169.74 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 105.69 82.10 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 168.83 168.39 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 126.62 96.72 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 109.34 65.19 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 147.95 141.22 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 137.01 112.03 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 162.22 137.52 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 127.16 132.82 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 167.88 189.32 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 149.25 119.85 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 138.03 126.72 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 156.53 106.81 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 130.09 108.75 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 166.08 137.22 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 144.30 146.60 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 169.90 120.01 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 159.82 134.15 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 157.50 163.12 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 165.34 177.34 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 178.47 168.33 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 185.73 166.72 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 156.38 135.09 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 123.00 126.66 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 125.83 100.60 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 122.96 103.27 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 135.33 128.23 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 170.81 110.23 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 145.51 109.81 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 159.92 162.77 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 176.48 181.90 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 154.82 121.60 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 138.45 129.50 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 132.14 100.13 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 140.50 98.93 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 160.33 145.28 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 137.05 121.09 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 106.79 81.90 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 139.22 111.67 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 141.63 133.92 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 142.01 127.40 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 153.65 152.04 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 104.18 99.36 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 139.29 123.84 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 214.30 128.18 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 169.55 96.62 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 224.14 163.06 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 193.31 123.43 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 208.14 130.08 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 258.00 174.26 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 135.56 59.64 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 236.80 162.20 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 205.22 116.36 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 241.32 198.01 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 188.29 161.49 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 187.34 122.82 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 205.67 155.62 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 164.84 82.15 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 174.91 96.01 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 194.51 147.38 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 195.71 142.65 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 271.11 232.74 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 269.56 141.57 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 164.54 86.54 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 217.13 166.42 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 162.13 95.32 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 261.08 165.50 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 173.93 127.75 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 210.90 163.82 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 227.49 183.82 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 169.93 130.33 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 171.51 134.33 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 198.01 118.98 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 6.21 0 0 6.21 218.08 178.55 Tm (l) Tj 0 Tr +ET +BT

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Fwd: [galaxy-user] Protein names
by Anton Nekrutenko 05 Mar '10

05 Mar '10

Begin forwarded message: > From: webb(a)bx.psu.edu > Date: March 5, 2010 1:44:01 PM EST > To: Tjaart de Beer <tdebeer(a)gmail.com> > Cc: Anton Nekrutenko <anton(a)bx.psu.edu>, Webb Miller > <webb(a)bx.psu.edu>, Aakrosh Ratan <ratan(a)cse.psu.edu> > Subject: Re: Fwd: [galaxy-user] Protein names > > Hi, > > The gene annotations are from RefSeq. As we processed the SNPs with > tools such as PolyPhen and Sift, we sometimes had to use other > names. My assumption was that people would load their favorite gene > annotations into Galaxy and use an "interval" join to attach the > desired names. Can you do something like that? Or is the problem > that you need to deal with alternate splice forms? > > Please keep asking until you have everything working. If necessary, > I can regenerate the file with other protein names. Thanks for your > patience. > > --Webb > > > Quoting Anton Nekrutenko <anton(a)bx.psu.edu>: > >> Webb: >> >> The question here is on where the protein names come from. Can you >> elaborate, so I send him a reply. >> >> Thanks, >> >> anton >> >> >> >> Begin forwarded message: >> >>> From: Tjaart de Beer <tdebeer(a)gmail.com> >>> Date: March 5, 2010 7:34:13 AM EST >>> To: galaxy-user(a)bx.psu.edu >>> Subject: [galaxy-user] Protein names >>> >>> Hi >>> >>> I am trying to parse some data from the Bushmen dataset and have >>> a question. >>> >>> Where do you get the protein names from? It does not correspond 100% >>> to the UniProt ID field in Uniprot entries nor is it Uniprot AC >>> numbers. Is there some kind of mapping I can use to get the >>> appropriate names or Uniprot entries? Would you be able to provide >>> with this mapping? I have been going through the Uniprot website >>> rather extensively and have failed to find any such downloadable >>> mapping. Hope you can help! >>> >>> Thanks! >>> >>> Dr. Tjaart de Beer >>> Thornton group >>> EMBL-EBI >>> Cambridge >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-user >> >> Anton Nekrutenko >> http://nekrut.bx.psu.edu >> http://usegalaxy.org >> >> >> >> > > > Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

1 0

Problem with displaying wiggle file in galaxy.
by Vipin TS 05 Mar '10

05 Mar '10

Dear Galaxy Team, I would like to visualize a wiggle format file in my galaxy instance. I made initial set up for visualization and I am not able to find my track display. Here I am attaching my screen shot, please find it. less from my wiggle file, track type=wiggle_0 name=test variableStep chrom=I I 3749 1 I 3750 1 I 3751 1 I 3752 1 I 3753 1 I 3754 1 I 3755 1 I 3756 1 I 3757 1 I 3758 1 I 3759 1 I 3760 1 I 3761 1 I 3762 1 I 3763 1 I 3764 1 I 3765 1 I 3766 3 I 3767 5 I 3768 6 I 3769 6 I 3770 6 I 3771 6 I 3772 6 It will be great if you can suggest me a way to solve the display problem. Many thanks, Vipin

3 3

Python 2.6
by SHAUN WEBB 05 Mar '10

05 Mar '10

Hi, I just wanted to check if Galaxy is now fully compatible with Python 2.6. Thanks for your help Shaun webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 1

