# HG changeset patch # User peterjc # Date 1527508676 14400 # Node ID 13aa389f4eebb534728bb1e3449cbf9ff93a48c1 # Parent d724d9af93eefa626f975a5fea6bfa815d14d87d planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 16ef84e19ea373838bbfb921b9ef2cd4b02b8788-dirty diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastn_chimera_vs_rhodopsin_db.tabular --- a/test-data/blastn_chimera_vs_rhodopsin_db.tabular Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastn_chimera_vs_rhodopsin_db.tabular Mon May 28 07:57:56 2018 -0400 @@ -1,8 +1,8 @@ -chimera NM_001009242 92.308 1014 78 0 8881 9894 34 1047 0.0 1441 -chimera GQ290312 91.527 956 81 0 8881 9836 4 959 0.0 1317 -chimera AB062417 87.586 1015 124 2 8881 9894 34 1047 0.0 1175 -chimera GQ290303 91.515 330 28 0 8881 9210 4 333 8.28e-130 455 -chimera GQ290303 91.358 243 19 2 9542 9783 3127 3368 1.46e-92 331 -chimera GQ290303 94.220 173 10 0 9208 9380 1410 1582 1.50e-72 265 -chimera GQ290303 92.941 170 12 0 9375 9544 2854 3023 1.51e-67 248 -chimera GQ290303 95.588 68 3 0 9781 9848 4222 4289 7.43e-26 110 +chimera NM_001009242.1 92.308 1014 78 0 8881 9894 34 1047 0.0 1441 +chimera GQ290312.1 91.527 956 81 0 8881 9836 4 959 0.0 1317 +chimera AB062417.1 87.586 1015 124 2 8881 9894 34 1047 0.0 1175 +chimera GQ290303.1 91.515 330 28 0 8881 9210 4 333 8.28e-130 455 +chimera GQ290303.1 91.358 243 19 2 9542 9783 3127 3368 1.46e-92 331 +chimera GQ290303.1 94.220 173 10 0 9208 9380 1410 1582 1.50e-72 265 +chimera GQ290303.1 92.941 170 12 0 9375 9544 2854 3023 1.51e-67 248 +chimera GQ290303.1 95.588 68 3 0 9781 9848 4222 4289 7.43e-26 110 diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular --- a/test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular Mon May 28 07:57:56 2018 -0400 @@ -1,11 +1,11 @@ chimera ENA|AB011145|AB011145.1 100.000 4560 0 0 1 4560 121 4680 0.0 8421 chimera ENA|M10051|M10051.1 99.931 4331 3 0 4560 8890 60 4390 0.0 7982 chimera ENA|BC112106|BC112106.1 100.000 1093 0 0 8881 9973 121 1213 0.0 2019 -chimera NM_001009242 92.308 1014 78 0 8881 9894 34 1047 0.0 1441 -chimera GQ290312 91.527 956 81 0 8881 9836 4 959 0.0 1317 -chimera AB062417 87.586 1015 124 2 8881 9894 34 1047 0.0 1175 -chimera GQ290303 91.515 330 28 0 8881 9210 4 333 1.70e-129 455 -chimera GQ290303 91.358 243 19 2 9542 9783 3127 3368 2.98e-92 331 -chimera GQ290303 94.220 173 10 0 9208 9380 1410 1582 3.07e-72 265 -chimera GQ290303 92.941 170 12 0 9375 9544 2854 3023 3.09e-67 248 -chimera GQ290303 95.588 68 3 0 9781 9848 4222 4289 1.52e-25 110 +chimera NM_001009242.1 92.308 1014 78 0 8881 9894 34 1047 0.0 1441 +chimera GQ290312.1 91.527 956 81 0 8881 9836 4 959 0.0 1317 +chimera AB062417.1 87.586 1015 124 2 8881 9894 34 1047 0.0 1175 +chimera GQ290303.1 91.515 330 28 0 8881 9210 4 333 1.70e-129 455 +chimera GQ290303.1 91.358 243 19 2 9542 9783 3127 3368 2.98e-92 331 +chimera GQ290303.1 94.220 173 10 0 9208 9380 1410 1582 3.07e-72 265 +chimera GQ290303.1 92.941 170 12 0 9375 9544 2854 3023 3.09e-67 248 +chimera GQ290303.1 95.588 68 3 0 9781 9848 4222 4289 1.52e-25 110 diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastn_chimera_vs_three_human_max1.txt --- a/test-data/blastn_chimera_vs_three_human_max1.txt Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastn_chimera_vs_three_human_max1.txt Mon May 28 07:57:56 2018 -0400 @@ -1,4 +1,4 @@ -BLASTN 2.5.0+ +BLASTN 2.7.1+ Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb @@ -346,7 +346,7 @@ Database: Just 3 human mRNA sequences - Posted date: Dec 2, 2016 10:38 AM + Posted date: Oct 31, 2017 4:23 PM Number of letters in database: 10,732 Number of sequences in database: 3 diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastn_rhodopsin_vs_three_human.xml --- a/test-data/blastn_rhodopsin_vs_three_human.xml Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastn_rhodopsin_vs_three_human.xml Mon May 28 07:57:56 2018 -0400 @@ -2,7 +2,7 @@ blastn - BLASTN 2.5.0+ + BLASTN 2.7.1+ Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14. Query_1 diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastp_four_human_vs_rhodopsin.tabular --- a/test-data/blastp_four_human_vs_rhodopsin.tabular Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin.tabular Mon May 28 07:57:56 2018 -0400 @@ -1,6 +1,6 @@ -P08100 NP_001009242 96.552 348 12 0 1 348 1 348 0.0 701 +P08100 NP_001009242.1 96.552 348 12 0 1 348 1 348 0.0 701 P08100 0811197A 93.103 348 23 1 1 348 1 347 0.0 673 -P08100 ADB45242 94.817 328 17 0 11 338 1 328 0.0 653 -P08100 ADB45229 94.817 328 17 0 11 338 1 328 0.0 631 -P08100 P56514 84.795 342 51 1 1 341 1 342 0.0 619 -P08100 BAB21486 82.164 342 60 1 1 341 1 342 0.0 599 +P08100 ADB45242.1 94.817 328 17 0 11 338 1 328 0.0 653 +P08100 ADB45229.1 94.817 328 17 0 11 338 1 328 0.0 631 +P08100 P56514.1 84.795 342 51 1 1 341 1 342 0.0 619 +P08100 BAB21486.1 82.164 342 60 1 1 341 1 342 0.0 599 diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastp_four_human_vs_rhodopsin.xml --- a/test-data/blastp_four_human_vs_rhodopsin.xml Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Mon May 28 07:57:56 2018 -0400 @@ -2,7 +2,7 @@ blastp - BLASTP 2.5.0+ + BLASTP 2.7.1+ Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Q9BS26 diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastp_four_human_vs_rhodopsin_ext.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Mon May 28 07:57:56 2018 -0400 @@ -1,6 +1,6 @@ -P08100 NP_001009242 96.552 348 12 0 1 348 1 348 0.0 701 gi|57163783|ref|NP_001009242.1| 1808 336 343 0 98.56 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 348 N/A +P08100 NP_001009242.1 96.552 348 12 0 1 348 1 348 0.0 701 gi|57163783|ref|NP_001009242.1| 1808 336 343 0 98.56 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 348 N/A P08100 0811197A 93.103 348 23 1 1 348 1 347 0.0 673 gi|223523|prf||0811197A 1736 324 336 1 96.55 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 347 N/A -P08100 ADB45242 94.817 328 17 0 11 338 1 328 0.0 653 gi|283855846|gb|ADB45242.1| 1684 311 321 0 97.87 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 N/A -P08100 ADB45229 94.817 328 17 0 11 338 1 328 0.0 631 gi|283855823|gb|ADB45229.1| 1627 311 323 0 98.48 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 N/A -P08100 P56514 84.795 342 51 1 1 341 1 342 0.0 619 gi|3024260|sp|P56514.1|OPSD_BUFBU 1595 290 322 1 94.15 