[galaxy-commits] commit/galaxy-central: jgoecks: Make Cuffcompare wrapper compatible with v1.0.3

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389/ changeset: f4b98c453389 user: jgoecks date: 2011-06-09 18:06:07 summary: Make Cuffcompare wrapper compatible with v1.0.3 affected #: 6 files (890 bytes) --- a/test-data/cuffcompare_out1.tmap Thu Jun 09 11:38:37 2011 -0400 +++ b/test-data/cuffcompare_out1.tmap Thu Jun 09 12:06:07 2011 -0400 @@ -1,51 +1,51 @@ ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 27.255658 0.000000 65.800979 1.741935 31 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 9.999117 0.000000 19.998234 0.639053 169 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 17.776896 9.153835 26.399957 1.136139 404 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.11.1 - -- - u CUFF.13 CUFF.13.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.13.1 - -- - u CUFF.15 CUFF.15.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.15.1 - -- - u CUFF.17 CUFF.17.1 100 8.710571 0.000000 21.029179 0.556701 97 CUFF.17.1 - -- - u CUFF.19 CUFF.19.1 100 29.337687 3.097262 55.578113 1.875000 72 CUFF.19.1 - -- - u CUFF.21 CUFF.21.1 100 13.851236 0.000000 33.439842 0.885246 61 CUFF.21.1 - -- - u CUFF.23 CUFF.23.1 100 23.470150 0.000000 50.571145 1.500000 54 CUFF.23.1 - -- - u CUFF.25 CUFF.25.1 100 14.567679 5.354270 23.781089 0.931034 290 CUFF.25.1 - -- - u CUFF.27 CUFF.27.1 100 34.253732 0.000000 73.806535 2.189189 37 CUFF.27.1 - -- - u CUFF.29 CUFF.29.1 100 107.103219 71.402146 142.804292 6.845070 142 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 122.650461 40.883487 204.417435 7.838710 31 CUFF.31.1 - -- - u CUFF.33 CUFF.33.1 100 109.527366 26.732460 192.322273 7.000000 27 CUFF.33.1 - -- - u CUFF.35 CUFF.35.1 100 96.747183 61.420107 132.074259 6.183206 131 CUFF.35.1 - -- - u CUFF.37 CUFF.37.1 100 104.085013 53.596365 154.573660 6.652174 69 CUFF.37.1 - -- - u CUFF.39 CUFF.39.1 100 23.912983 0.000000 51.525317 1.528302 53 CUFF.39.1 - -- - u CUFF.41 CUFF.41.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.41.1 - -- - u CUFF.43 CUFF.43.1 100 10.561567 0.000000 25.497879 0.675000 80 CUFF.43.1 - -- - u CUFF.45 CUFF.45.1 100 20.708956 2.186303 39.231609 1.323529 102 CUFF.45.1 - -- - u CUFF.47 CUFF.47.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.47.1 - -- - u CUFF.49 CUFF.49.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.49.1 - -- - u CUFF.51 CUFF.51.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.51.1 - -- - u CUFF.53 CUFF.53.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.53.1 - -- - u CUFF.55 CUFF.55.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.55.1 - -- - u CUFF.57 CUFF.57.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.57.1 - -- - u CUFF.59 CUFF.59.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.59.1 - -- - u CUFF.61 CUFF.61.1 100 45.263860 0.000000 97.530065 2.892857 28 CUFF.61.1 - -- - u CUFF.63 CUFF.63.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.63.1 - -- - u CUFF.65 CUFF.65.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.65.1 - -- - u CUFF.67 CUFF.67.1 100 12.998852 0.000000 31.382005 0.830769 65 CUFF.67.1 - -- - u CUFF.69 CUFF.69.1 100 10.058636 0.000000 24.283695 0.642857 84 CUFF.69.1 - -- - u CUFF.71 CUFF.71.1 100 8.621688 0.000000 20.814595 0.551020 98 CUFF.71.1 - -- - u CUFF.73 CUFF.73.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.73.1 - -- - u CUFF.75 CUFF.75.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.75.1 - -- - u CUFF.77 CUFF.77.1 100 16.248565 0.000000 39.227507 1.038462 52 CUFF.77.1 - -- - u CUFF.79 CUFF.79.