[hg] galaxy 3476: Fix for sharing histories that include restric...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/adda1b9e31fa changeset: 3476:adda1b9e31fa user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Mar 03 17:00:50 2010 -0500 description: Fix for sharing histories that include restricted datasets. diffstat: lib/galaxy/web/controllers/history.py | 12 +++++++----- 1 files changed, 7 insertions(+), 5 deletions(-) diffs (31 lines): diff -r a2cb4b0ccf6b -r adda1b9e31fa lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Wed Mar 03 15:37:43 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Wed Mar 03 17:00:50 2010 -0500 @@ -908,7 +908,7 @@ else: # Only deal with datasets that have not been purged for hda in history.activatable_datasets: - if trans.app.security_agent.dataset_is_public( hda.dataset ): + if trans.app.security_agent.can_access_dataset( send_to_user.all_roles(), hda.dataset ): # The no_change_needed dictionary is a special case. If both of can_change # and cannot_change are empty, no_change_needed will used for sharing. Otherwise # unique_no_change_needed will be used for displaying, so we need to populate both. @@ -924,12 +924,14 @@ no_change_needed[ send_to_user ][ history ] = [ hda ] else: no_change_needed[ send_to_user ][ history ].append( hda ) - elif not trans.app.security_agent.can_access_dataset( send_to_user.all_roles(), hda.dataset ): + else: # The user with which we are sharing the history does not have access permission on the current dataset - if trans.app.security_agent.can_manage_dataset( user_roles, hda.dataset ) and not hda.dataset.library_associations: + if trans.app.security_agent.can_manage_dataset( user_roles, hda.dataset ): # The current user has authority to change permissions on the current dataset because - # they have permission to manage permissions on the dataset and the dataset is not associated - # with a library. + # they have permission to manage permissions on the dataset. + # NOTE: ( gvk )There may be problems if the dataset also has an ldda, but I don't think so + # because the user with which we are sharing will not have the "manage permission" permission + # on the dataset in their history. Keep an eye on this though... if unique: # Build the dictionaries for display, containing unique histories only if history not in can_change:

1 0

[hg] galaxy 3475: Updated Bowtie wrapper for new fastqcssanger d...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a2cb4b0ccf6b changeset: 3475:a2cb4b0ccf6b user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Wed Mar 03 15:37:43 2010 -0500 description: Updated Bowtie wrapper for new fastqcssanger datatype, and added equCab2 to builds.txt so sam_to_bam and sam_pileup will pass diffstat: test-data/bowtie_in1.fastqcssanger | 4 +++ test-data/bowtie_in1.fastqsanger | 4 --- test-data/bowtie_in3.fastqcssanger | 4 +++ test-data/bowtie_in3.fastqsanger | 4 --- test-data/bowtie_in4.fastqcssanger | 4 +++ test-data/bowtie_in4.fastqsanger | 4 --- tool-data/shared/ucsc/builds.txt | 1 + tools/sr_mapping/bowtie_color_wrapper.xml | 32 +++++++++++++++--------------- 8 files changed, 29 insertions(+), 28 deletions(-) diffs (183 lines): diff -r f0e32644688b -r a2cb4b0ccf6b test-data/bowtie_in1.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in1.fastqcssanger Wed Mar 03 15:37:43 2010 -0500 @@ -0,0 +1,4 @@ +@869_1532_1255/1 +G2102223311000312223321002 ++ +=;8:?@=?;;9:8;=>;5A?;<8>< diff -r f0e32644688b -r a2cb4b0ccf6b test-data/bowtie_in1.fastqsanger --- a/test-data/bowtie_in1.fastqsanger Wed Mar 03 15:18:09 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@869_1532_1255/1 -G2102223311000312223321002 -+ -=;8:?@=?;;9:8;=>;5A?;<8>< diff -r f0e32644688b -r a2cb4b0ccf6b test-data/bowtie_in3.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in3.fastqcssanger Wed Mar 03 15:37:43 2010 -0500 @@ -0,0 +1,4 @@ +@869_1532_1255/1 +G2102223311000312223321002 ++ +=;8:?@=?;;9:8;=>;5A?;<8>< diff -r f0e32644688b -r a2cb4b0ccf6b test-data/bowtie_in3.fastqsanger --- a/test-data/bowtie_in3.fastqsanger Wed Mar 03 15:18:09 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@869_1532_1255/1 -G2102223311000312223321002 -+ -=;8:?@=?;;9:8;=>;5A?;<8>< diff -r f0e32644688b -r a2cb4b0ccf6b test-data/bowtie_in4.