details: http://www.bx.psu.edu/hg/galaxy/rev/82b63d47a0d8 changeset: 3117:82b63d47a0d8 user: Greg Von Kuster <greg@bx.psu.edu> date: Fri Nov 20 15:35:30 2009 -0500 description: Rename test files for taxonomy tools and set ftype for test's input datasets. diffstat: test-data/find_diag_hits.dat | 2 - test-data/find_diag_hits.tabular | 2 + test-data/poisson2test1.out | 5 -- test-data/poisson2test1.tabular | 5 ++ test-data/poisson2test1.txt | 5 -- test-data/poisson2test1_out.tabular | 5 ++ test-data/poisson2test2.out | 52 -------------------------- test-data/poisson2test2.tabular | 52 ++++++++++++++++++++++++++ test-data/poisson2test2.txt | 52 -------------------------- test-data/poisson2test2_out.tabular | 52 ++++++++++++++++++++++++++ test-data/t2t_report.dat | 15 ------- test-data/t2t_report.tabular | 15 +++++++ test-data/taxonomy2gi-input.tabular | 4 ++ test-data/taxonomy2gi-input.txt | 4 -- test-data/taxonomy2gi-output.tabular | 4 ++ test-data/taxonomy2gi-output.txt | 4 -- test-data/taxonomyGI.dat | 5 -- test-data/taxonomyGI.tabular | 5 ++ test-data/taxonomyGI.taxonomy | 5 ++ test-data/taxonomyGI.txt | 5 -- tools/taxonomy/example_dataset_missing_nodes.txt | 6 --- tools/taxonomy/find_diag_hits.xml | 4 +- tools/taxonomy/gi2taxonomy.xml | 4 +- tools/taxonomy/poisson2test.xml | 8 ++-- tools/taxonomy/t2t_report.xml | 4 +- 25 files changed, 159 insertions(+), 165 deletions(-) diffs (467 lines): diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/find_diag_hits.dat --- a/test-data/find_diag_hits.dat Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Primates 4 order -Homo 2 genus diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/find_diag_hits.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_diag_hits.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,2 @@ +Primates 4 order +Homo 2 genus diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test1.out --- a/test-data/poisson2test1.out Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -Acinetobacter 37 7 2.109 2.315 0.017468 0.010302 0.087342 0.051510 -Acyrthosiphon 70 21 1.549 1.612 0.060722 0.053481 0.303609 0.267406 -aedes 61 13 2.425 2.625 0.007645 0.004329 0.038223 0.021643 -Aeromonas 169 0 8.623 14.372 0.000000 0.000000 0.000000 0.000000 -anopheles 145 97 -3.217 -3.102 0.000647 0.000960 0.003234 0.004801 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poisson2test1.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,5 @@ +Acinetobacter 37 7 +Acyrthosiphon 70 21 +aedes 61 13 +Aeromonas 169 0 +anopheles 145 97 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test1.txt --- a/test-data/poisson2test1.txt Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -Acinetobacter 37 7 -Acyrthosiphon 70 21 -aedes 61 13 -Aeromonas 169 0 -anopheles 145 97 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test1_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poisson2test1_out.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,5 @@ +Acinetobacter 37 7 2.109 2.315 0.017468 0.010302 0.087342 0.051510 +Acyrthosiphon 70 21 1.549 1.612 0.060722 0.053481 0.303609 0.267406 +aedes 61 13 2.425 2.625 0.007645 0.004329 0.038223 0.021643 +Aeromonas 169 0 8.623 14.372 0.000000 0.000000 0.000000 0.000000 +anopheles 145 97 -3.217 -3.102 0.000647 0.000960 0.003234 0.004801 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test2.out --- a/test-data/poisson2test2.out Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ -Acyrthosiphon pisum 55 54 -4.303 -4.049 0.000008 0.000026 0.000438 0.001340 -Aedes aegypti 246 72 3.064 3.198 0.001093 0.000693 0.056838 0.036029 -Anopheles gambiae 337 168 -1.323 -1.307 0.092930 0.095535 1.000000 1.000000 -Apis mellifera 33 11 0.800 0.823 0.211855 0.205213 1.000000 1.000000 -Aspergillus niger 292 29 8.371 9.916 0.000000 