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 354 N/A -P08100 BAB21486 82.164 342 60 1 1 341 1 342 0.0 599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354 N/A +P08100 ADB45242.1 94.817 328 17 0 11 338 1 328 0.0 653 gi|283855846|gb|ADB45242.1| 1684 311 321 0 97.87 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 N/A +P08100 ADB45229.1 94.817 328 17 0 11 338 1 328 0.0 631 gi|283855823|gb|ADB45229.1| 1627 311 323 0 98.48 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 N/A +P08100 P56514.1 84.795 342 51 1 1 341 1 342 0.0 619 gi|3024260|sp|P56514.1|OPSD_BUFBU 1595 290 322 1 94.15 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 354 N/A +P08100 BAB21486.1 82.164 342 60 1 1 341 1 342 0.0 599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354 N/A diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastx_rhodopsin_vs_four_human.xml --- a/test-data/blastx_rhodopsin_vs_four_human.xml Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Mon May 28 07:57:56 2018 -0400 @@ -2,7 +2,7 @@ blastx - BLASTX 2.5.0+ + BLASTX 2.7.1+ Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query_1 diff -r d724d9af93ee -r 13aa389f4eeb test-data/cd00003_and_cd00008.pin Binary file test-data/cd00003_and_cd00008.pin has changed diff -r d724d9af93ee -r 13aa389f4eeb test-data/four_human_proteins.dbinfo.txt --- a/test-data/four_human_proteins.dbinfo.txt Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/four_human_proteins.dbinfo.txt Mon May 28 07:57:56 2018 -0400 @@ -1,7 +1,7 @@ Database: Just 4 human proteins 4 sequences; 3,297 total residues -Date: Dec 2, 2016 10:38 AM Longest sequence: 1,382 residues +Date: Oct 31, 2017 4:23 PM Longest sequence: 1,382 residues Volumes: - /mnt/shared/users/pc40583/repositories/galaxy_blast/test-data/four_human_proteins_taxid.fasta + /mnt/galaxy/repositories/galaxy_blast/test-data/four_human_proteins_taxid.fasta diff -r d724d9af93ee -r 13aa389f4eeb test-data/four_human_proteins.fasta.pin Binary file test-data/four_human_proteins.fasta.pin has changed diff -r d724d9af93ee -r 13aa389f4eeb test-data/four_human_proteins_taxid.fasta.pin Binary file test-data/four_human_proteins_taxid.fasta.pin has changed diff -r d724d9af93ee -r 13aa389f4eeb test-data/rhodopsin_nucs.dbinfo.txt --- a/test-data/rhodopsin_nucs.dbinfo.txt Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/rhodopsin_nucs.dbinfo.txt Mon May 28 07:57:56 2018 -0400 @@ -1,7 +1,7 @@ Database: Rhodopsin nucleotides 6 sequences; 10,296 total bases -Date: Dec 2, 2016 10:38 AM Longest sequence: 4,301 bases +Date: Oct 31, 2017 4:23 PM Longest sequence: 4,301 bases Volumes: - /mnt/shared/users/pc40583/repositories/galaxy_blast/test-data/rhodopsin_nucs.fasta + /mnt/galaxy/repositories/galaxy_blast/test-data/rhodopsin_nucs.fasta diff -r d724d9af93ee -r 13aa389f4eeb test-data/rhodopsin_nucs.fasta.nin Binary file test-data/rhodopsin_nucs.fasta.nin has changed diff -r d724d9af93ee -r 13aa389f4eeb test-data/tblastn_four_human_vs_rhodopsin.html --- a/test-data/tblastn_four_human_vs_rhodopsin.html Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Mon May 28 07:57:56 2018 -0400 @@ -1,9 +1,9 @@ -BLAST Search Results +BLAST Search Results 
 