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in4.fastqcssanger Wed Mar 03 15:37:43 2010 -0500 @@ -0,0 +1,4 @@ +@869_1532_1255/2 +T1301222000112122113330022 ++ +;89<:==5<8>69;8=<9;<>9:=< diff -r f0e32644688b -r a2cb4b0ccf6b test-data/bowtie_in4.fastqsanger --- a/test-data/bowtie_in4.fastqsanger Wed Mar 03 15:18:09 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@869_1532_1255/2 -T1301222000112122113330022 -+ -;89<:==5<8>69;8=<9;<>9:=< diff -r f0e32644688b -r a2cb4b0ccf6b tool-data/shared/ucsc/builds.txt --- a/tool-data/shared/ucsc/builds.txt Wed Mar 03 15:18:09 2010 -0500 +++ b/tool-data/shared/ucsc/builds.txt Wed Mar 03 15:37:43 2010 -0500 @@ -786,6 +786,7 @@ aeroHydr_ATCC7966 Aeromonas hydrophila subsp. hydrophila ATCC 7966 (aeroHydr_ATCC7966) baciAnth_AMES Bacillus anthracis str. Ames (baciAnth_AMES) shewOnei Shewanella oneidensis MR-1 (shewOnei) +equCab2 Horse Sep. 2007 (equCab2) arabidopsis Arabidopsis thaliana TAIR9 arabidopsis_tair8 Arabidopsis thaliana TAIR8 araTha1 Arabidopsis thaliana TAIR7 diff -r f0e32644688b -r a2cb4b0ccf6b tools/sr_mapping/bowtie_color_wrapper.xml --- a/tools/sr_mapping/bowtie_color_wrapper.xml Wed Mar 03 15:18:09 2010 -0500 +++ b/tools/sr_mapping/bowtie_color_wrapper.xml Wed Mar 03 15:37:43 2010 -0500 @@ -210,7 +210,7 @@ <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own"> <option value="indexPreSet">Default</option> <option value="indexFull">Set your own</option> - </param> + </param> <when value="indexPreSet" /> <when value="indexFull"> <conditional name="autoBehavior"> @@ -259,7 +259,7 @@ <option value="paired">Paired-end</option> </param> <when value="single"> - <param name="sInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="sInput1" type="data" format="fastqcssanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> <conditional name="sParams"> <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> <option value="preSet">Commonly used</option> @@ -317,8 +317,8 @@ </conditional>  </when>  <when value="paired"> - <param name="pInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> - <param name="pInput2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="pInput1" type="data" format="fastqcssanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="pInput2" type="data" format="fastqcssanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" /> <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)"> <option value="ff">FF (for SOLiD)</option> @@ -401,14 +401,14 @@ <test>  <param name="genomeSource" value="indexed" /> <param name="index" value="equCab2chrM" /> <param name="sPaired" value="single" /> - <param name="sInput1" ftype="fastqsanger" value="bowtie_in1.fastqsanger" /> + <param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" /> <param name="sSettingsType" value="preSet" /> <param name="suppressHeader" value="true" /> <output name="output" ftype="sam" file="bowtie_out1.sam" /> @@ -417,7 +417,7 @@  @@ -425,8 +425,8 @@ <param name="ownFile" value="chr_m.fasta" /> <param name="indexSettings" value="indexPreSet" /> <param name="sPaired" value="paired" /> - <param name="pInput1" ftype="fastqsanger" value="bowtie_in3.fastqsanger" /> - <param name="pInput2" ftype="fastqsanger" value="bowtie_in4.fastqsanger" /> + <param name="pInput1" ftype="fastqcssanger" value="bowtie_in3.fastqcssanger" /> + <param name="pInput2" ftype="fastqcssanger" value="bowtie_in4.fastqcssanger" /> <param name="pMaxInsert" value="1000" /> <param name="pMateOrient" value="ff" /> <param name="pSettingsType" value="full" /> @@ -460,14 +460,14 @@ <test>  <param name="genomeSource" value="indexed" /> <param name="index" value="equCab2chrM" /> <param name="sPaired" value="single" /> - <param name="sInput1" ftype="fastqsanger" value="bowtie_in1.fastqsanger" /> + <param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" /> <param name="sSettingsType" value="full" /> <param name="sSkip" value="0" /> <param name="sAlignLimit" value="-1" /> @@ -496,7 +496,7 @@  @@ -517,8 +517,8 @@ <param name="seed" value="-1" /> <param name="cutoff" value="-1" /> <param name="sPaired" value="paired" /> - <param name="pInput1" ftype="fastqsanger" value="bowtie_in3.fastqsanger" /> - <param name="pInput2" ftype="fastqsanger" value="bowtie_in4.fastqsanger" /> + <param name="pInput1" ftype="fastqcssanger" value="bowtie_in3.fastqcssanger" /> + <param name="pInput2" ftype="fastqcssanger" value="bowtie_in4.fastqcssanger" /> <param name="pMaxInsert" value="1000" /> <param name="pMateOrient" value="ff" /> <param name="pSettingsType" value="preSet" /> @@ -558,7 +558,7 @@ The output is in SAM format, and has the following columns:: Column Description - -------- -------------------------------------------------------- + -------- -------------------------------------------------------- 1 QNAME Query (pair) NAME 2 FLAG bitwise FLAG 3 RNAME Reference sequence NAME @@ -571,7 +571,7 @@ 10 SEQ query SEQuence on the same strand as the reference 11 QUAL query QUALity (ASCII-33 gives the Phred base quality) 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE - + The flags are as follows:: Flag Description