0.000000 0.000000 0.000000 -Batrachochytrium dendrobatidis 17 14 -1.765 -1.678 0.038749 0.046690 1.000000 1.000000 -Bombyx mori 2 16 5.373 5.103 0.000000 0.000000 0.000002 0.000009 -Bos taurus 16 71 10.338 9.621 0.000000 0.000000 0.000000 0.000000 -Branchiostoma floridae 44 1 4.126 5.667 0.000018 0.000000 0.000959 0.000000 -Caenorhabditis briggsae 269 121 -0.202 -0.201 0.420141 0.420309 1.000000 1.000000 -Caenorhabditis remanei 35 29 -2.563 -2.435 0.005191 0.007450 0.269927 0.387398 -Chlamydomonas reinhardtii 85 13 3.716 4.183 0.000101 0.000014 0.005267 0.000747 -Citrus sinensis 14 2 1.568 1.780 0.058457 0.037576 1.000000 1.000000 -Culex pipiens 408 81 6.717 7.331 0.000000 0.000000 0.000000 0.000000 -Daphnia pulex 213 75 1.663 1.701 0.048160 0.044463 1.000000 1.000000 -Drosophila ananassae 3 20 5.872 5.539 0.000000 0.000000 0.000000 0.000001 -Drosophila grimshawi 14 10 -1.182 -1.134 0.118667 0.128417 1.000000 1.000000 -Drosophila pseudoobscura 28 22 -2.064 -1.967 0.019519 0.024570 1.000000 1.000000 -Drosophila willistoni 4 18 5.220 4.860 0.000000 0.000001 0.000005 0.000031 -Emiliania huxleyi 56 13 2.113 2.264 0.017321 0.011791 0.900675 0.613145 -Glycine max 4019 1831 -1.235 -1.231 0.108478 0.109251 1.000000 1.000000 -Helobdella robusta 33 1 3.496 4.684 0.000237 0.000001 0.012302 0.000073 -Homo sapiens 59 6 3.732 4.409 0.000095 0.000005 0.004933 0.000270 -Hyaloperonospora parasitica 48 10 2.201 2.389 0.013860 0.008448 0.720722 0.439307 -Hydra magnipapillata 9 65 10.697 10.120 0.000000 0.000000 0.000000 0.000000 -Medicago truncatula 62 42 -2.176 -2.096 0.014777 0.018033 0.768379 0.937696 -Mimulus guttatus 12 9 -1.224 -1.170 0.110516 0.120942 1.000000 1.000000 -Mus musculus 18 5 0.918 0.964 0.179337 0.167614 1.000000 1.000000 -Mycosphaerella fijiensis 42 7 2.472 2.755 0.006711 0.002933 0.348951 0.152533 -Nasonia vitripennis 10 12 2.443 2.277 0.007288 0.011379 0.378990 0.591708 -Nectria haematococca 67 2 4.987 6.692 0.000000 0.000000 0.000016 0.000000 -Oryza sativa 6068 2561 1.768 1.775 0.038558 0.037957 1.000000 1.000000 -Paramecium tetraurelia 749 296 1.565 1.582 0.058782 0.056837 1.000000 1.000000 -Pediculus humanus 49 40 -2.947 -2.802 0.001606 0.002538 0.083501 0.131991 -Phakopsora pachyrhizi 66 53 -3.311 -3.152 0.000464 0.000811 0.024152 0.042153 -Physcomitrella patens 304 36 7.993 9.276 0.000000 0.000000 0.000000 0.000000 -Phytophthora ramorum 174 56 2.044 2.111 0.020488 0.017390 1.000000 0.904295 -Phytophthora sojae 10 0 2.098 3.496 0.017969 0.000236 0.934412 0.012278 -Pinus taeda 0 26 7.687 8.498 0.000000 0.000000 0.000000 0.000000 -Populus balsamifera 43 4 3.281 3.916 0.000517 0.000045 0.026903 0.002339 -Pristionchus pacificus 4 14 4.349 4.025 0.000007 0.000028 0.000355 0.001481 -Rattus norvegicus 11 3 0.741 0.780 0.229238 0.217720 1.000000 1.000000 -Rhodnius prolixus 24 17 -1.516 -1.456 0.064729 0.072722 1.000000 1.000000 -Ricinus communis 75 14 3.036 3.338 0.001198 0.000422 0.062288 0.021926 -Schistosoma mansoni 80 15 3.124 3.433 0.000891 0.000298 0.046328 0.015504 -Schmidtea mediterranea 307 277 -8.853 -8.368 0.000000 0.000000 0.000000 0.000000 -Selaginella moellendorffii 27 10 0.466 0.474 0.320629 0.317714 1.000000 1.000000 -Sorghum bicolor 306 72 4.857 5.197 0.000001 0.000000 0.000031 0.000005 -Strongylocentrotus purpuratus 182 34 4.727 5.196 0.000001 0.000000 0.000059 0.000005 -Trypanosoma cruzi 23 0 3.181 5.302 0.000733 0.000000 0.038134 0.000003 -Volvox carteri 64 2 4.854 6.487 0.000001 0.000000 0.000031 0.000000 -Zea mays 583 263 -0.336 -0.335 0.368487 0.368792 1.000000 1.000000 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poisson2test2.