diff --git a/lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml b/lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
deleted file mode 100644
index 9bccf112f2d..00000000000
--- a/lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
+++ /dev/null
@@ -1,722 +0,0 @@
-
-
-
- tblastn
- TBLASTN 2.2.25+
- 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
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
- BLOSUM80
- 1e-10
- 10
- 1
- F
-
-
-
-
- 1
- Query_1
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
-
- 0
- 0
- 19
- 127710
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 2
- Query_1
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
-
- 0
- 0
- 19
- 127710
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 3
- Query_1
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
-
- 0
- 0
- 19
- 127710
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 4
- Query_1
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
-
- 0
- 0
- 19
- 127710
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 5
- Query_1
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
-
- 0
- 0
- 19
- 127710
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 6
- Query_1
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
-
- 0
- 0
- 19
- 127710
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 7
- Query_2
- sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
- 1161
-
-
-
- 0
- 0
- 23
- 370988
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 8
- Query_2
- sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
- 1161
-
-
-
- 0
- 0
- 23
- 370988
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 9
- Query_2
- sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
- 1161
-
-
-
- 0
- 0
- 23
- 370988
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 10
- Query_2
- sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
- 1161
-
-
-
- 0
- 0
- 23
- 370988
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 11
- Query_2
- sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
- 1161
-
-
-
- 0
- 0
- 23
- 370988
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 12
- Query_2
- sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
- 1161
-
-
-
- 0
- 0
- 23
- 370988
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 13
- Query_3
- sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4
- 1382
-
-
-
- 0
- 0
- 24
- 441350
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 14
- Query_3
- sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4
- 1382
-
-
-
- 0
- 0
- 24
- 441350
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 15
- Query_3
- sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4
- 1382
-
-
-
- 0
- 0
- 24
- 441350
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 16
- Query_3
- sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4
- 1382
-
-
-
- 0
- 0
- 24
- 441350
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 17
- Query_3
- sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4
- 1382
-
-
-
- 0
- 0
- 24
- 441350
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 18
- Query_3
- sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4
- 1382
-
-
-
- 0
- 0
- 24
- 441350
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 19
- Query_4
- sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
- 348
-
-
- 1
- Subject_1
- gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA
- Subject_1
- 1047
-
-
- 1
- 732.392902459534
- 1689
- 0
- 1
- 348
- 1
- 1044
- 0
- 1
- 336
- 343
- 0
- 348
- MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
- MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA
- MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA
-
-
-
-
-
-
- 0
- 0
- 18
- 109230
- 0.071
- 0.299
- 0.27
-
-
-
-
- 20
- Query_4
- sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
- 348
-
-
- 1
- Subject_2
- gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds
- Subject_2
- 1574
-
-
- 1
- 646.119739014374
- 1489
- 0
- 1
- 341
- 42
- 1067
- 0
- 3
- 290
- 320
- 1
- 342
- MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE
- MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE
- MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S+ GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF+ QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA SKTE
-
-
-
-
-
-
- 0
- 0
- 18
- 109230
- 0.071
- 0.299
- 0.27
-
-
-
-
- 21
- Query_4
- sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
- 348
-
-
- 1
- Subject_3
- gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds
- Subject_3
- 4301
-
-
- 1
- 151.343146656381
- 342
- 1.39566684546685e-72
- 239
- 312
- 3147
- 3368
- 0
- 3
- 69
- 73
- 0
- 74
- ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ
- ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ
- ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ
-
-
- 2
- 126.323929257285
- 284
- 1.39566684546685e-72
- 177
- 235
- 2855
- 3031
- 0
- 2
- 54
- 57
- 0
- 59
- RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA
- RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS
- RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE +
-
-
- 3
- 229.420359574251
- 523
- 9.84654801241353e-65
- 11
- 121
- 1
- 333
- 0
- 1
- 107
- 109
- 0