1 0

[hg] galaxy 3474: Update tool_conf.xml.main to use the new FASTQ...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f0e32644688b changeset: 3474:f0e32644688b user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Mar 03 15:18:09 2010 -0500 description: Update tool_conf.xml.main to use the new FASTQ tools. Minor updates to help text for a few of the FASTQ tools. diffstat: tool_conf.xml.main | 15 +++++++++++++-- tools/fastq/fastq_filter.xml | 2 +- tools/fastq/fastq_groomer.xml | 5 ++++- tools/fastq/fastq_manipulation.xml | 10 +++++----- tools/fastq/fastq_trimmer.xml | 2 +- 5 files changed, 24 insertions(+), 10 deletions(-) diffs (116 lines): diff -r d6d156b04767 -r f0e32644688b tool_conf.xml.main --- a/tool_conf.xml.main Wed Mar 03 14:34:31 2010 -0500 +++ b/tool_conf.xml.main Wed Mar 03 15:18:09 2010 -0500 @@ -265,20 +265,31 @@ </section> <label text="NGS Toolbox Beta" id="ngs" /> <section name="NGS: QC and manipulation" id="cshl_library_information"> - <label text="Generic FASTQ data" id="fastq" /> + <label text="Illumina data" id="illumina" /> + <tool file="fastq/fastq_groomer.xml" /> + <tool file="fastq/fastq_paired_end_splitter.xml" /> + <tool file="fastq/fastq_paired_end_joiner.xml" /> + <tool file="fastq/fastq_stats.xml" /> +  <label text="Roche-454 data" id="454" /> <tool file="metag_tools/short_reads_figure_score.xml" /> <tool file="metag_tools/short_reads_trim_seq.xml" /> + <tool file="fastq/fastq_combiner.xml" /> <label text="AB-SOLiD data" id="solid" /> <tool file="next_gen_conversion/solid2fastq.xml" /> <tool file="solid_tools/solid_qual_stats.xml" /> <tool file="solid_tools/solid_qual_boxplot.xml" /> + <label text="Generic FASTQ manipulation" id="generic_fastq" /> + <tool file="fastq/fastq_filter.xml" /> + <tool file="fastq/fastq_trimmer.xml" /> + <tool file="fastq/fastq_manipulation.xml" /> + <tool file="fastq/fastq_to_fasta.xml" /> </section> <section name="NGS: Mapping" id="ngs_mapping"> <label text="Illumina" id="illumina"/> diff -r d6d156b04767 -r f0e32644688b tools/fastq/fastq_filter.xml --- a/tools/fastq/fastq_filter.xml Wed Mar 03 14:34:31 2010 -0500 +++ b/tools/fastq/fastq_filter.xml Wed Mar 03 15:18:09 2010 -0500 @@ -16,7 +16,7 @@ <param name="paired_end" label="This is paired end data" type="boolean" truevalue="paired_end" falsevalue="single_end" checked="False"/> <repeat name="fastq_filters" title="Quality Filter on a Range of Bases" help="The above settings do not apply to these filters."> <conditional name="offset_type"> - <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Absolute for e.g. fixed length reads.<br>Percentage for e.g. variable length reads."> + <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)"> <option value="offsets_absolute" selected="true">Absolute Values</option> <option value="offsets_percent">Percentage of Read Length</option> </param> diff -r d6d156b04767 -r f0e32644688b tools/fastq/fastq_groomer.xml --- a/tools/fastq/fastq_groomer.xml Wed Mar 03 14:34:31 2010 -0500 +++ b/tools/fastq/fastq_groomer.xml Wed Mar 03 15:18:09 2010 -0500 @@ -317,7 +317,7 @@ When converting, if a quality score falls outside of the target score range, it will be coerced to the closest available value (i.e. the minimum or maximum). -When converting between Solexa and the other formats, quality scores are mapped between Solexa and PHRED scales using the equations found in Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16. +When converting between Solexa and the other formats, quality scores are mapped between Solexa and PHRED scales using the equations found in `Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.`_ When converting between color space (csSanger) and base/sequence space (Sanger, Illumina, Solexa) formats, adapter bases are lost or gained; if gained, the base 'G' is used as the adapter. You cannot convert a color space read to base space if there is no adapter present in the color space sequence. Any masked or ambiguous nucleotides in base space will be converted to 'N's when determining color space encoding. @@ -340,5 +340,8 @@ Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format + +.. _Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.: http://www.ncbi.nlm.nih.gov/pubmed/20015970 + </help> </tool> diff -r d6d156b04767 -r f0e32644688b tools/fastq/fastq_manipulation.xml --- a/tools/fastq/fastq_manipulation.xml Wed Mar 03 14:34:31 2010 -0500 +++ b/tools/fastq/fastq_manipulation.xml Wed Mar 03 15:18:09 2010 -0500 @@ -89,25 +89,25 @@ </when> <when value="trim"> <conditional name="offset_type"> - <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Absolute for e.g. fixed length reads.<br>Percentage for e.g. variable length reads."> + <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)"> <option value="offsets_absolute" selected="true">Absolute Values</option> <option value="offsets_percent">Percentage of Read Length</option> </param> <when value="offsets_absolute"> - <param name="left_column_offset" label="Absolute Left Base Offset" value="0" type="integer" help="Values start at 0, increasing from the left"> + <param name="left_column_offset" label="Offset from 5' end" value="0" type="integer" help="Values start at 0, increasing from the left"> <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> </param> - <param name="right_column_offset" label="Absolute Right Base Offset" value="0" type="integer" help="Values start at 0, increasing from the right"> + <param name="right_column_offset" label="Offset from 3' end" value="0" type="integer" help="Values start at 0, increasing from the right"> <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> </param> </when> <when value="offsets_percent"> - <param name="left_column_offset" label="Percentage Left Base Offset" value="0" type="float"> + <param name="left_column_offset" label="Offset from 5' end" value="0" type="float"> <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> </param> - <param name="right_column_offset" label="Percentage Right Base Offset" value="0" type="float"> + <param name="right_column_offset" label="Offset from 3' end" value="0" type="float"> <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> </param> </when> diff -r d6d156b04767 -r f0e32644688b tools/fastq/fastq_trimmer.xml --- a/tools/fastq/fastq_trimmer.xml Wed Mar 03 14:34:31 2010 -0500 +++ b/tools/fastq/fastq_trimmer.xml Wed Mar 03 15:18:09 2010 -0500 @@ -4,7 +4,7 @@ <inputs> <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ File"/> <conditional name="offset_type"> - <param name="base_offset_type" type="select" label="Define Base Offsets as"> + <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)"> <option value="offsets_absolute" selected="true">Absolute Values</option> <option value="offsets_percent">Percentage of Read Length</option> </param>