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,52 @@ +Acyrthosiphon pisum 55 54 +Aedes aegypti 246 72 +Anopheles gambiae 337 168 +Apis mellifera 33 11 +Aspergillus niger 292 29 +Batrachochytrium dendrobatidis 17 14 +Bombyx mori 2 16 +Bos taurus 16 71 +Branchiostoma floridae 44 1 +Caenorhabditis briggsae 269 121 +Caenorhabditis remanei 35 29 +Chlamydomonas reinhardtii 85 13 +Citrus sinensis 14 2 +Culex pipiens 408 81 +Daphnia pulex 213 75 +Drosophila ananassae 3 20 +Drosophila grimshawi 14 10 +Drosophila pseudoobscura 28 22 +Drosophila willistoni 4 18 +Emiliania huxleyi 56 13 +Glycine max 4019 1831 +Helobdella robusta 33 1 +Homo sapiens 59 6 +Hyaloperonospora parasitica 48 10 +Hydra magnipapillata 9 65 +Medicago truncatula 62 42 +Mimulus guttatus 12 9 +Mus musculus 18 5 +Mycosphaerella fijiensis 42 7 +Nasonia vitripennis 10 12 +Nectria haematococca 67 2 +Oryza sativa 6068 2561 +Paramecium tetraurelia 749 296 +Pediculus humanus 49 40 +Phakopsora pachyrhizi 66 53 +Physcomitrella patens 304 36 +Phytophthora ramorum 174 56 +Phytophthora sojae 10 0 +Pinus taeda 0 26 +Populus balsamifera 43 4 +Pristionchus pacificus 4 14 +Rattus norvegicus 11 3 +Rhodnius prolixus 24 17 +Ricinus communis 75 14 +Schistosoma mansoni 80 15 +Schmidtea mediterranea 307 277 +Selaginella moellendorffii 27 10 +Sorghum bicolor 306 72 +Strongylocentrotus purpuratus 182 34 +Trypanosoma cruzi 23 0 +Volvox carteri 64 2 +Zea mays 583 263 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test2.txt --- a/test-data/poisson2test2.txt Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ -Acyrthosiphon pisum 55 54 -Aedes aegypti 246 72 -Anopheles gambiae 337 168 -Apis mellifera 33 11 -Aspergillus niger 292 29 -Batrachochytrium dendrobatidis 17 14 -Bombyx mori 2 16 -Bos taurus 16 71 -Branchiostoma floridae 44 1 -Caenorhabditis briggsae 269 121 -Caenorhabditis remanei 35 29 -Chlamydomonas reinhardtii 85 13 -Citrus sinensis 14 2 -Culex pipiens 408 81 -Daphnia pulex 213 75 -Drosophila ananassae 3 20 -Drosophila grimshawi 14 10 -Drosophila pseudoobscura 28 22 -Drosophila willistoni 4 18 -Emiliania huxleyi 56 13 -Glycine max 4019 1831 -Helobdella robusta 33 1 -Homo sapiens 59 6 -Hyaloperonospora parasitica 48 10 -Hydra magnipapillata 9 65 -Medicago truncatula 62 42 -Mimulus guttatus 12 9 -Mus musculus 18 5 -Mycosphaerella fijiensis 42 7 -Nasonia vitripennis 10 12 -Nectria haematococca 67 2 -Oryza sativa 6068 2561 -Paramecium tetraurelia 749 296 -Pediculus humanus 49 40 -Phakopsora pachyrhizi 66 53 -Physcomitrella patens 304 36 -Phytophthora ramorum 174 56 -Phytophthora sojae 10 0 -Pinus taeda 0 26 -Populus balsamifera 43 4 -Pristionchus pacificus 4 14 -Rattus norvegicus 11 3 -Rhodnius prolixus 24 17 -Ricinus communis 75 14 -Schistosoma mansoni 80 15 -Schmidtea mediterranea 307 277 -Selaginella moellendorffii 27 10 -Sorghum bicolor 306 72 -Strongylocentrotus purpuratus 182 34 -Trypanosoma cruzi 23 0 -Volvox carteri 64 2 -Zea mays 583 263 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test2_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poisson2test2_out.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,52 @@ +Acyrthosiphon pisum 55 54 -4.303 -4.049 0.000008 0.000026 0.000438 0.001340 +Aedes aegypti 246 72 3.064 3.198 0.001093 0.000693 0.056838 0.036029 +Anopheles gambiae 337 168 -1.323 -1.307 0.092930 0.095535 1.000000 1.000000 +Apis mellifera 33 11 0.800 0.823 0.211855 0.205213 1.000000 1.000000 +Aspergillus niger 292 29 8.371 9.916 0.000000 0.000000 0.000000 0.000000 +Batrachochytrium dendrobatidis 17 14 -1.765 -1.678 0.038749 0.046690 1.000000 1.000000 +Bombyx mori 2 16 5.373 5.103 0.000000 0.000000 0.000002 0.000009 +Bos taurus 16 71 10.338 9.621 0.000000 0.000000 0.000000 0.000000 +Branchiostoma floridae 44 1 4.126 5.667 0.000018 0.000000 0.000959 0.000000 +Caenorhabditis briggsae 269 121 -0.202 -0.201 0.420141 0.420309 1.000000 1.000000 +Caenorhabditis remanei 35 29 -2.563 -2.435 0.005191 