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.79.1 - -- - u CUFF.81 CUFF.81.1 100 13.201959 0.000000 31.872349 0.843750 64 CUFF.81.1 - -- - u CUFF.83 CUFF.83.1 100 13.201959 0.000000 28.446269 0.843750 96 CUFF.83.1 - -- - u CUFF.85 CUFF.85.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.85.1 - -- - u CUFF.87 CUFF.87.1 100 17.243375 0.000000 41.629191 1.102041 49 CUFF.87.1 - -- - u CUFF.89 CUFF.89.1 100 16.567165 0.000000 39.996674 1.058824 51 CUFF.89.1 - -- - u CUFF.91 CUFF.91.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.91.1 - -- - u CUFF.93 CUFF.93.1 100 21.664754 0.000000 52.303342 1.384615 39 CUFF.93.1 - -- - u CUFF.95 CUFF.95.1 100 46.940300 0.000000 101.142289 3.000000 27 CUFF.95.1 - -- - u CUFF.97 CUFF.97.1 100 21.481154 0.000000 46.285454 1.372881 59 CUFF.97.1 - -- - u CUFF.99 CUFF.99.1 100 14.567679 0.000000 35.169489 0.931034 58 CUFF.99.1 - +- - u CUFF.1 CUFF.1.1 100 0.000000 0.000000 0.000000 0.000000 41 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 100 0.000000 0.000000 0.000000 0.000000 31 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 100 0.000000 0.000000 0.000000 0.000000 169 CUFF.7.1 - +- - u CUFF.9 CUFF.9.1 100 0.000000 0.000000 0.000000 0.000000 404 CUFF.9.1 - +- - u CUFF.11 CUFF.11.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.11.1 - +- - u CUFF.13 CUFF.13.1 100 0.000000 0.000000 0.000000 0.000000 79 CUFF.13.1 - +- - u CUFF.15 CUFF.15.1 100 0.000000 0.000000 0.000000 0.000000 79 CUFF.15.1 - +- - u CUFF.17 CUFF.17.1 100 0.000000 0.000000 0.000000 0.000000 97 CUFF.17.1 - +- - u CUFF.19 CUFF.19.1 100 0.000000 0.000000 0.000000 0.000000 72 CUFF.19.1 - +- - u CUFF.21 CUFF.21.1 100 0.000000 0.000000 0.000000 0.000000 61 CUFF.21.1 - +- - u CUFF.23 CUFF.23.1 100 0.000000 0.000000 0.000000 0.000000 54 CUFF.23.1 - +- - u CUFF.25 CUFF.25.1 100 0.000000 0.000000 0.000000 0.000000 290 CUFF.25.1 - +- - u CUFF.27 CUFF.27.1 100 0.000000 0.000000 0.000000 0.000000 37 CUFF.27.1 - +- - u CUFF.29 CUFF.29.1 100 0.000000 0.000000 0.000000 0.000000 142 CUFF.29.1 - +- - u CUFF.31 CUFF.31.1 100 0.000000 0.000000 0.000000 0.000000 31 CUFF.31.1 - +- - u CUFF.33 CUFF.33.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.33.1 - +- - u CUFF.35 CUFF.35.1 100 0.000000 0.000000 0.000000 0.000000 131 CUFF.35.1 - +- - u CUFF.37 CUFF.37.1 100 0.000000 0.000000 0.000000 0.000000 69 CUFF.37.1 - +- - u CUFF.39 CUFF.39.1 100 0.000000 0.000000 0.000000 0.000000 53 CUFF.39.1 - +- - u CUFF.41 CUFF.41.1 100 0.000000 0.000000 0.000000 0.000000 79 CUFF.41.1 - +- - u CUFF.43 CUFF.43.1 100 0.000000 0.000000 0.000000 0.000000 80 CUFF.43.1 - +- - u CUFF.45 CUFF.45.1 100 0.000000 0.000000 0.000000 0.000000 102 CUFF.45.1 - +- - u CUFF.47 CUFF.47.1 100 0.000000 0.000000 0.000000 0.000000 41 CUFF.47.1 - +- - u CUFF.49 CUFF.49.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.49.1 - +- - u CUFF.51 CUFF.51.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.51.1 - +- - u CUFF.53 CUFF.53.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.53.1 - +- - u CUFF.55 CUFF.55.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.55.1 - +- - u CUFF.57 CUFF.57.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.57.1 - +- - u CUFF.59 CUFF.59.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.59.1 - +- - u CUFF.61 CUFF.61.1 100 0.000000 0.000000 0.000000 0.000000 28 CUFF.61.1 - +- - u CUFF.63 CUFF.63.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.63.1 - +- - u CUFF.65 CUFF.65.1 100 0.000000 0.000000 0.000000 0.000000 55 CUFF.65.1 - +- - u CUFF.67 CUFF.67.1 100 0.000000 0.000000 0.000000 0.000000 65 CUFF.67.1 - +- - u CUFF.69 CUFF.69.1 100 0.000000 0.000000 0.000000 0.000000 84 CUFF.69.1 - +- - u CUFF.71 CUFF.71.1 100 0.000000 0.000000 0.000000 0.000000 98 CUFF.71.1 - +- - u CUFF.73 CUFF.73.1 100 0.000000 0.000000 0.000000 0.000000 55 CUFF.73.1 - +- - u CUFF.75 CUFF.75.