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[hg] galaxy 3473: Changes for some FASTQ tools. Move several opt...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/d6d156b04767 changeset: 3473:d6d156b04767 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Mar 03 14:34:31 2010 -0500 description: Changes for some FASTQ tools. Move several options of the Groomer tool under an advanced options conditional. Update help for groomer, filter and manipulation tools. diffstat: tools/fastq/fastq_filter.xml | 10 +- tools/fastq/fastq_groomer.xml | 277 ++++++++++++++++++------------------ tools/fastq/fastq_manipulation.xml | 2 +- 3 files changed, 142 insertions(+), 147 deletions(-) diffs (526 lines): diff -r bfcf6a3249c7 -r d6d156b04767 tools/fastq/fastq_filter.xml --- a/tools/fastq/fastq_filter.xml Wed Mar 03 14:30:32 2010 -0500 +++ b/tools/fastq/fastq_filter.xml Wed Mar 03 14:34:31 2010 -0500 @@ -16,7 +16,7 @@ <param name="paired_end" label="This is paired end data" type="boolean" truevalue="paired_end" falsevalue="single_end" checked="False"/> <repeat name="fastq_filters" title="Quality Filter on a Range of Bases" help="The above settings do not apply to these filters."> <conditional name="offset_type"> - <param name="base_offset_type" type="select" label="Define Base Offsets as"> + <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Absolute for e.g. fixed length reads.<br>Percentage for e.g. variable length reads."> <option value="offsets_absolute" selected="true">Absolute Values</option> <option value="offsets_percent">Percentage of Read Length</option> </param> @@ -289,15 +289,15 @@ <help> This tool allows you to build complex filters to be applied to each read in a FASTQ file. -Basic Options: +**Basic Options:** * You can specify a minimum and maximum read lengths. * You can specify minimum and maximum per base quality scores, with optionally specifying the number of bases that are allowed to deviate from this range (default of 0 deviant bases). * If your data is paired-end, select the proper checkbox; this will cause each read to be internally split down the middle and filters applied to each half using the offsets specified. -Advance Options: +**Advance Options:** * You can specify any number of advanced filters. - * Offsets are defined, starting at zero, increasing from the ends of the reads. For example, a quality string of "ABCDEFG", with offsets of 1 and 1 specified will yield "BCDEF". - * You can specify either absolute offset values, or percentage offset values. When using the percent-based method, offsets are rounded to the nearest integer. + * 5' and 3' offsets are defined, starting at zero, increasing from the respective end of the reads. For example, a quality string of "ABCDEFG", with 5' and 3' offsets of 1 and 1, respectively, specified will yield "BCDEF". + * You can specify either absolute offset values, or percentage offset values. *Absolute Values* based offsets are useful for fixed length reads (e.g. Illumina or SOLiD data). *Percentage of Read Length* based offsets are useful for variable length reads (e.g. 454 data). When using the percent-based method, offsets are rounded to the nearest integer. * The user specifies the aggregating action (min, max, sum, mean) to perform on the quality score values found between the specified offsets to be used with the user defined comparison operation and comparison value. * If a set of offsets is specified that causes the remaining quality score list to be of length zero, then the read will **pass** the quality filter unless the size range filter is used to remove these reads. diff -r bfcf6a3249c7 -r d6d156b04767 tools/fastq/fastq_groomer.xml --- a/tools/fastq/fastq_groomer.xml Wed Mar 03 14:30:32 2010 -0500 +++ b/tools/fastq/fastq_groomer.xml Wed Mar 03 14:34:31 2010 -0500 @@ -1,6 +1,17 @@ -<tool id="fastq_groomer" name="FASTQ Groomer" version="1.0.1"> +<tool id="fastq_groomer" name="FASTQ Groomer" version="1.0.2"> <description>convert between various FASTQ quality formats</description> - <command interpreter="python">fastq_groomer.py '$input_file' '$input_type' '$output_file' '$output_type' '$force_quality_encoding' '$summarize_input'</command> + <command interpreter="python">fastq_groomer.py '$input_file' '$input_type' '$output_file' +#if str( $options_type['options_type_selector'] ) == 'basic': +#if str( $input_type ) == 'cssanger': +'cssanger' +#else: +'sanger' +#end if +'ascii' 'summarize_input' +#else: +'${options_type.output_type}' '${options_type.force_quality_encoding}' '${options_type.summarize_input}' +#end if +</command> <inputs> <param name="input_file" type="data" format="fastq" label="File to groom" /> <param name="input_type" type="select" label="Input FASTQ quality scores type"> @@ -9,63 +20,110 @@ <option value="sanger" selected="True">Sanger</option> <option value="cssanger">Color Space Sanger</option> </param> - <param name="output_type" type="select" label="Output FASTQ quality scores type"> - <option value="solexa">Solexa</option> - <option value="illumina">Illumina 1.3+</option> - <option value="sanger" selected="True">Sanger (recommended)</option> - <option value="cssanger">Color Space Sanger</option> + <conditional name="options_type"> + <param name="options_type_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> </param> - <param name="force_quality_encoding" type="select" label="Force Quality Score encoding"> - <option value="None">Use Source Encoding</option> - <option value="ascii" selected="True">ASCII</option> - <option value="decimal">Decimal</option> - </param> - <param name="summarize_input" type="select" label="Summarize input data"> - <option value="summarize_input" selected="True">Summarize Input</option> - <option value="dont_summarize_input">Do not Summarize Input (faster)</option> - </param> + <when value="basic"> +  + </when> + <when value="advanced"> + <param name="output_type" type="select" label="Output FASTQ quality scores type" help="Galaxy tools are designed to work with the Sanger Quality score format."> + <option value="solexa">Solexa</option> + <option value="illumina">Illumina 1.3+</option> + <option value="sanger" selected="True">Sanger (recommended)</option> + <option value="cssanger">Color Space Sanger</option> + </param> + <param name="force_quality_encoding" type="select" label="Force Quality Score encoding"> + <option value="None">Use Source Encoding</option> + <option value="ascii" selected="True">ASCII</option> + <option value="decimal">Decimal</option> + </param> + <param name="summarize_input" type="select" label="Summarize input data"> + <option value="summarize_input" selected="True">Summarize Input</option> + <option value="dont_summarize_input">Do not Summarize Input (faster)</option> + </param> + </when> + </conditional> </inputs> <outputs> - <data name="output_file" format="fastq"> + <data name="output_file" format="fastqsanger"> <change_format> - <when input="output_type" value="solexa" format="fastqsolexa" /> - <when input="output_type" value="illumina" format="fastqillumina" /> - <when input="output_type" value="sanger" format="fastqsanger" /> - <when input="output_type" value="cssanger" format="fastqcssanger" /> + <when input="input_type" value="cssanger" format="fastqcssanger" /> + <when input="options_type.output_type" value="solexa" format="fastqsolexa" /> + <when input="options_type.output_type" value="illumina" format="fastqillumina" /> + <when input="options_type.output_type" value="sanger" format="fastqsanger" /> + <when input="options_type.output_type" value="cssanger" format="fastqcssanger" /> </change_format> </data> </outputs> <tests>   +  + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> + <param name="input_type" value="sanger" /> + <param name="options_type_selector" value="basic" /> + <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> + </test> + <test> + <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> + <param name="input_type" value="cssanger" /> + <param name="options_type_selector" value="basic" /> + <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> + </test> + <test> + <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> + <param name="input_type" value="illumina" /> + <param name="options_type_selector" value="basic" /> + <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" /> + </test> + <test> + <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> + <param name="input_type" value="solexa" /> + <param name="options_type_selector" value="basic" /> + <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" /> + </test> + <test> + <param name="input_file" value="sanger_full_range_as_illumina.fastqillumina" ftype="fastq" /> + <param name="input_type" value="sanger" /> + <param name="options_type_selector" value="basic" /> + <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" /> + </test>  <test> - <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastqillumina" /> + <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> <param name="input_type" value="illumina" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="illumina" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="illumina_full_range_original_illumina.fastqillumina" /> </test> <test> - <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastqillumina" /> + <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> <param name="input_type" value="illumina" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="sanger" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" /> </test> <test> - <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastqillumina" /> + <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> <param name="input_type" value="illumina" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="solexa" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="illumina_full_range_as_solexa.fastqsolexa" /> </test> <test> - <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastqillumina" /> + <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> <param name="input_type" value="illumina" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="cssanger" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> @@ -73,32 +131,36 @@ </test>  <test> - <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> <param name="input_type" value="sanger" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="sanger" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> </test> <test> - <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> <param name="input_type" value="sanger" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="illumina" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" /> </test> <test> - <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> <param name="input_type" value="sanger" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="solexa" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" /> </test> <test> - <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> <param