- 111
- VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG
- VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG
- VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG
-
-
- 4
- 122.873002719478
- 276
- 1.40732096096596e-32
- 119
- 177
- 1404
- 1580
- 0
- 3
- 55
- 56
- 0
- 59
- LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR
- LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR
- L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR
-
-
- 5
- 57.7367643183824
- 125
- 5.60065526485586e-13
- 312
- 337
- 4222
- 4299
- 0
- 1
- 23
- 24
- 0
- 26
- QFRNCMLTTICCGKNPLGDDEASATV
- QFRNCMLTTLCCGKNPLGDDEASTTA
- QFRNCMLTT+CCGKNPLGDDEAS T
-
-
-
-
-
-
- 0
- 0
- 18
- 109230
- 0.071
- 0.299
- 0.27
-
-
-
-
- 22
- Query_4
- sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
- 348
-
-
- 1
- Subject_4
- gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds
- Subject_4
- 983
-
-
- 1
- 658.197981896696
- 1517
- 0
- 11
- 336
- 1
- 978
- 0
- 1
- 310
- 322
- 0
- 326
- VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT
- VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT
- VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T
-
-
-
-
-
-
- 0
- 0
- 18
- 109230
- 0.071
- 0.299
- 0.27
-
-
-
-
- 23
- Query_4
- sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
- 348
-
-
- 1
- Subject_5
- gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds
- Subject_5
- 1047
-
-
- 1
- 711.255977415469
- 1640
- 0
- 1
- 348
- 1
- 1044
- 0
- 1
- 325
- 337
- 0
- 348
- MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
- MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA
- MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA
-
-
-
-
-
-
- 0
- 0
- 18
- 109230
- 0.071
- 0.299
- 0.27
-
-
-
-
- 24
- Query_4
- sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
- 348
-
-
- 1
- Subject_6
- gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds
- Subject_6
- 1344
-
-
- 1
- 626.708277239213
- 1444
- 0
- 1
- 341
- 23
- 1048
- 0
- 2
- 281
- 311
- 1
- 342
- MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE
- MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE
- MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR CM+TT+CCGKNP +D ASAT SKTE
-
-
-
-
-
-
- 0
- 0
- 18
- 109230
- 0.071
- 0.299
- 0.27
-
-
-
-
-
diff --git a/test-data/tblastn_four_human_vs_rhodopsin.xml b/test-data/tblastn_four_human_vs_rhodopsin.xml
deleted file mode 100644
index 9bccf112f2d..00000000000
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml
+++ /dev/null
@@ -1,722 +0,0 @@
-
-
-
- tblastn
- TBLASTN 2.2.25+
- 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
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
- BLOSUM80
- 1e-10
- 10
- 1
- F
-
-
-
-
- 1
- Query_1
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
-
- 0
- 0
- 19
- 127710
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 2
- Query_1
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
-
- 0
- 0
- 19
- 127710
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 3
- Query_1
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
-
- 0
- 0
- 19
- 127710
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 4
- Query_1
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
-
- 0
- 0
- 19
- 127710
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 5
- Query_1
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
-
- 0
- 0
- 19
- 127710
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 6
- Query_1
- sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- 406
-
-
-
- 0
- 0
- 19
- 127710
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 7
- Query_2
- sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
- 1161
-
-
-
- 0
- 0
- 23
- 370988
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 8
- Query_2
- sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
- 1161
-
-
-
- 0
- 0
- 23
- 370988
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 9
- Query_2
- sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
- 1161
-
-
-
- 0
- 0
- 23
- 370988
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 10
- Query_2
- sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
- 1161
-
-
-
- 0
- 0
- 23
- 370988
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 11
- Query_2
- sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
- 1161
-
-
-
- 0
- 0
- 23
- 370988
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 12
- Query_2
- sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
- 1161
-
-
-
- 0
- 0
- 23
- 370988
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 13
- Query_3
- sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4
- 1382
-
-
-
- 0
- 0
- 24
- 441350
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 14
- Query_3
- sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4
- 1382
-
-
-
- 0
- 0
- 24
- 441350
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 15
- Query_3
- sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4
- 1382
-
-
-
- 0
- 0
- 24
- 441350
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 16
- Query_3
- sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4
- 1382
-
-
-
- 0
- 0
- 24
- 441350
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 17
- Query_3
- sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4
- 1382
-
-
-
- 0
- 0
- 24
- 441350
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 18
- Query_3
- sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4
- 1382
-
-
-
- 0
- 0
- 24
- 441350
- 0.071
- 0.299
- 0.27
-
-
- No hits found
-
-
- 19
- Query_4
- sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
- 348
-
-
- 1
- Subject_1
- gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA
- Subject_1
- 1047
-
-
- 1
- 732.392902459534
- 1689
- 0
- 1
- 348
- 1
- 1044
- 0
- 1
- 336
- 343
- 0
- 348
- MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
- MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA
- MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA
-
-
-
-
-
-
- 0
- 0
- 18
- 109230
- 0.071
- 0.299
- 0.27
-
-
-
-
- 20
- Query_4
- sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
- 348
-
-
- 1
- Subject_2
- gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds
- Subject_2
- 1574
-
-
- 1
- 646.119739014374
- 1489
- 0
- 1
- 341
- 42
- 1067
- 0
- 3
- 290
- 320
- 1
- 342
- MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE
- MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE
- MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S+ GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF+ QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA SKTE
-
-
-
-
-
-
- 0
- 0
- 18
- 109230
- 0.071
- 0.299
- 0.27
-
-
-
-
- 21
- Query_4
- sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
- 348
-
-
- 1
- Subject_3
- gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds
- Subject_3
- 4301
-
-
- 1
- 151.343146656381
- 342
- 1.39566684546685e-72
- 239
- 312
- 3147
- 3368
- 0
- 3
- 69
- 73
- 0
- 74
- ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ
- ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ
- ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ
-
-
- 2
- 126.323929257285
- 284
- 1.39566684546685e-72
- 177
- 235
- 2855
- 3031
- 0
- 2
- 54
- 57
- 0
- 59
- RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA
- RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS
- RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE +
-
-
- 3
- 229.420359574251
- 523
- 9.84654801241353e-65
- 11
- 121
- 1
- 333
- 0
- 1
- 107
- 109
- 0
- 111
- VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG
- VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG
- VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG
-
-
- 4
- 122.873002719478
- 276
- 1.40732096096596e-32
- 119
- 177
- 1404
- 1580
- 0
- 3
- 55
- 56
- 0
- 59
- LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR
- LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR
- L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR
-
-
- 5
- 57.7367643183824
- 125
- 5.60065526485586e-13
- 312
- 337
- 4222
- 4299
- 0
- 1
- 23
- 24
- 0
- 26
- QFRNCMLTTICCGKNPLGDDEASATV
- QFRNCMLTTLCCGKNPLGDDEASTTA
- QFRNCMLTT+CCGKNPLGDDEAS T
-
-
-
-
-
-
- 0
- 0
- 18
- 109230
- 0.071
- 0.299
- 0.27
-
-
-
-
- 22
- Query_4
- sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
- 348
-
-
- 1
- Subject_4
- gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds
- Subject_4
- 983
-
-
- 1
- 658.197981896696
- 1517
- 0
- 11
- 336
- 1
- 978
- 0
- 1
- 310
- 322
- 0
- 326
- VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT
- VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT
- VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T
-
-
-
-
-
-
- 0
- 0
- 18
- 109230
- 0.071
- 0.299
- 0.27
-
-
-
-
- 23
- Query_4
- sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
- 348
-
-
- 1
- Subject_5
- gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds
- Subject_5
- 1047
-
-
- 1
- 711.255977415469
- 1640
- 0
- 1
- 348
- 1
- 1044
- 0
- 1
- 325
- 337
- 0
- 348
- MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
- MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA
- MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA
-
-
-
-
-
-
- 0
- 0
- 18
- 109230
- 0.071
- 0.299
- 0.27
-
-
-
-
- 24
- Query_4
- sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
- 348
-
-
- 1
- Subject_6
- gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds
- Subject_6
- 1344
-
-
- 1
- 626.708277239213
- 1444
- 0
- 1
- 341
- 23
- 1048
- 0
- 2
- 281
- 311
- 1
- 342
- MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE
- MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE
- MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR CM+TT+CCGKNP +D ASAT SKTE
-
-
-
-
-
-
- 0
- 0
- 18
- 109230
- 0.071
- 0.299
- 0.27
-
-
-
-
-
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 17a4b5421d9..d9eafeba58c 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -244,14 +244,6 @@
-
diff --git a/tools/ncbi_blast_plus/blastxml_to_tabular.py b/tools/ncbi_blast_plus/blastxml_to_tabular.py
deleted file mode 100644
index 7098fec2d2b..00000000000
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py
+++ /dev/null
@@ -1,254 +0,0 @@
-#!/usr/bin/env python
-"""Convert a BLAST XML file to 12 column tabular output
-
-Takes three command line options, input BLAST XML filename, output tabular
-BLAST filename, output format (std for standard 12 columns, or ext for the
-extended 24 columns offered in the BLAST+ wrappers).
