details: http://www.bx.psu.edu/hg/galaxy/rev/ab1c33257cb3 changeset: 3323:ab1c33257cb3 user: gua110 date: Wed Feb 03 13:53:16 2010 -0500 description: Added functional tests for a couple of my tools with multiple outputs/pdf outputs.
diffstat:
test-data/5_liftover_mapped.bed | 131 ++ test-data/5_liftover_unmapped.bed | 6 + test-data/regr_inp.tabular | 10 + test-data/regr_out.pdf | 1590 ++++++++++++++++++++++++++++++ test-data/regr_out.tabular | 10 + tools/extract/liftOver_wrapper.xml | 8 +- tools/regVariation/linear_regression.xml | 9 +- 7 files changed, 1758 insertions(+), 6 deletions(-)
diffs (1819 lines):
diff -r 5c268e401913 -r ab1c33257cb3 test-data/5_liftover_mapped.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/5_liftover_mapped.bed Wed Feb 03 13:53:16 2010 -0500 @@ -0,0 +1,131 @@ +chr7 116197893 116197920 CCDS5763.1_cds_0_0_chr7_115444713_f 0 + +chr7 116222929 116223015 CCDS5763.1_cds_1_0_chr7_115468539_f 0 + +chr7 116237938 116238188 CCDS5763.1_cds_2_0_chr7_115483025_f 0 + +chr7 116239076 116239412 CCDS5763.1_cds_3_0_chr7_115484166_f 0 + +chr7 116240675 116240891 CCDS5763.1_cds_4_0_chr7_115485765_f 0 + +chr7 116241233 116241396 CCDS5763.1_cds_5_0_chr7_115486323_f 0 + +chr7 116246193 116246382 CCDS5763.1_cds_6_0_chr7_115491299_f 0 + +chr7 116222929 116223015 CCDS5764.1_cds_0_0_chr7_115468539_f 0 + +chr7 116237938 116238188 CCDS5764.1_cds_1_0_chr7_115483025_f 0 + +chr7 116239076 116239412 CCDS5764.1_cds_2_0_chr7_115484166_f 0 + +chr7 116240675 116240891 CCDS5764.1_cds_3_0_chr7_115485765_f 0 + +chr7 116241233 116241396 CCDS5764.1_cds_4_0_chr7_115486323_f 0 + +chr7 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/5_liftover_unmapped.bed Wed Feb 03 13:53:16 2010 -0500 @@ -0,0 +1,6 @@ +#Partially deleted in new +chr7 116549075 116549353 CCDS5771.1_cds_2_0_chr7_116549076_r 0 - +#Deleted in new +chr7 116953508 116953641 CCDS5774.1_cds_2_0_chr7_116953509_r 0 - +#Deleted in new +chr7 116955071 116955135 CCDS5774.1_cds_3_0_chr7_116955072_r 0 - diff -r 5c268e401913 -r ab1c33257cb3 test-data/regr_inp.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/regr_inp.tabular Wed Feb 03 13:53:16 2010 -0500 @@ -0,0 +1,10 @@ +7 33 42 +4 41 33 +16 7 75 +3 49 28 +21 5 91 +8 31 55 +7 35 52 +5 30 16 +15 10 69 +20 10 94 diff -r 5c268e401913 -r ab1c33257cb3 test-data/regr_out.pdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/regr_out.pdf Wed Feb 03 13:53:16 2010 -0500 @@ -0,0 +1,1590 @@ +%PDF-1.4 +%âãÏÓ\r +1 0 obj +<< +/CreationDate (D:20100112163009) +/ModDate (D:20100112163009) +/Title (R Graphics Output) +/Producer (R 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Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 379.95 501.55 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 465.93 437.10 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 479.16 431.73 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 462.62 367.28 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 396.48 462.17 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 396.48 506.93 Tm (l) Tj 0 Tr +ET +Q q 42.77 203.09 157.15 150.82 re W n +Q q 38.02 198.34 166.66 160.32 re W n +Q q +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +42.77 203.09 m +199.92 203.09 l +199.92 353.90 l +42.77 353.90 l +42.77 203.09 l +S +42.77 224.19 m 42.77 340.56 l S +42.77 224.19 m 38.02 224.19 l S +42.77 262.98 m 38.02 262.98 l S +42.77 301.77 m 38.02 301.77 l S +42.77 340.56 m 38.02 340.56 l S +BT +0.000 0.000 0.000 rg +/F2 1 Tf 0.00 8.00 -8.00 0.00 31.36 221.97 Tm (5) Tj +ET +BT +/F2 1 Tf 0.00 8.00 -8.00 0.00 31.36 258.53 Tm (10) Tj +ET +BT +/F2 1 Tf 0.00 8.00 -8.00 0.00 31.36 297.32 Tm (15) Tj +ET +BT +/F2 1 Tf 0.00 8.00 -8.00 0.00 31.36 336.11 Tm (20) Tj +ET +Q q 42.77 203.09 157.15 150.82 re W n +0.000 0.000 1.