name="input_type" value="sanger" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="cssanger" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> @@ -106,32 +168,36 @@ </test>  <test> - <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa" /> + <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> <param name="input_type" value="solexa" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="solexa" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" /> </test> <test> - <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa" /> + <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> <param name="input_type" value="solexa" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="illumina" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="solexa_full_range_as_illumina.fastqillumina" /> </test> <test> - <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa" /> + <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> <param name="input_type" value="solexa" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="sanger" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" /> </test> <test> - <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa" /> + <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> <param name="input_type" value="solexa" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="cssanger" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> @@ -139,32 +205,36 @@ </test>  <test> - <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" /> + <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> <param name="input_type" value="cssanger" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="cssanger" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> </test> <test> - <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" /> + <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> <param name="input_type" value="cssanger" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="sanger" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> </test> <test> - <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" /> + <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> <param name="input_type" value="cssanger" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="illumina" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" /> </test> <test> - <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" /> + <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> <param name="input_type" value="cssanger" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="solexa" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> @@ -172,24 +242,27 @@ </test>  <test> - <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" /> <param name="input_type" value="sanger" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="sanger" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="wrapping_as_sanger.fastqsanger" /> </test> <test> - <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" /> <param name="input_type" value="sanger" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="illumina" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="wrapping_as_illumina.fastqillumina" /> </test> <test> - <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" /> <param name="input_type" value="sanger" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="solexa" /> <param name="force_quality_encoding" value="None" /> <param name="summarize_input" value="summarize_input" /> @@ -198,16 +271,18 @@   <test> - <param name="input_file" value="sanger_full_range_as_decimal_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="input_file" value="sanger_full_range_as_decimal_sanger.fastqsanger" ftype="fastq" /> <param name="input_type" value="sanger" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="sanger" /> <param name="force_quality_encoding" value="ascii" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> </test> <test> - <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> <param name="input_type" value="sanger" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="sanger" /> <param name="force_quality_encoding" value="decimal" /> <param name="summarize_input" value="summarize_input" /> @@ -215,16 +290,18 @@ </test>  <test> - <param name="input_file" value="solexa_full_range_as_decimal_solexa.fastqsolexa" ftype="fastqsolexa" /> + <param name="input_file" value="solexa_full_range_as_decimal_solexa.fastqsolexa" ftype="fastq" /> <param name="input_type" value="solexa" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="solexa" /> <param name="force_quality_encoding" value="ascii" /> <param name="summarize_input" value="summarize_input" /> <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" /> </test> <test> - <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa" /> + <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> <param name="input_type" value="solexa" /> + <param name="options_type_selector" value="advanced" /> <param name="output_type" value="solexa" /> <param name="force_quality_encoding" value="decimal" /> <param name="summarize_input" value="summarize_input" /> @@ -236,6 +313,8 @@ This tool offers several conversions options relating to the FASTQ format. +When using *Basic* options, the output will be *sanger* formatted or *cssanger* formatted (when the input is Color Space Sanger). + When converting, if a quality score falls outside of the target score range, it will be coerced to the closest available value (i.e. the minimum or maximum). When converting between Solexa and the other formats, quality scores are mapped between Solexa and PHRED scales using the equations found in Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16. @@ -244,106 +323,22 @@ ----- -**Examples** +**Quality Score Comparison** -1. Converting the Solexa FASTQ data:: +:: - @Solexa scores from -5 to 62 inclusive (in that order) - ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT - + - ;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ - @Solexa scores from 62 to -5 inclusive (in that order) - TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA - + - ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<; + SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS + ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII + ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX + !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ + | | | | | | + 33 59 64 73 104 126 + + S - Sanger Phred+33, 93 values (0, 93) (0 to 60 expected in raw reads) + I - Illumina 1.3 Phred+64, 62 values (0, 62) (0 to 40 expected in raw reads) + X - Solexa Solexa+64, 67 values (-5, 62) (-5 to 40 expected in raw reads) -- will produce the following Sanger FASTQ data:: - - @Solexa scores from -5 to 62 inclusive (in that order) - ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT - + - ""##$$%%&&'()*++,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_ - @Solexa scores from 62 to -5 inclusive (in that order) - TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA - + - _^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,++*)('&&%%$$##"" - -- will produce the following Illumina 1.3+ FASTQ data:: - - @Solexa scores from -5 to 62 inclusive (in that order) - ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT - + - AABBCCDDEEFGHIJJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ - @Solexa scores from 62 to -5 inclusive (in that order) - TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA - + - ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJJIHGFEEDDCCBBAA - -2. Converting the Illumina 1.3+ FASTQ data:: - - @Illumina PHRED scores from 0 to 62 inclusive (in that order) - ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG - + - @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ - @Illumina PHRED scores from 62 to 0 inclusive (in that order) - GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA - + - ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@ - -- will produce the following Sanger FASTQ data:: - - @Illumina PHRED scores from 0 to 62 inclusive (in that order) - ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG - + - !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_ - @Illumina PHRED scores from 62 to 0 inclusive (in that order) - GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA - + - _^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! - -- will produce the following Solexa FASTQ data:: - - @Illumina PHRED scores from 0 to 62 inclusive (in that order) - ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG - + - ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ - @Illumina PHRED scores from 62 to 0 inclusive (in that order) - GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA - + - ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJHGFECB@>;; - -3. Converting standard Sanger FASTQ:: - - @Sanger PHRED scores from 0 to 93 inclusive (in that order) - ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC - + - !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ - @Sanger PHRED scores from 93 to 0 inclusive (in that order) - CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA - + - ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! - -- will produce the following Solexa FASTQ data:: - - @Sanger PHRED scores from 0 to 93 inclusive (in that order) - ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC - + - ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - @Sanger PHRED scores from 93 to 0 inclusive (in that order) - CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA - + - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJHGFECB@>;; - -- will produce the following Illumina 1.3+ FASTQ data:: - - @Sanger PHRED scores from 0 to 93 inclusive (in that order) - ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC - + - @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - @Sanger PHRED scores from 93 to 0 inclusive (in that order) - CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA - + - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@ +Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format </help> </tool> diff -r bfcf6a3249c7 -r d6d156b04767 tools/fastq/fastq_manipulation.xml --- a/tools/fastq/fastq_manipulation.xml Wed Mar 03 14:30:32 2010 -0500 +++ b/tools/fastq/fastq_manipulation.xml Wed Mar 03 14:34:31 2010 -0500 @@ -89,7 +89,7 @@ </when> <when value="trim"> <conditional name="offset_type"> - <param name="base_offset_type" type="select" label="Define Base Offsets as"> + <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Absolute for e.g. fixed length reads.<br>Percentage for e.g. variable length reads."> <option value="offsets_absolute" selected="true">Absolute Values</option> <option value="offsets_percent">Percentage of Read Length</option> </param>