0.007450 0.269927 0.387398 +Chlamydomonas reinhardtii 85 13 3.716 4.183 0.000101 0.000014 0.005267 0.000747 +Citrus sinensis 14 2 1.568 1.780 0.058457 0.037576 1.000000 1.000000 +Culex pipiens 408 81 6.717 7.331 0.000000 0.000000 0.000000 0.000000 +Daphnia pulex 213 75 1.663 1.701 0.048160 0.044463 1.000000 1.000000 +Drosophila ananassae 3 20 5.872 5.539 0.000000 0.000000 0.000000 0.000001 +Drosophila grimshawi 14 10 -1.182 -1.134 0.118667 0.128417 1.000000 1.000000 +Drosophila pseudoobscura 28 22 -2.064 -1.967 0.019519 0.024570 1.000000 1.000000 +Drosophila willistoni 4 18 5.220 4.860 0.000000 0.000001 0.000005 0.000031 +Emiliania huxleyi 56 13 2.113 2.264 0.017321 0.011791 0.900675 0.613145 +Glycine max 4019 1831 -1.235 -1.231 0.108478 0.109251 1.000000 1.000000 +Helobdella robusta 33 1 3.496 4.684 0.000237 0.000001 0.012302 0.000073 +Homo sapiens 59 6 3.732 4.409 0.000095 0.000005 0.004933 0.000270 +Hyaloperonospora parasitica 48 10 2.201 2.389 0.013860 0.008448 0.720722 0.439307 +Hydra magnipapillata 9 65 10.697 10.120 0.000000 0.000000 0.000000 0.000000 +Medicago truncatula 62 42 -2.176 -2.096 0.014777 0.018033 0.768379 0.937696 +Mimulus guttatus 12 9 -1.224 -1.170 0.110516 0.120942 1.000000 1.000000 +Mus musculus 18 5 0.918 0.964 0.179337 0.167614 1.000000 1.000000 +Mycosphaerella fijiensis 42 7 2.472 2.755 0.006711 0.002933 0.348951 0.152533 +Nasonia vitripennis 10 12 2.443 2.277 0.007288 0.011379 0.378990 0.591708 +Nectria haematococca 67 2 4.987 6.692 0.000000 0.000000 0.000016 0.000000 +Oryza sativa 6068 2561 1.768 1.775 0.038558 0.037957 1.000000 1.000000 +Paramecium tetraurelia 749 296 1.565 1.582 0.058782 0.056837 1.000000 1.000000 +Pediculus humanus 49 40 -2.947 -2.802 0.001606 0.002538 0.083501 0.131991 +Phakopsora pachyrhizi 66 53 -3.311 -3.152 0.000464 0.000811 0.024152 0.042153 +Physcomitrella patens 304 36 7.993 9.276 0.000000 0.000000 0.000000 0.000000 +Phytophthora ramorum 174 56 2.044 2.111 0.020488 0.017390 1.000000 0.904295 +Phytophthora sojae 10 0 2.098 3.496 0.017969 0.000236 0.934412 0.012278 +Pinus taeda 0 26 7.687 8.498 0.000000 0.000000 0.000000 0.000000 +Populus balsamifera 43 4 3.281 3.916 0.000517 0.000045 0.026903 0.002339 +Pristionchus pacificus 4 14 4.349 4.025 0.000007 0.000028 0.000355 0.001481 +Rattus norvegicus 11 3 0.741 0.780 0.229238 0.217720 1.000000 1.000000 +Rhodnius prolixus 24 17 -1.516 -1.456 0.064729 0.072722 1.000000 1.000000 +Ricinus communis 75 14 3.036 3.338 0.001198 0.000422 0.062288 0.021926 +Schistosoma mansoni 80 15 3.124 3.433 0.000891 0.000298 0.046328 0.015504 +Schmidtea mediterranea 307 277 -8.853 -8.368 0.000000 0.000000 0.000000 0.000000 +Selaginella moellendorffii 27 10 0.466 0.474 0.320629 0.317714 1.000000 1.000000 +Sorghum bicolor 306 72 4.857 5.197 0.000001 0.000000 0.000031 0.000005 +Strongylocentrotus purpuratus 182 34 4.727 5.196 0.000001 0.000000 0.000059 0.000005 +Trypanosoma cruzi 23 0 3.181 5.302 0.000733 0.000000 0.038134 0.000003 +Volvox carteri 64 2 4.854 6.487 0.000001 0.000000 0.000031 0.000000 +Zea mays 583 263 -0.336 -0.335 0.368487 0.368792 1.000000 1.000000 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/t2t_report.dat --- a/test-data/t2t_report.dat Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -root root 5 -superkingdom Eukaryota 5 -kingdom Metazoa 5 -phylum Chordata 5 -subphylum Craniata 5 -superclass Gnathostomata 5 -class Mammalia 5 -superorder Euarchontoglires 4 -order Primates 4 -suborder Haplorrhini 3 -superfamily Hominoidea 3 -family Hominidae 3 -genus Homo 2 -species Homo sapiens 2 -subspecies Homo sapiens neanderthalensis 1 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/t2t_report.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t2t_report.