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.75.1 - +- - u CUFF.77 CUFF.77.1 100 0.000000 0.000000 0.000000 0.000000 52 CUFF.77.1 - +- - u CUFF.79 CUFF.79.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.79.1 - +- - u CUFF.81 CUFF.81.1 100 0.000000 0.000000 0.000000 0.000000 64 CUFF.81.1 - +- - u CUFF.83 CUFF.83.1 100 0.000000 0.000000 0.000000 0.000000 96 CUFF.83.1 - +- - u CUFF.85 CUFF.85.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.85.1 - +- - u CUFF.87 CUFF.87.1 100 0.000000 0.000000 0.000000 0.000000 49 CUFF.87.1 - +- - u CUFF.89 CUFF.89.1 100 0.000000 0.000000 0.000000 0.000000 51 CUFF.89.1 - +- - u CUFF.91 CUFF.91.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.91.1 - +- - u CUFF.93 CUFF.93.1 100 0.000000 0.000000 0.000000 0.000000 39 CUFF.93.1 - +- - u CUFF.95 CUFF.95.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.95.1 - +- - u CUFF.97 CUFF.97.1 100 0.000000 0.000000 0.000000 0.000000 59 CUFF.97.1 - +- - u CUFF.99 CUFF.99.1 100 0.000000 0.000000 0.000000 0.000000 58 CUFF.99.1 - --- a/test-data/cuffcompare_out3.tmap Thu Jun 09 11:38:37 2011 -0400 +++ b/test-data/cuffcompare_out3.tmap Thu Jun 09 12:06:07 2011 -0400 @@ -1,51 +1,51 @@ ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 21.226627 0.000000 59.889707 1.205672 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 29.709524 19.806349 39.612698 1.687500 576 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 34.072933 23.364686 44.781179 1.935341 565 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 32.531777 24.582998 40.480555 1.847804 979 CUFF.11.1 - -- - u CUFF.13 CUFF.13.1 100 16.582060 0.000000 35.729373 0.941860 86 CUFF.13.1 - -- - u CUFF.15 CUFF.15.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.15.1 - -- - u CUFF.17 CUFF.17.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.17.1 - -- - u CUFF.19 CUFF.19.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.19.1 - -- - u CUFF.21 CUFF.21.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.21.1 - -- - u CUFF.23 CUFF.23.1 100 16.205195 0.000000 34.917342 0.920455 88 CUFF.23.1 - -- - u CUFF.25 CUFF.25.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.25.1 - -- - u CUFF.26 CUFF.26.1 100 29.709524 0.000000 71.725135 1.687500 32 CUFF.26.1 - -- - u CUFF.29 CUFF.29.1 100 13.581496 0.000000 32.788633 0.771429 70 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 22.635827 0.000000 45.271655 1.285714 84 CUFF.31.1 - -- - u CUFF.33 CUFF.33.1 100 23.767619 0.000000 57.380108 1.350000 40 CUFF.33.1 - -- - u CUFF.35 CUFF.35.1 100 11.317914 0.000000 27.323861 0.642857 84 CUFF.35.1 - -- - u CUFF.37 CUFF.37.1 100 11.500461 0.000000 24.780049 0.653226 124 CUFF.37.1 - -- - u CUFF.39 CUFF.39.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.39.1 - -- - u CUFF.41 CUFF.41.1 100 43.213852 0.000000 93.112911 2.454545 33 CUFF.41.1 - -- - u CUFF.43 CUFF.43.1 100 23.474191 0.000000 46.948383 1.333333 81 CUFF.43.1 - -- - u CUFF.45 CUFF.45.1 100 20.667495 0.000000 49.895746 1.173913 46 CUFF.45.1 - -- - u CUFF.47 CUFF.47.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.47.1 - -- - u CUFF.49 CUFF.49.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.49.1 - -- - u CUFF.51 CUFF.51.1 100 14.948188 7.228977 22.667399 0.849057 477 CUFF.51.1 - -- - u CUFF.53 CUFF.53.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.53.1 - -- - u CUFF.55 CUFF.55.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.55.1 - -- - u CUFF.57 CUFF.57.