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 95.14 237.99 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 78.35 214.72 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 156.70 307.82 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 69.02 206.96 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 186.55 346.61 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 119.39 245.75 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 113.79 237.99 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 46.63 222.48 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 145.51 300.06 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 192.14 338.85 Tm (l) Tj 0 Tr +ET +Q q 209.42 203.09 157.15 150.82 re W n +Q q 204.67 198.34 166.66 160.32 re W n +Q q +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +209.42 203.09 m +366.58 203.09 l +366.58 353.90 l +209.42 353.90 l +209.42 203.09 l +S +Q q 209.42 203.09 157.15 150.82 re W n +BT +0.000 0.000 0.000 rg +/F2 1 Tf 16.00 0.00 -0.00 16.00 277.33 272.87 Tm (x.1) Tj +ET +Q q 376.08 203.09 157.15 150.82 re W n +Q q 371.33 198.34 166.66 160.32 re W n +Q q +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +376.08 203.09 m +533.23 203.09 l +533.23 353.90 l +376.08 353.90 l +376.08 203.09 l +S +Q q 376.08 203.09 157.15 150.82 re W n +0.000 0.000 1.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 472.54 237.99 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 499.00 214.72 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 386.56 307.82 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 525.46 206.96 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 379.95 346.61 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 465.93 245.75 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 479.16 237.99 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 462.62 222.48 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 396.48 300.06 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 396.48 338.85 Tm (l) Tj 0 Tr +ET +Q q 42.77 42.77 157.15 150.82 re W n +Q q 38.02 38.02 166.66 160.32 re W n +Q q +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +42.77 42.77 m +199.92 42.77 l +199.92 193.58 l +42.77 193.58 l +42.77 42.77 l +S +56.05 42.77 m 167.98 42.77 l S +56.05 42.77 m 56.05 38.02 l S +93.36 42.77 m 93.36 38.02 l S +130.67 42.77 m 130.67 38.02 l S +167.98 42.77 m 167.98 38.02 l S +BT +0.000 0.000 0.000 rg +/F2 1 Tf 8.00 0.00 -0.00 8.00 51.60 25.66 Tm (20) Tj +ET +BT +/F2 1 Tf 8.00 0.00 -0.00 8.00 88.91 25.66 Tm (40) Tj +ET +BT +/F2 1 Tf 8.00 0.00 -0.00 8.00 126.22 25.66 Tm (60) Tj +ET +BT +/F2 1 Tf 8.00 0.00 -0.00 8.00 163.53 25.66 Tm (80) Tj +ET +Q q 42.77 42.77 157.15 150.82 re W n +0.000 0.000 1.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 95.14 135.51 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 78.35 160.90 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 156.70 52.99 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 69.02 186.29 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 186.55 46.64 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 119.39 129.16 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 113.79 141.85 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 46.63 125.98 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 145.51 62.51 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 192.14 62.51 Tm (l) Tj 0 Tr +ET +Q q 209.42 42.77 157.15 150.82 re W n +Q q 204.67 38.02 166.66 160.32 re W n +Q q +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +209.42 42.77 m +366.58 42.77 l +366.58 193.58 l +209.42 193.58 l +209.42 42.77 l +S +Q q 209.42 42.77 157.15 150.82 re W n +0.000 0.000 1.