1 0

[hg] galaxy 3472: Enhance change_format tag of tool outputs to a...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/bfcf6a3249c7 changeset: 3472:bfcf6a3249c7 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Mar 03 14:30:32 2010 -0500 description: Enhance change_format tag of tool outputs to allow the use of Grouping Constructs. Objects can be accessed using the previously accepted bare name or using the same style as used within templates (e.g. the tool command tag). e.g. <outputs> <data name="output_file" format="fastqsanger"> <change_format> <when input="input_type" value="cssanger" format="fastqcssanger" /> <when input="options_type.output_type" value="solexa" format="fastqsolexa" /> <when input="options_type.output_type" value="illumina" format="fastqillumina" /> <when input="options_type.output_type" value="sanger" format="fastqsanger" /> <when input="options_type.output_type" value="cssanger" format="fastqcssanger" /> </change_format> </data> </outputs> or <outputs> <data name="output_file" format="fastqsanger"> <change_format> <when input="$input_type" value="cssanger" format="fastqcssanger" /> <when input="${options_type.output_type}" value="solexa" format="fastqsolexa" /> <when input="${options_type.output_type}" value="illumina" format="fastqillumina" /> <when input="${options_type.output_type}" value="sanger" format="fastqsanger" /> <when input="${options_type.output_type}" value="cssanger" format="fastqcssanger" /> </change_format> </data> </outputs> where 'options_type' is the name of the grouping parameter and 'output_type' is the name of a parameter found in this group and 'input_type' is the name of a parameter not found within a group. diffstat: lib/galaxy/tools/actions/__init__.py | 14 +++++++++++--- 1 files changed, 11 insertions(+), 3 deletions(-) diffs (27 lines): diff -r d51de35b53d8 -r bfcf6a3249c7 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Wed Mar 03 13:51:29 2010 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Wed Mar 03 14:30:32 2010 -0500 @@ -213,12 +213,20 @@ ext = input_ext #process change_format tags if output.change_format: + params = make_dict_copy( incoming ) #FIXME: The wrapping of inputs should only be done once per call to execute; currently happens here and possibly when generating output dataset name + wrap_values( tool.inputs, params ) for change_elem in output.change_format: for when_elem in change_elem.findall( 'when' ): - check = incoming.get( when_elem.get( 'input' ), None ) + check = when_elem.get( 'input', None ) if check is not None: - if check == when_elem.get( 'value', None ): - ext = when_elem.get( 'format', ext ) + try: + if '$' not in check: + #allow a simple name or more complex specifications + check = '${%s}' % check + if str( fill_template( check, context = params ) ) == when_elem.get( 'value', None ): + ext = when_elem.get( 'format', ext ) + except: #bad tag input value; possibly referencing a param within a different conditional when block or other nonexistent grouping construct + continue else: check = when_elem.get( 'input_dataset', None ) if check is not None:

1 0

[hg] galaxy 3471: Fixed broken functional tests
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/d51de35b53d8 changeset: 3471:d51de35b53d8 user: rc date: Wed Mar 03 13:51:29 2010 -0500 description: Fixed broken functional tests diffstat: test/base/twilltestcase.py | 16 +++++++++++----- test/functional/test_forms_and_requests.py | 18 +++++++++--------- 2 files changed, 20 insertions(+), 14 deletions(-) diffs (109 lines): diff -r 0291f870f2c9 -r d51de35b53d8 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Mar 03 13:40:26 2010 -0500 +++ b/test/base/twilltestcase.py Wed Mar 03 13:51:29 2010 -0500 @@ -1281,12 +1281,12 @@ def check_request_grid(self, state, request_name, deleted=False): self.home() self.visit_url('%s/requests/list?sort=create_time&f-state=%s&f-deleted=%s' \ - % (self.url, state, str(deleted))) + % (self.url, state.replace(' ', '+'), str(deleted))) self.check_page_for_string( request_name ) def check_request_admin_grid(self, state, request_name, deleted=False): self.home() self.visit_url('%s/requests_admin/list?sort=create_time&f-state=%s&f-deleted=%s' \ - % (self.url, state, str(deleted))) + % (self.url, state.replace(' ', '+'), str(deleted))) self.check_page_for_string( request_name ) def create_request_type( self, name, desc, request_form_id, sample_form_id, states ): self.home() @@ -1327,14 +1327,20 @@ self.check_page_for_string( new_desc ) def add_samples( self, request_id, request_name, samples ): self.home() - self.visit_url( "%s/requests/list?sort=-create_time&operation=show_request&id=%s" % ( self.url, self.security.encode_id( request_id ) )) + url = "%s/requests/list?sort=-create_time&operation=show_request&id=%s" % ( self.url, self.security.encode_id( request_id ) ) + self.visit_url( url ) self.check_page_for_string( 'Sequencing Request "%s"' % request_name ) + self.check_page_for_string( 'There are no samples.' ) + # this redundant stmt below is add so that the second form in + # the page gets selected + tc.fv( "2", "request_id", request_id ) for sample_index, sample in enumerate(samples): tc.submit( "add_sample_button" ) + self.check_page_for_string( 'Sequencing Request "%s"' % request_name ) sample_name, fields = sample - tc.fv( "1", "sample_%i_name" % sample_index, sample_name ) + tc.fv( "2", "sample_%i_name" % sample_index, sample_name ) for field_index, field_value in enumerate(fields): - tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) + tc.fv( "2", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) tc.submit( "save_samples_button" ) for sample_name, fields in samples: self.check_page_for_string( sample_name ) diff -r 0291f870f2c9 -r d51de35b53d8 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Wed Mar 03 13:40:26 2010 -0500 +++ b/test/functional/test_forms_and_requests.py Wed Mar 03 13:51:29 2010 -0500 @@ -231,12 +231,12 @@ request_one.desc+' (Re-described)', fields) sa_session.refresh( request_one ) # check if the request is showing in the 'new' filter - self.check_request_grid(state='New', request_name=request_one.name) + self.check_request_grid(state=request_one.states.NEW, request_name=request_one.name) # submit the request self.submit_request( request_one.id, request_one.name ) sa_session.refresh( request_one ) # check if the request is showing in the 'submitted' filter - self.check_request_grid(state='Submitted', request_name=request_one.name) + self.check_request_grid(state=request_one.states.SUBMITTED, request_name=request_one.name) # check if the request's state is now set to 'submitted' assert request_one.state is not request_one.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \ % ( request_one.name, request_one.states.SUBMITTED ) @@ -245,7 +245,7 @@ # goto admin manage requests page self.logout() self.login( email='test(a)bx.psu.edu' ) - self.check_request_admin_grid(state='Submitted', request_name=request_one.name) + self.check_request_admin_grid(state=request_one.states.SUBMITTED, request_name=request_one.name) self.visit_url( "%s/requests_admin/list?sort=-create_time&operation=show_request&id=%s" \ % ( self.url, self.security.encode_id( request_one.id ) )) self.check_page_for_string( 'Sequencing Request "%s"' % request_one.name ) @@ -261,9 +261,9 @@ self.logout() self.login( email='test1(a)bx.psu.edu' ) # check if the request's state is now set to 'complete' -# self.check_request_grid(state='Complete', request_name=request_one.name) -# assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" \ -# % ( request_one.name, request_one.states.COMPLETE ) + self.check_request_grid(state='Complete', request_name=request_one.name) + assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" \ + % ( request_one.name, request_one.states.COMPLETE ) def test_040_admin_create_request_on_behalf_of_regular_user( self ): """Testing creating and submitting a request as an admin on behalf of a regular user""" self.logout() @@ -281,7 +281,7 @@ galaxy.model.Request.table.c.deleted==False ) ) \ .first() # check if the request is showing in the 'new' filter - self.check_request_admin_grid(state='New', request_name=request_two.name) + self.check_request_admin_grid(state=request_two.states.NEW, request_name=request_two.name) # check if the request's state is now set to 'new' assert request_two.state is not request_two.states.NEW, "The state of the request '%s' should be set to '%s'" \ % ( request_two.name, request_two.states.NEW ) @@ -294,7 +294,7 @@ self.submit_request_as_admin( request_two.id, request_two.name ) sa_session.refresh( request_two ) # check if the request is showing in the 'submitted' filter - self.check_request_admin_grid(state='Submitted', request_name=request_two.name) + self.check_request_admin_grid(state=request_two.states.SUBMITTED, request_name=request_two.name) # check if the request's state is now set to 'submitted' assert request_two.state is not request_two.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \ % ( request_two.name, request_two.states.SUBMITTED ) @@ -308,7 +308,7 @@ self.reject_request( request_two.id, request_two.name, "Rejection test comment" ) sa_session.refresh( request_two ) # check if the request is showing in the 'rejected' filter - self.check_request_admin_grid(state='Rejected', request_name=request_two.name) + self.check_request_admin_grid(state=request_two.states.REJECTED, request_name=request_two.name) # check if the request's state is now set to 'submitted' assert request_two.state is not request_two.states.REJECTED, "The state of the request '%s' should be set to '%s'" \ % ( request_two.name, request_two.states.REJECTED )

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