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.57.1 - -- - u CUFF.59 CUFF.59.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.59.1 - -- - u CUFF.61 CUFF.61.1 100 13.204233 0.000000 31.877838 0.750000 72 CUFF.61.1 - -- - u CUFF.63 CUFF.63.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.63.1 - -- - u CUFF.65 CUFF.65.1 100 31.170648 0.000000 62.341295 1.770492 61 CUFF.65.1 - -- - u CUFF.67 CUFF.67.1 100 15.681351 3.378764 27.983938 0.890700 197 CUFF.67.1 - -- - u CUFF.69 CUFF.69.1 100 18.799247 8.750627 28.847866 1.067797 354 CUFF.69.1 - -- - u CUFF.71 CUFF.71.1 100 22.635827 0.000000 54.647722 1.285714 42 CUFF.71.1 - -- - u CUFF.73 CUFF.73.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.73.1 - -- - u CUFF.75 CUFF.75.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.75.1 - -- - u CUFF.77 CUFF.77.1 100 17.605644 0.000000 52.816931 1.000000 27 CUFF.77.1 - -- - u CUFF.79 CUFF.79.1 100 13.390208 0.000000 32.326821 0.760563 71 CUFF.79.1 - -- - u CUFF.81 CUFF.81.1 100 11.211141 1.183592 21.238690 0.636792 212 CUFF.81.1 - -- - u CUFF.83 CUFF.83.1 100 21.126772 0.000000 51.004540 1.200000 45 CUFF.83.1 - -- - u CUFF.85 CUFF.85.1 100 19.014095 0.000000 38.028190 1.080000 100 CUFF.85.1 - -- - u CUFF.87 CUFF.87.1 100 24.170460 0.000000 52.080103 1.372881 59 CUFF.87.1 - -- - u CUFF.89 CUFF.89.1 100 29.709524 0.000000 64.015126 1.687500 48 CUFF.89.1 - -- - u CUFF.91 CUFF.91.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.91.1 - -- - u CUFF.93 CUFF.93.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.93.1 - -- - u CUFF.95 CUFF.95.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.95.1 - -- - u CUFF.97 CUFF.97.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.97.1 - -- - u CUFF.99 CUFF.99.1 100 19.602160 0.000000 39.204320 1.113402 97 CUFF.99.1 - +- - u CUFF.1 CUFF.1.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 100 0.000000 0.000000 0.000000 0.000000 576 CUFF.7.1 - +- - u CUFF.9 CUFF.9.1 100 0.000000 0.000000 0.000000 0.000000 565 CUFF.9.1 - +- - u CUFF.11 CUFF.11.1 100 0.000000 0.000000 0.000000 0.000000 979 CUFF.11.1 - +- - u CUFF.13 CUFF.13.1 100 0.000000 0.000000 0.000000 0.000000 86 CUFF.13.1 - +- - u CUFF.15 CUFF.15.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.15.1 - +- - u CUFF.17 CUFF.17.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.17.1 - +- - u CUFF.19 CUFF.19.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.19.1 - +- - u CUFF.21 CUFF.21.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.21.1 - +- - u CUFF.23 CUFF.23.1 100 0.000000 0.000000 0.000000 0.000000 88 CUFF.23.1 - +- - u CUFF.25 CUFF.25.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.25.1 - +- - u CUFF.26 CUFF.26.1 100 0.000000 0.000000 0.000000 0.000000 32 CUFF.26.1 - +- - u CUFF.29 CUFF.29.1 100 0.000000 0.000000 0.000000 0.000000 70 CUFF.29.1 - +- - u CUFF.31 CUFF.31.1 100 0.000000 0.000000 0.000000 0.000000 84 CUFF.31.1 - +- - u CUFF.33 CUFF.33.1 100 0.000000 0.000000 0.000000 0.000000 40 CUFF.33.1 - +- - u CUFF.35 CUFF.35.1 100 0.000000 0.000000 0.000000 0.000000 84 CUFF.35.1 - +- - u CUFF.37 CUFF.37.1 100 0.000000 0.000000 0.000000 0.000000 124 CUFF.37.1 - +- - u CUFF.39 CUFF.39.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.39.1 - +- - u CUFF.41 CUFF.41.1 100 0.000000 0.000000 0.000000 0.000000 33 CUFF.41.1 - +- - u CUFF.43 CUFF.43.1 100 0.000000 0.000000 0.000000 0.000000 81 CUFF.43.1 - +- - u CUFF.45 CUFF.45.1 100 0.000000 0.000000 0.000000 0.000000 46 CUFF.45.1 - +- - u CUFF.47 CUFF.47.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.47.1 - +- - u CUFF.49 CUFF.49.