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 245.63 135.51 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 221.37 160.90 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 318.38 52.99 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 213.29 186.29 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 358.80 46.64 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 253.71 129.16 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 245.63 141.85 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 229.46 125.98 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 310.30 62.51 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 4.94 0 0 4.94 350.72 62.51 Tm (l) Tj 0 Tr +ET +Q q 376.08 42.77 157.15 150.82 re W n +Q q 371.33 38.02 166.66 160.32 re W n +Q q +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +376.08 42.77 m +533.23 42.77 l +533.23 193.58 l +376.08 193.58 l +376.08 42.77 l +S +398.44 42.77 m 530.72 42.77 l S +398.44 42.77 m 398.44 38.02 l S +431.51 42.77 m 431.51 38.02 l S +464.58 42.77 m 464.58 38.02 l S +497.65 42.77 m 497.65 38.02 l S +530.72 42.77 m 530.72 38.02 l S +BT +0.000 0.000 0.000 rg +/F2 1 Tf 8.00 0.00 -0.00 8.00 393.99 25.66 Tm (10) Tj +ET +BT +/F2 1 Tf 8.00 0.00 -0.00 8.00 427.06 25.66 Tm (20) Tj +ET +BT +/F2 1 Tf 8.00 0.00 -0.00 8.00 460.13 25.66 Tm (30) Tj +ET +BT +/F2 1 Tf 8.00 0.00 -0.00 8.00 493.20 25.66 Tm (40) Tj +ET +BT +/F2 1 Tf 8.00 0.00 -0.00 8.00 526.27 25.66 Tm (50) Tj +ET +533.23 64.22 m 533.23 191.17 l S +533.23 64.22 m 537.98 64.22 l S +533.23 95.96 m 537.98 95.96 l S +533.23 127.70 m 537.98 127.70 l S +533.23 159.43 m 537.98 159.43 l S +533.23 191.17 m 537.98 191.17 l S +BT +/F2 1 Tf 0.00 8.00 -8.00 0.00 550.34 59.77 Tm (10) Tj +ET +BT +/F2 1 Tf 0.00 8.00 -8.00 0.00 550.34 91.51 Tm (20) Tj +ET +BT +/F2 1 Tf 0.00 8.00 -8.00 0.00 550.34 123.25 Tm (30) Tj +ET +BT +/F2 1 Tf 0.00 8.00 -8.00 0.00 550.34 154.99 Tm (40) Tj +ET +BT +/F2 1 Tf 0.00 8.00 -8.00 0.00 550.34 186.72 Tm (50) Tj +ET +Q q 376.08 42.77 157.15 150.82 re W n +BT +0.000 0.000 0.000 rg +/F2 1 Tf 16.00 0.00 -0.00 16.00 443.98 112.55 Tm (x.2) Tj +ET +Q q +BT +0.000 0.000 0.000 rg +/F3 1 Tf 14.00 0.00 -0.00 14.00 228.88 549.39 Tm (Scatterplot Matrix) Tj +ET +Q +endstream +endobj +7 0 obj +9361 +endobj +8 0 obj +<< +/Type /Page +/Parent 3 0 R +/Contents 9 0 R +/Resources 4 0 R +>> +endobj +9 0 obj +<< +/Length 10 0 R +>> +stream +q +Q q 59.04 73.44 486.72 443.52 re W n +Q q +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +91.71 73.44 m 481.63 73.44 l S +91.71 73.44 m 91.71 66.24 l S +156.70 73.44 m 156.70 66.24 l S +221.68 73.44 m 221.68 66.24 l S +286.67 73.44 m 286.67 66.24 l S +351.66 73.44 m 351.66 66.24 l S +416.64 73.44 m 416.64 66.24 l S +481.63 73.44 m 481.63 66.24 l S +BT +0.000 0.000 0.000 rg +/F2 1 Tf 12.00 0.00 -0.00 12.00 85.04 47.52 Tm (30) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 150.02 47.52 Tm (40) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 215.01 47.52 Tm (50) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 280.00 47.52 Tm (60) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 344.98 47.52 Tm (70) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 409.97 47.52 Tm (80) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 474.96 47.52 Tm (90) Tj +ET +59.04 147.85 m 59.04 487.37 l S +59.04 147.85 m 51.84 147.85 l S +59.04 232.73 m 51.84 232.73 l S +59.04 317.61 m 51.84 317.61 l S +59.04 402.49 m 51.84 402.49 l S +59.04 487.37 m 51.84 487.37 l S +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 137.67 Tm (-10) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 225.89 Tm (-5) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 314.27 Tm (0) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 