-TBLASTN 2.5.0+
+TBLASTN 2.7.1+
 
 
 
 
   tblastn
-  TBLASTN 2.5.0+
+  TBLASTN 2.7.1+
   Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
   
   Query_1
diff -r d724d9af93ee -r 13aa389f4eeb test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular
--- a/test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular	Mon May 28 07:57:56 2018 -0400
@@ -1,10 +1,10 @@
-P08100	NM_001009242	96.552	348	12	0	1	348	1	1044	0.0	732
-P08100	AB062417	93.391	348	23	0	1	348	1	1044	0.0	711
-P08100	GQ290312	95.092	326	16	0	11	336	1	978	0.0	658
-P08100	U59921	84.795	342	51	1	1	341	42	1067	0.0	646
-P08100	AB043817	82.164	342	60	1	1	341	23	1048	0.0	626
-P08100	GQ290303	93.243	74	5	0	239	312	3147	3368	1.34e-71	151
-P08100	GQ290303	91.525	59	5	0	177	235	2855	3031	1.34e-71	126
-P08100	GQ290303	96.396	111	4	0	11	121	1	333	3.31e-67	229
-P08100	GQ290303	93.220	59	4	0	119	177	1404	1580	2.31e-32	122
-P08100	GQ290303	88.462	26	3	0	312	337	4222	4299	3.61e-12	57.7
+P08100	NM_001009242.1	96.552	348	12	0	1	348	1	1044	0.0	732
+P08100	AB062417.1	93.391	348	23	0	1	348	1	1044	0.0	711
+P08100	GQ290312.1	95.092	326	16	0	11	336	1	978	0.0	658
+P08100	U59921.1	84.795	342	51	1	1	341	42	1067	0.0	646
+P08100	AB043817.1	82.164	342	60	1	1	341	23	1048	0.0	626
+P08100	GQ290303.1	93.243	74	5	0	239	312	3147	3368	1.34e-71	151
+P08100	GQ290303.1	91.525	59	5	0	177	235	2855	3031	1.34e-71	126
+P08100	GQ290303.1	96.396	111	4	0	11	121	1	333	3.31e-67	229
+P08100	GQ290303.1	93.220	59	4	0	119	177	1404	1580	2.31e-32	122
+P08100	GQ290303.1	88.462	26	3	0	312	337	4222	4299	3.61e-12	57.7
diff -r d724d9af93ee -r 13aa389f4eeb test-data/three_human_mRNA.dbinfo.txt
--- a/test-data/three_human_mRNA.dbinfo.txt	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/three_human_mRNA.dbinfo.txt	Mon May 28 07:57:56 2018 -0400
@@ -1,7 +1,7 @@
 Database: Just 3 human mRNA sequences
 	3 sequences; 10,732 total bases
 
-Date: Dec 2, 2016  10:38 AM	Longest sequence: 4,796 bases
+Date: Oct 31, 2017  4:23 PM	Longest sequence: 4,796 bases
 
 Volumes:
-	/mnt/shared/users/pc40583/repositories/galaxy_blast/test-data/three_human_mRNA.fasta
+	/mnt/galaxy/repositories/galaxy_blast/test-data/three_human_mRNA.fasta
diff -r d724d9af93ee -r 13aa389f4eeb test-data/three_human_mRNA.fasta.nin
Binary file test-data/three_human_mRNA.fasta.nin has changed
diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/README.rst
--- a/tools/ncbi_blast_plus/README.rst	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/README.rst	Mon May 28 07:57:56 2018 -0400
@@ -255,6 +255,10 @@
         - Support for ``-window_size``, ``-threshold``, ``-comp_based_stats``
           and revising ``-word_size`` to avoid using zero to mean  default
           (contribution from Caleb Easterly).
+v0.3.0  - Updated for NCBI BLAST+ 2.7.1,
+        - Depends on BioConda or legacy ToolShed ``package_blast_plus_2_7_1``.
+        - Document the BLAST+ 2.6.0 change in the standard 12 column output
+          from ``qacc,sacc,...`` to ``qaccver,saccver,...`` instead.
 ======= ======================================================================
 
 
diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Mon May 28 07:57:56 2018 -0400
@@ -86,7 +86,7 @@
 More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_.
 