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,15 @@ +root root 5 +superkingdom Eukaryota 5 +kingdom Metazoa 5 +phylum Chordata 5 +subphylum Craniata 5 +superclass Gnathostomata 5 +class Mammalia 5 +superorder Euarchontoglires 4 +order Primates 4 +suborder Haplorrhini 3 +superfamily Hominoidea 3 +family Hominidae 3 +genus Homo 2 +species Homo sapiens 2 +subspecies Homo sapiens neanderthalensis 1 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomy2gi-input.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy2gi-input.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,4 @@ +2 9913 +4 9646 +15 9915 +16 9771 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomy2gi-input.txt --- a/test-data/taxonomy2gi-input.txt Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -2 9913 -4 9646 -15 9915 -16 9771 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomy2gi-output.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy2gi-output.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,4 @@ +9913 9913 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos taurus n 2 +9646 9646 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria Carnivora Caniformia n Ursidae n n n Ailuropoda n Ailuropoda melanoleuca n 4 +9915 9915 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos indicus n 15 +9771 9771 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria Cetacea Mysticeti n Balaenopteridae n n n Balaenoptera n Balaenoptera musculus n 16 \ No newline at end of file diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomy2gi-output.txt --- a/test-data/taxonomy2gi-output.txt Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -9913 9913 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos taurus n 2 -9646 9646 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria Carnivora Caniformia n Ursidae n n n Ailuropoda n Ailuropoda melanoleuca n 4 -9915 9915 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos indicus n 15 -9771 9771 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria Cetacea Mysticeti n Balaenopteridae n n n Balaenoptera n Balaenoptera musculus n 16 \ No newline at end of file diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomyGI.dat --- a/test-data/taxonomyGI.dat Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -9606 9606 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n 12583 -40674 40674 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n n n n n n n n n n n n n 410771 -63221 63221 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens Homo sapiens neanderthalensis 2286205 -9604 9604 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n n n n n 23236241 -9443 9443 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates n n n n n n n n n n 33001686 \ No newline at end of file diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomyGI.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomyGI.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,5 @@ +33001686 9443 +23236241 9604 +12583 9606 +410771 40674 +2286205 63221 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomyGI.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomyGI.taxonomy Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,5 @@ +9606 9606 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n 12583 +40674 40674 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n n n n n n n n n n n n n 410771 +63221 63221 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens Homo sapiens neanderthalensis 2286205 +9604 9604 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n n n n n 23236241 +9443 9443 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates n n n n n n n n n n 33001686 \ No newline at end of file diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomyGI.txt --- a/test-data/taxonomyGI.txt Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -33001686 