399.15 Tm (5) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 480.69 Tm (10) Tj +ET +59.04 73.44 m +545.76 73.44 l +545.76 516.96 l +59.04 516.96 l +59.04 73.44 l +S +Q q +BT +0.000 0.000 0.000 rg +/F2 1 Tf 12.00 0.00 -0.00 12.00 268.54 18.72 Tm [(Fitted v) 25 (alues)] TJ +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 12.96 268.86 Tm (Residuals) Tj +ET +Q q 59.04 73.44 486.72 443.52 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 7.48 0 0 7.48 166.43 315.79 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 101.40 332.89 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 349.78 397.05 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 111.06 222.76 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 524.77 211.55 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 192.03 469.62 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 178.19 454.85 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 74.10 115.59 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 330.06 346.71 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 516.81 283.29 Tm (l) Tj 0 Tr +ET +1.000 0.000 0.000 RG +77.07 141.77 m +104.36 215.63 l +114.02 240.45 l +169.39 389.46 l +181.15 422.49 l +194.99 463.49 l +333.02 381.33 l +352.74 378.55 l +519.77 253.25 l +527.73 247.63 l +S +Q q +BT +0.000 0.000 0.000 rg +/F2 1 Tf 12.00 0.00 -0.00 12.00 99.28 4.32 Tm [(function (f) 30 (or) -25 (m) 10 (ula, data, subset, w) 10 (eights) 15 (, na.action, method = "qr", model = ...)] TJ +ET +Q q +BT +0.000 0.000 0.000 rg +/F2 1 Tf 12.00 0.00 -0.00 12.00 251.72 523.44 Tm (Residuals vs Fitted) Tj +ET +Q q +BT +0.000 0.000 0.000 rg +/F2 1 Tf 9.00 0.00 -0.00 9.00 80.67 113.16 Tm (8) Tj +ET +BT +/F2 1 Tf 9.00 0.00 -0.00 9.00 186.39 470.06 Tm (6) Tj +ET +BT +/F2 1 Tf 9.00 0.00 -0.00 9.00 172.54 455.29 Tm (7) Tj +ET +Q q 59.04 73.44 486.72 443.52 re W n +0.745 0.745 0.745 RG +0.75 w +[ 0.00 4.00] 0 d +1 J +1 j +10.00 M +59.04 317.61 m 545.76 317.61 l S +Q +endstream +endobj +10 0 obj +3090 +endobj +11 0 obj +<< +/Type /Page +/Parent 3 0 R +/Contents 12 0 R +/Resources 4 0 R +>> +endobj +12 0 obj +<< +/Length 13 0 R +>> +stream +q +Q q 59.04 73.44 486.72 443.52 re W n +Q q 59.04 73.44 486.72 443.52 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 7.48 0 0 7.48 281.58 323.65 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 317.30 340.84 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 394.93 412.99 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 203.95 210.25 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 153.67 203.79 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 524.77 469.29 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 445.20 457.77 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 74.10 87.27 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 354.14 356.10 Tm (l) Tj 0 Tr +ET +BT +/F1 1 Tf 1 Tr 7.48 0 0 7.48 244.74 284.34 Tm (l) Tj 0 Tr +ET +Q q +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +83.86 73.44 m 520.94 73.44 l S +83.86 73.44 m 83.86 66.24 l S +156.71 73.44 m 156.71 66.24 l S +229.55 73.44 m 229.55 66.24 l S +302.40 73.44 m 302.40 66.24 l S +375.25 73.44 m 375.25 66.24 l S +448.09 73.44 m 448.09 66.24 l S +520.94 73.44 m 520.94 66.24 l S +BT +0.000 0.000 0.000 rg +/F2 1 Tf 12.00 0.00 -0.00 12.00 72.02 47.52 Tm (-1.5) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 144.86 47.52 Tm (-1.0) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 217.71 47.52 Tm (-0.5) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 294.06 47.52 Tm (0.0) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 366.91 47.52 Tm (0.5) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 439.75 47.52 Tm (1.0) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 512.60 47.52 Tm (1.5) Tj +ET +59.04 100.87 m 59.04 437.81 l S +59.04 100.87 m 51.84 100.87 l S +59.04 213.18 m 51.84 213.18 l S +59.04 325.50 m 51.84 325.50 l S +59.04 437.81 m 51.84 437.81 l S +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 94.03 Tm (-2) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 206.34 Tm (-1) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 322.16 Tm (0) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 434.48 Tm (1) Tj +ET +59.04 73.44 m +545.76 73.44 l +545.76 516.96 l +59.04 516.96 l +59.04 73.44 l +S +Q q +BT +0.000 0.000 0.000 rg +/F2 1 Tf 12.00 0.00 -0.00 12.00 245.71 18.72 Tm (Theoretical Quantiles) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 12.96 234.26 Tm [(Standardiz) 15 (ed residuals)] TJ +ET +Q q 59.04 73.44 486.72 443.52 re W n +0.498 0.498 0.498 RG +0.75 w +[ 0.00 4.00] 0 d +1 J +1 j +10.00 M +59.04 105.88 m 545.76 526.86 l S +Q q +BT +0.000 0.000 0.000 rg +/F2 1 Tf 12.00 0.00 -0.00 12.00 99.28 4.32 Tm [(function (f) 30 (or) -25 (m) 10 (ula, data, subset, w) 10 (eights) 15 (, na.action, method = "qr", model = ...)] TJ +ET +Q q +BT +0.000 0.000 0.000 rg +/F2 1 Tf 12.00 0.00 -0.00 12.00 268.41 523.44 Tm [(Nor) -25 (mal Q-Q)] TJ +ET +Q q +BT +0.000 0.000 0.000 rg +/F2 1 Tf 9.00 0.00 -0.00 9.00 80.67 87.71 Tm (8) Tj +ET +BT +/F2 1 Tf 9.00 0.00 -0.00 9.00 519.13 469.73 Tm (6) Tj +ET +BT +/F2 1 Tf 9.00 0.00 -0.00 9.00 439.56 458.21 Tm (7) Tj +ET +Q +endstream +endobj +13 0 obj +2841 +endobj +14 0 obj +<< +/Type /Page +/Parent 3 0 R +/Contents 15 0 R +/Resources 4 0 R +>> +endobj +15 0 obj +<< +/Length 16 0 R +>> +stream +q +Q q 59.04 73.44 486.72 443.52 re W n +Q q +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +91.71 73.44 m 481.63 73.44 l S +91.71 73.44 m 91.71 66.24 l S +156.70 73.44 m 156.70 66.24 l S +221.68 73.44 m 221.68 66.24 l S +286.67 73.44 m 286.67 66.24 l S +351.66 73.44 m 351.66 66.24 l S +416.64 73.44 m 416.64 66.24 l S +481.63 73.44 m 481.63 66.24 l S +BT +0.000 0.000 0.000 rg +/F2 1 Tf 12.00 0.00 -0.00 12.00 85.04 47.52 Tm (30) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 150.02 47.52 Tm (40) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 215.01 47.52 Tm (50) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 280.00 47.52 Tm (60) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 344.98 47.52 Tm (70) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 409.97 47.52 Tm (80) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 474.96 47.52 Tm (90) Tj +ET +59.04 89.87 m 59.04 515.16 l S +59.04 89.87 m 51.84 89.87 l S +59.04 231.63 m 51.84 231.63 l S +59.04 373.39 m 51.84 373.39 l S +59.04 515.16 m 51.84 515.16 l S +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 81.53 Tm (0.0) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 223.29 Tm (0.5) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 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+/F2 1 Tf 12.00 0.00 -0.00 12.00 102.24 83.53 Tm (Cook's distance) Tj +ET +Q q +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +545.76 151.77 m 545.76 516.96 l S +545.76 151.77 m 545.76 151.77 l S +545.76 205.89 m 545.76 205.89 l S +545.76 467.22 m 545.76 467.22 l S +BT +1.000 0.000 0.000 rg +/F2 1 Tf 9.00 0.00 -0.00 9.00 549.36 148.54 Tm (1) Tj +ET +BT +/F2 1 Tf 9.00 0.00 -0.00 9.00 549.36 202.66 Tm (0.5) Tj +ET +BT +/F2 1 Tf 9.00 0.00 -0.00 9.00 549.36 463.98 Tm (0.5) Tj +ET +BT +0.000 0.000 0.000 rg +/F2 1 Tf 12.00 0.00 -0.00 12.00 242.10 523.44 Tm [(Residuals vs Le) 30 (v) 25 (er) 10 (age)] TJ +ET +Q q +BT +0.000 0.000 0.000 rg +/F2 1 Tf 9.00 0.00 -0.00 9.00 496.58 113.16 Tm (8) Tj +ET +BT +/F2 1 Tf 9.00 0.00 -0.00 9.00 519.13 227.13 Tm (4) Tj +ET +BT +/F2 1 Tf 9.00 0.00 -0.00 9.00 467.56 221.14 Tm (5) Tj +ET +Q +endstream +endobj +19 0 obj +6882 +endobj +3 0 obj +<< +/Type /Pages +/Kids [ +5 0 R +8 0 R +11 0 R +14 0 R +17 0 R +] +/Count 5 +/MediaBox [0 0 576 576] +>> +endobj +4 0 obj +<< +/ProcSet [/PDF /Text] +/Font << /F1 21 0 R /F2 22 0 R /F3 23 0 R >> +/ExtGState << >> +>> +endobj +20 0 obj +<< +/Type /Encoding +/BaseEncoding /WinAnsiEncoding +/Differences [ 45/minus 96/quoteleft +144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent +/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +>> +endobj +21 0 obj +<< +/Type /Font +/Subtype /Type1 +/Name /F1 +/BaseFont /ZapfDingbats +>> +endobj +22 0 obj << +/Type /Font +/Subtype /Type1 +/Name /F2 +/BaseFont /Helvetica +/Encoding 20 0 R +>> endobj +23 0 obj << +/Type /Font +/Subtype /Type1 +/Name /F3 +/BaseFont /Helvetica-Bold +/Encoding 20 0 R +>> endobj +xref +0 24 +0000000000 65535 f +0000000021 00000 n +0000000164 00000 n +0000027491 00000 n +0000027601 00000 n +0000000213 00000 n +0000000293 00000 n +0000009707 00000 n +0000009727 00000 n +0000009807 00000 n +0000012951 00000 n +0000012972 00000 n +0000013054 00000 n +0000015950 00000 n +0000015971 00000 n +0000016053 00000 n +0000020430 00000 n +0000020451 00000 n +0000020533 00000 n +0000027470 00000 n +0000027706 00000 n +0000027964 00000 n +0000028048 00000 n +0000028146 00000 n +trailer +<< +/Size 24 +/Info 1 0 R +/Root 2 0 R +>> +startxref +28249 +%%EOF diff -r 5c268e401913 -r ab1c33257cb3 test-data/regr_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/regr_out.tabular Wed Feb 03 13:53:16 2010 -0500 @@ -0,0 +1,10 @@ +Y-intercept -28.1169126094 +p-value (Y-intercept) 0.294263204753 +Slope (c1) 5.74713412453 +p-value (c1) 0.0017328770415 +Slope (c2) 0.904274537427 +p-value (c2) 0.114667546826 +R-squared 0.938805439971 +Adjusted R-squared 0.921321279962 +F-statistic {'dendf': 7.0, 'value': 53.694626422997374, 'numdf': 2.0} +Sigma 7.43450071131 diff -r 5c268e401913 -r ab1c33257cb3 tools/extract/liftOver_wrapper.xml --- a/tools/extract/liftOver_wrapper.xml Wed Feb 03 12:21:29 2010 -0500 +++ b/tools/extract/liftOver_wrapper.xml Wed Feb 03 13:53:16 2010 -0500 @@ -14,7 +14,7 @@ <filter type="data_meta" ref="input" key="dbkey" column="0" /> </options> </param> - <param name="minMatch" size="10" type="float" value="0.10" label="Minimum ratio of bases that must remap" /> + <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" /> </inputs> <outputs> <data format="input" name="out_file1" /> @@ -23,17 +23,17 @@ <requirements> <requirement type="binary">liftOver</requirement> </requirements> - <!-- + <tests> <test> <param name="input" value="5.bed" dbkey="hg18" ftype="bed" /> <param name="to_dbkey" value="/depot/data2/galaxy/hg18/liftOver/hg18ToPanTro2.over.chain" /> - <param name="misMatch" value="0.95" /> + <param name="minMatch" value="0.95" /> <output name="out_file1" file="5_liftover_mapped.bed"/> <output name="out_file2" file="5_liftover_unmapped.bed"/> </test> </tests> - --> + <help>
.. class:: warningmark diff -r 5c268e401913 -r ab1c33257cb3 tools/regVariation/linear_regression.xml --- a/tools/regVariation/linear_regression.xml Wed Feb 03 12:21:29 2010 -0500 +++ b/tools/regVariation/linear_regression.xml Wed Feb 03 13:53:16 2010 -0500 @@ -24,8 +24,13 @@ <requirement type="python-module">rpy</requirement> </requirements> <tests> - <!-- Testing this tool will not be possible because this tool produces a pdf output file. - --> + <test> + <param name="input1" value="regr_inp.tabular"/> + <param name="response_col" value="3"/> + <param name="predictor_cols" value="1,2"/> + <output name="out_file1" file="regr_out.tabular"/> + <output name="out_file2" file="regr_out.pdf"/> + </test> </tests> <help>