 .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/
-.. _DUST: http://www.ncbi.nlm.nih.gov/pubmed/16796549
+.. _DUST: https://www.ncbi.nlm.nih.gov/pubmed/16796549
 
 **References**
 
diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/ncbi_macros.xml
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Mon May 28 07:57:56 2018 -0400
@@ -1,5 +1,5 @@
 
-    0.2.02
+    0.3.0
     
         
         
@@ -7,7 +7,7 @@
 
     
         
-            blast
+            blast
         
         @BINARY@ -version
     
@@ -288,7 +288,7 @@
 
     
         
-            
+            
             
             
             
@@ -312,7 +312,7 @@
 
     
         
-            
+            
             
             
             
@@ -678,8 +678,8 @@
 ====== ========= ============================================
 Column NCBI name Description
 ------ --------- --------------------------------------------
-     1 qacc      Query accession
-     2 sacc      Subject accession (database hit)
+     1 qaccver   Query accession dot version
+     2 saccver   Subject accession dot version (database hit)
      3 pident    Percentage of identical matches
      4 length    Alignment length
      5 mismatch  Number of mismatches
diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/ncbi_makeblastdb.xml
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Mon May 28 07:57:56 2018 -0400
@@ -110,7 +110,7 @@
             
             
                 
-                
+                
                 
                 
                 
@@ -129,7 +129,7 @@
             
             
                 
-                
+                
                 
                 
                 
@@ -147,7 +147,7 @@
             
             
                 
-                
+                
                 
                 
                 
@@ -166,7 +166,7 @@
             
             
                 
-                
+                
                 
                 
                 
diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Mon May 28 07:57:56 2018 -0400
@@ -75,15 +75,15 @@
 (PSSMs) and are available for a number of domain collections including:
 
 *CDD* - NCBI curarated meta-collection of domains, see
-http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains
+https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains
 
 *Kog* - PSSMs from automatically aligned sequences and sequence
 fragments classified in the KOGs resource, the eukaryotic
-counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/
+counterpart to COGs, see https://www.ncbi.nlm.nih.gov/COG/
 
 *Cog* - PSSMs from automatically aligned sequences and sequence
 fragments classified in the COGs resource, which focuses primarily
-on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/
+on prokaryotes, see https://www.ncbi.nlm.nih.gov/COG/
 
 *Pfam* - PSSMs from Pfam-A seed alignment database, see
 http://xfam.org/
@@ -92,11 +92,11 @@
 http://smart.embl-heidelberg.de/
 
 *Tigr* - PSSMs from TIGRFAM database of protein families, see
-http://www.jcvi.org/cms/research/projects/tigrfams/overview/
+ftp://ftp.jcvi.org/pub/data/TIGRFAMs/
 
 *Prk* - PSSms from automatically aligned stable clusters in the
 Protein Clusters database, see
-http://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters
+https://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters
 
 The exact list of domain databases offered will depend on how your
 local Galaxy has been configured.
diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Mon May 28 07:57:56 2018 -0400
@@ -73,15 +73,15 @@
 (PSSMs) and are available for a number of domain collections including:
 
 *CDD* - NCBI curarated meta-collection of domains, see
-http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains
+https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains
 
 *Kog* - PSSMs from automatically aligned sequences and sequence
 fragments classified in the KOGs resource, the eukaryotic
-counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/
+counterpart to COGs, see https://www.ncbi.nlm.nih.gov/COG/
 
 *Cog* - PSSMs from automatically aligned sequences and sequence
 fragments classified in the COGs resource, which focuses primarily
-on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/
+on prokaryotes, see https://www.ncbi.nlm.nih.gov/COG/
 
 *Pfam* - PSSMs from Pfam-A seed alignment database, see
 http://xfam.org/
@@ -90,11 +90,11 @@
 http://smart.embl-heidelberg.de/
 
 *Tigr* - PSSMs from TIGRFAM database of protein families, see
-http://www.jcvi.org/cms/research/projects/tigrfams/overview/
+ftp://ftp.jcvi.org/pub/data/TIGRFAMs/
 
 *Prk* - PSSms from automatically aligned stable clusters in the
 Protein Clusters database, see
-http://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters
+https://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters
 
 The exact list of domain databases offered will depend on how your
 local Galaxy has been configured.
diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Mon May 28 07:57:56 2018 -0400
@@ -88,7 +88,7 @@
 More information about segmasker can be found in the `BLAST Command Line Applications User Manual`_.
 
 .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/
-.. _SEG: http://www.ncbi.nlm.nih.gov/pubmed/8743706
+.. _SEG: https://www.ncbi.nlm.nih.gov/pubmed/8743706
 
 **References**