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.49.1 - +- - u CUFF.51 CUFF.51.1 100 0.000000 0.000000 0.000000 0.000000 477 CUFF.51.1 - +- - u CUFF.53 CUFF.53.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.53.1 - +- - u CUFF.55 CUFF.55.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.55.1 - +- - u CUFF.57 CUFF.57.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.57.1 - +- - u CUFF.59 CUFF.59.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.59.1 - +- - u CUFF.61 CUFF.61.1 100 0.000000 0.000000 0.000000 0.000000 72 CUFF.61.1 - +- - u CUFF.63 CUFF.63.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.63.1 - +- - u CUFF.65 CUFF.65.1 100 0.000000 0.000000 0.000000 0.000000 61 CUFF.65.1 - +- - u CUFF.67 CUFF.67.1 100 0.000000 0.000000 0.000000 0.000000 197 CUFF.67.1 - +- - u CUFF.69 CUFF.69.1 100 0.000000 0.000000 0.000000 0.000000 354 CUFF.69.1 - +- - u CUFF.71 CUFF.71.1 100 0.000000 0.000000 0.000000 0.000000 42 CUFF.71.1 - +- - u CUFF.73 CUFF.73.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.73.1 - +- - u CUFF.75 CUFF.75.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.75.1 - +- - u CUFF.77 CUFF.77.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.77.1 - +- - u CUFF.79 CUFF.79.1 100 0.000000 0.000000 0.000000 0.000000 71 CUFF.79.1 - +- - u CUFF.81 CUFF.81.1 100 0.000000 0.000000 0.000000 0.000000 212 CUFF.81.1 - +- - u CUFF.83 CUFF.83.1 100 0.000000 0.000000 0.000000 0.000000 45 CUFF.83.1 - +- - u CUFF.85 CUFF.85.1 100 0.000000 0.000000 0.000000 0.000000 100 CUFF.85.1 - +- - u CUFF.87 CUFF.87.1 100 0.000000 0.000000 0.000000 0.000000 59 CUFF.87.1 - +- - u CUFF.89 CUFF.89.1 100 0.000000 0.000000 0.000000 0.000000 48 CUFF.89.1 - +- - u CUFF.91 CUFF.91.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.91.1 - +- - u CUFF.93 CUFF.93.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.93.1 - +- - u CUFF.95 CUFF.95.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.95.1 - +- - u CUFF.97 CUFF.97.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.97.1 - +- - u CUFF.99 CUFF.99.1 100 0.000000 0.000000 0.000000 0.000000 97 CUFF.99.1 - --- a/test-data/cuffcompare_out6.tracking Thu Jun 09 11:38:37 2011 -0400 +++ b/test-data/cuffcompare_out6.tracking Thu Jun 09 12:06:07 2011 -0400 @@ -1,100 +1,100 @@ -TCONS_00000001 XLOC_000001 - u q1:CUFF.1|CUFF.1.1|100|20.607936|0.000000|49.751960|1.317073|- - -TCONS_00000002 XLOC_000002 - u q1:CUFF.3|CUFF.3.1|100|27.255658|0.000000|65.800979|1.741935|- - -TCONS_00000003 XLOC_000006 - u q1:CUFF.29|CUFF.29.1|100|107.103219|71.402146|142.804292|6.845070|- - -TCONS_00000004 XLOC_000006 - u q1:CUFF.31|CUFF.31.1|100|122.650461|40.883487|204.417435|7.838710|- - -TCONS_00000005 XLOC_000006 - u q1:CUFF.33|CUFF.33.1|100|109.527366|26.732460|192.322273|7.000000|- - -TCONS_00000006 XLOC_000008 - 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u - q2:CUFF.9|CUFF.9.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000057 XLOC_000009 - u - q2:CUFF.13|CUFF.13.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000058 XLOC_000012 - u - q2:CUFF.15|CUFF.15.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000059 XLOC_000017 - u - q2:CUFF.17|CUFF.17.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000060 XLOC_000023 - u - q2:CUFF.19|CUFF.19.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000061 XLOC_000024 - u - q2:CUFF.23|CUFF.23.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000062 XLOC_000026 - u - q2:CUFF.21|CUFF.21.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000063 XLOC_000027 - u - q2:CUFF.26|CUFF.26.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000064 XLOC_000028 - u - q2:CUFF.25|CUFF.25.