9443 -23236241 9604 -12583 9606 -410771 40674 -2286205 63221 diff -r 436de91e08b0 -r 82b63d47a0d8 tools/taxonomy/example_dataset_missing_nodes.txt --- a/tools/taxonomy/example_dataset_missing_nodes.txt Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -Species_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus1 subgenus1 species1 subspecies1 -Species_2 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus2 n species2 subspecies2 -Species_3 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 n subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species3 subspecies3 -Species_4 4 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum4 subphylum4 superclass4 class4 subclass4 superorder4 order4 suborder4 superfamily4 family4 subfamily4 tribe4 subtribe4 genus4 subgenus4 species4 subspecies4 -Species_5 5 root superkingdom1 kingdom1 subkingdom1 superphylum1 n subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species5 subspecies5 - diff -r 436de91e08b0 -r 82b63d47a0d8 tools/taxonomy/find_diag_hits.xml --- a/tools/taxonomy/find_diag_hits.xml Fri Nov 20 15:25:13 2009 -0500 +++ b/tools/taxonomy/find_diag_hits.xml Fri Nov 20 15:35:30 2009 -0500 @@ -37,11 +37,11 @@ </outputs> <tests> <test> - <param name="input1" value="taxonomyGI.dat" ftype="taxonomy"/> + <param name="input1" value="taxonomyGI.taxonomy" ftype="taxonomy"/> <param name="id_col" value="1" /> <param name="rank_list" value="order,genus" /> <param name="out_format" value="counts" /> - <output name="out_file1" file="find_diag_hits.dat" ftype="tabular"/> + <output name="out_file1" file="find_diag_hits.tabular" /> </test> </tests> diff -r 436de91e08b0 -r 82b63d47a0d8 tools/taxonomy/gi2taxonomy.xml --- a/tools/taxonomy/gi2taxonomy.xml Fri Nov 20 15:25:13 2009 -0500 +++ b/tools/taxonomy/gi2taxonomy.xml Fri Nov 20 15:35:30 2009 -0500 @@ -14,10 +14,10 @@ </requirements> <tests> <test> - <param name="input" value="taxonomy2gi-input.txt"/> + <param name="input" ftype="tabular" value="taxonomy2gi-input.tabular"/> <param name="giField" value="1"/> <param name="idField" value="2"/> - <output name="out_file1" file="taxonomy2gi-output.txt"/> + <output name="out_file1" file="taxonomy2gi-output.tabular"/> </test> </tests> diff -r 436de91e08b0 -r 82b63d47a0d8 tools/taxonomy/poisson2test.xml --- a/tools/taxonomy/poisson2test.xml Fri Nov 20 15:25:13 2009 -0500 +++ b/tools/taxonomy/poisson2test.xml Fri Nov 20 15:35:30 2009 -0500 @@ -16,20 +16,20 @@ </outputs> <tests> <test> - <param name="input1" value="poisson2test1.txt"/> + <param name="input1" value="poisson2test1.tabular" ftype="tabular"/> <param name="input2" value="2" /> <param name="input3" value="3" /> <param name="input4" value="0.44" /> <param name="input5" value="0" /> - <output name="output1" file="poisson2test1.out" /> + <output name="output1" file="poisson2test1_out.tabular" /> </test> <test> - <param name="input1" value="poisson2test2.txt"/> + <param name="input1" value="poisson2test2.tabular" ftype="tabular"/> <param name="input2" value="2" /> <param name="input3" value="3" /> <param name="input4" value="0.44" /> <param name="input5" value="0" /> - <output name="output1" file="poisson2test2.out" /> + <output name="output1" file="poisson2test2_out.tabular" /> </test> </tests> <help> diff -r 436de91e08b0 -r 82b63d47a0d8 tools/taxonomy/t2t_report.xml --- a/tools/taxonomy/t2t_report.xml Fri Nov 20 15:25:13 2009 -0500 +++ b/tools/taxonomy/t2t_report.xml Fri Nov 20 15:35:30 2009 -0500 @@ -12,8 +12,8 @@ </requirements> <tests> <test> - <param name="input" value="taxonomyGI.dat" ftype="taxonomy"/> - <output name="out_file1" file="t2t_report.dat"/> + <param name="input" value="taxonomyGI.taxonomy" ftype="taxonomy"/> + <output name="out_file1" file="t2t_report.tabular"/> </test> </tests>