-
-The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart
-qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which
-mean:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
- 1 qseqid Query Seq-id (ID of your sequence)
- 2 sseqid Subject Seq-id (ID of the database hit)
- 3 pident Percentage of identical matches
- 4 length Alignment length
- 5 mismatch Number of mismatches
- 6 gapopen Number of gap openings
- 7 qstart Start of alignment in query
- 8 qend End of alignment in query
- 9 sstart Start of alignment in subject (database hit)
- 10 send End of alignment in subject (database hit)
- 11 evalue Expectation value (E-value)
- 12 bitscore Bit score
-====== ========= ============================================
-
-The additional columns offered in the Galaxy BLAST+ wrappers are:
-
-====== ============= ===========================================
-Column NCBI name Description
------- ------------- -------------------------------------------
- 13 sallseqid All subject Seq-id(s), separated by a ';'
- 14 score Raw score
- 15 nident Number of identical matches
- 16 positive Number of positive-scoring matches
- 17 gaps Total number of gaps
- 18 ppos Percentage of positive-scoring matches
- 19 qframe Query frame
- 20 sframe Subject frame
- 21 qseq Aligned part of query sequence
- 22 sseq Aligned part of subject sequence
- 23 qlen Query sequence length
- 24 slen Subject sequence length
-====== ============= ===========================================
-
-Most of these fields are given explicitly in the XML file, others some like
-the percentage identity and the number of gap openings must be calculated.
-
-Be aware that the sequence in the extended tabular output or XML direct from
-BLAST+ may or may not use XXXX masking on regions of low complexity. This
-can throw the off the calculation of percentage identity and gap openings.
-[In fact, both BLAST 2.2.24+ and 2.2.25+ have a subtle bug in this regard,
-with these numbers changing depending on whether or not the low complexity
-filter is used.]
-
-This script attempts to produce identical output to what BLAST+ would have done.
-However, check this with "diff -b ..." since BLAST+ sometimes includes an extra
-space character (probably a bug).
-"""
-import sys
-import re
-
-if sys.version_info[:2] >= ( 2, 5 ):
- import xml.etree.cElementTree as ElementTree
-else:
- from galaxy import eggs
- import pkg_resources; pkg_resources.require( "elementtree" )
- from elementtree import ElementTree
-
-def stop_err( msg ):
- sys.stderr.write("%s\n" % msg)
- sys.exit(1)
-
-#Parse Command Line
-try:
- in_file, out_file, out_fmt = sys.argv[1:]
-except:
- stop_err("Expect 3 arguments: input BLAST XML file, output tabular file, out format (std or ext)")
-
-if out_fmt == "std":
- extended = False
-elif out_fmt == "x22":
- stop_err("Format argument x22 has been replaced with ext (extended 24 columns)")
-elif out_fmt == "ext":
- extended = True
-else:
- stop_err("Format argument should be std (12 column) or ext (extended 24 columns)")
-
-
-# get an iterable
-try:
- context = ElementTree.iterparse(in_file, events=("start", "end"))
-except:
- stop_err("Invalid data format.")
-# turn it into an iterator
-context = iter(context)
-# get the root element
-try:
- event, root = context.next()
-except:
- stop_err( "Invalid data format." )
-
-
-re_default_query_id = re.compile("^Query_\d+$")
-assert re_default_query_id.match("Query_101")
-assert not re_default_query_id.match("Query_101a")
-assert not re_default_query_id.match("MyQuery_101")
-re_default_subject_id = re.compile("^Subject_\d+$")
-assert re_default_subject_id.match("Subject_1")
-assert not re_default_subject_id.match("Subject_")
-assert not re_default_subject_id.match("Subject_12a")
-assert not re_default_subject_id.match("TheSubject_1")
-
-
-outfile = open(out_file, 'w')
-blast_program = None
-for event, elem in context:
- if event == "end" and elem.tag == "BlastOutput_program":
- blast_program = elem.text
- # for every tag
- if event == "end" and elem.tag == "Iteration":
- #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA
- # sp|Q9BS26|ERP44_HUMAN
- # Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
- # 406
- #
- #
- #Or, from BLAST 2.2.24+ run online
- # Query_1
- # Sample
- # 516
- # ...