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000065 XLOC_000029 - u - q2:CUFF.29|CUFF.29.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000066 XLOC_000031 - u - q2:CUFF.31|CUFF.31.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000067 XLOC_000033 - u - q2:CUFF.33|CUFF.33.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000068 XLOC_000036 - u - q2:CUFF.35|CUFF.35.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000069 XLOC_000037 - u - q2:CUFF.37|CUFF.37.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000070 XLOC_000038 - u - q2:CUFF.39|CUFF.39.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000071 XLOC_000039 - u - q2:CUFF.41|CUFF.41.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000072 XLOC_000041 - u - q2:CUFF.43|CUFF.43.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000073 XLOC_000043 - u - q2:CUFF.45|CUFF.45.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000074 XLOC_000045 - u - q2:CUFF.47|CUFF.47.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000075 XLOC_000047 - u - q2:CUFF.49|CUFF.49.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000076 XLOC_000049 - u - q2:CUFF.51|CUFF.51.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000077 XLOC_000050 - u - q2:CUFF.53|CUFF.53.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000078 XLOC_000051 - u - q2:CUFF.55|CUFF.55.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000079 XLOC_000053 - u - q2:CUFF.57|CUFF.57.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000080 XLOC_000054 - u - q2:CUFF.59|CUFF.59.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000081 XLOC_000055 - u - q2:CUFF.61|CUFF.61.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000082 XLOC_000056 - u - q2:CUFF.63|CUFF.63.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000083 XLOC_000058 - u - q2:CUFF.65|CUFF.65.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000084 XLOC_000059 - u - q2:CUFF.69|CUFF.69.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000085 XLOC_000060 - u - q2:CUFF.67|CUFF.67.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000086 XLOC_000061 - u - q2:CUFF.71|CUFF.71.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000087 XLOC_000063 - u - q2:CUFF.73|CUFF.73.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000088 XLOC_000064 - u - q2:CUFF.75|CUFF.75.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000089 XLOC_000066 - u - q2:CUFF.77|CUFF.77.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000090 XLOC_000067 - u - q2:CUFF.79|CUFF.79.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000091 XLOC_000068 - u - q2:CUFF.81|CUFF.81.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000092 XLOC_000069 - u - q2:CUFF.83|CUFF.83.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000093 XLOC_000070 - u - q2:CUFF.85|CUFF.85.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000094 XLOC_000072 - u - q2:CUFF.87|CUFF.87.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000095 XLOC_000074 - u - q2:CUFF.89|CUFF.89.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000096 XLOC_000076 - u - q2:CUFF.91|CUFF.91.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000097 XLOC_000078 - u - q2:CUFF.93|CUFF.93.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000098 XLOC_000079 - u - q2:CUFF.95|CUFF.95.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000099 XLOC_000081 - u - q2:CUFF.97|CUFF.97.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000100 XLOC_000082 - u - q2:CUFF.99|CUFF.99.1|100|0.000000|0.000000|0.000000|0.000000|- --- a/test-data/cuffcompare_out7.txt Thu Jun 09 11:38:37 2011 -0400 +++ b/test-data/cuffcompare_out7.txt Thu Jun 09 12:06:07 2011 -0400 @@ -1,19 +1,11 @@ -# Cuffcompare v1.0.1 | Command line was: -#cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf +# Cuffcompare v1.0.3 | Command line was: +#cuffcompare -o cc_output -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf # -#> Genomic sequence: chr1 -# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) -# (0 multi-transcript loci, ~1.0 transcripts per locus) -# Reference mRNAs : 0 in 0 loci (0 multi-exon) #= Summary for dataset: cuffcompare_in1.gtf : # Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) # (0 multi-transcript loci, ~1.0 transcripts per locus) # Reference mRNAs : 0 in 0 loci (0 multi-exon) -#> Genomic sequence: chr1 -# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) -# (0 multi-transcript loci, ~1.0 transcripts per locus) -# Reference mRNAs : 0 in 0 loci (0 multi-exon) #= Summary for dataset: cuffcompare_in2.gtf : # Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) --- a/tools/ngs_rna/cuffcompare_wrapper.py Thu Jun 09 11:38:37 2011 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.py Thu Jun 09 12:06:07 2011 -0400 @@ -116,7 +116,7 @@ raise Exception, stderr # check that there are results in the output file - cc_output_fname = "cc_output" + cc_output_fname = "cc_output.stats" if len( open( cc_output_fname, 'rb' ).read().strip() ) == 0: raise Exception, 'The main output file is empty, there may be an error with your input file or settings.' except Exception, e: --- a/tools/ngs_rna/cuffcompare_wrapper.xml Thu Jun 09 11:38:37 2011 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Thu Jun 09 12:06:07 2011 -0400 @@ -35,9 +35,7 @@ <inputs><param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/><repeat name="input_files" title="Additional GTF Input Files"> - <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""> - <validator type="unspecified_build" /> - </param> + <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""/></repeat><conditional name="annotation"><param name="use_ref_annotation" type="select" label="Use Reference Annotation"> @@ -73,13 +71,16 @@ </inputs><outputs> - <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" from_work_dir="cc_output" /> - <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: ${first_input.hid} data tmap file" from_work_dir="input1.tmap" /> - <data format="tabular" name="input1_refmap" label="${tool.name} on ${on_string}: data ${first_input.hid} refmap file" from_work_dir="input1.refmap"/> - <data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} tmap file" from_work_dir="input2.tmap"> + <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" + from_work_dir="cc_output.stats" /> + <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: ${first_input.hid} data tmap file" + from_work_dir="cc_output.input1.tmap" /> + <data format="tabular" name="input1_refmap" label="${tool.name} on ${on_string}: data ${first_input.hid} refmap file" + from_work_dir="cc_output.input1.refmap"/> + <data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} tmap file" from_work_dir="cc_output.input2.tmap"><filter>len( input_files ) > 0</filter></data> - <data format="tabular" name="input2_refmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} refmap file" from_work_dir="input2.refmap"> + <data format="tabular" name="input2_refmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} refmap file" from_work_dir="cc_output.input2.refmap"><filter>len( input_files ) > 0</filter></data><data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="cc_output.tracking"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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