- qseqid = elem.findtext("Iteration_query-ID")
- if re_default_query_id.match(qseqid):
- #Place holder ID, take the first word of the query definition
- qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
- qlen = int(elem.findtext("Iteration_query-len"))
-
- # for every within
- for hit in elem.findall("Iteration_hits/Hit"):
- #Expecting either this,
- # gi|3024260|sp|P56514.1|OPSD_BUFBU
- # RecName: Full=Rhodopsin
- # P56514
- #or,
- # Subject_1
- # gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]
- # Subject_1
- #
- #apparently depending on the parse_deflines switch
- sseqid = hit.findtext("Hit_id").split(None,1)[0]
- hit_def = sseqid + " " + hit.findtext("Hit_def")
- if re_default_subject_id.match(sseqid) \
- and sseqid == hit.findtext("Hit_accession"):
- #Place holder ID, take the first word of the subject definition
- hit_def = hit.findtext("Hit_def")
- sseqid = hit_def.split(None,1)[0]
- # for every within
- for hsp in hit.findall("Hit_hsps/Hsp"):
- nident = hsp.findtext("Hsp_identity")
- length = hsp.findtext("Hsp_align-len")
- pident = "%0.2f" % (100*float(nident)/float(length))
-
- q_seq = hsp.findtext("Hsp_qseq")
- h_seq = hsp.findtext("Hsp_hseq")
- m_seq = hsp.findtext("Hsp_midline")
- assert len(q_seq) == len(h_seq) == len(m_seq) == int(length)
- gapopen = str(len(q_seq.replace('-', ' ').split())-1 + \
- len(h_seq.replace('-', ' ').split())-1)
-
- mismatch = m_seq.count(' ') + m_seq.count('+') \
- - q_seq.count('-') - h_seq.count('-')
- #TODO - Remove this alternative mismatch calculation and test
- #once satisifed there are no problems
- expected_mismatch = len(q_seq) \
- - sum(1 for q,h in zip(q_seq, h_seq) \
- if q == h or q == "-" or h == "-")
- xx = sum(1 for q,h in zip(q_seq, h_seq) if q=="X" and h=="X")
- if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx):
- stop_err("%s vs %s mismatches, expected %i <= %i <= %i" \
- % (qseqid, sseqid, expected_mismatch - q_seq.count("X"),
- int(mismatch), expected_mismatch))
-
- #TODO - Remove this alternative identity calculation and test
- #once satisifed there are no problems
- expected_identity = sum(1 for q,h in zip(q_seq, h_seq) if q == h)
- if not (expected_identity - xx <= int(nident) <= expected_identity + q_seq.count("X")):
- stop_err("%s vs %s identities, expected %i <= %i <= %i" \
- % (qseqid, sseqid, expected_identity, int(nident),
- expected_identity + q_seq.count("X")))
-
-
- evalue = hsp.findtext("Hsp_evalue")
- if evalue == "0":
- evalue = "0.0"
- else:
- evalue = "%0.0e" % float(evalue)
-
- bitscore = float(hsp.findtext("Hsp_bit-score"))
- if bitscore < 100:
- #Seems to show one decimal place for lower scores
- bitscore = "%0.1f" % bitscore
- else:
- #Note BLAST does not round to nearest int, it truncates
- bitscore = "%i" % bitscore
-
- values = [qseqid,
- sseqid,
- pident,
- length, #hsp.findtext("Hsp_align-len")
- str(mismatch),
- gapopen,
- hsp.findtext("Hsp_query-from"), #qstart,
- hsp.findtext("Hsp_query-to"), #qend,
- hsp.findtext("Hsp_hit-from"), #sstart,
- hsp.findtext("Hsp_hit-to"), #send,
- evalue, #hsp.findtext("Hsp_evalue") in scientific notation
- bitscore, #hsp.findtext("Hsp_bit-score") rounded
- ]
-
- if extended:
- sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(">"))
- #print hit_def, "-->", sallseqid
- positive = hsp.findtext("Hsp_positive")
- ppos = "%0.2f" % (100*float(positive)/float(length))
- qframe = hsp.findtext("Hsp_query-frame")
- sframe = hsp.findtext("Hsp_hit-frame")
- if blast_program == "blastp":
- #Probably a bug in BLASTP that they use 0 or 1 depending on format
- if qframe == "0": qframe = "1"
- if sframe == "0": sframe = "1"
- slen = int(hit.findtext("Hit_len"))
- values.extend([sallseqid,
- hsp.findtext("Hsp_score"), #score,
- nident,
- positive,
- hsp.findtext("Hsp_gaps"), #gaps,
- ppos,
- qframe,
- sframe,
- #NOTE - for blastp, XML shows original seq, tabular uses XXX masking
- q_seq,
- h_seq,
- str(qlen),
- str(slen),
- ])
- #print "\t".join(values)
- outfile.write("\t".join(values) + "\n")
- # prevents ElementTree from growing large datastructure
- root.clear()
- elem.clear()
-outfile.close()
diff --git a/tools/ncbi_blast_plus/blastxml_to_tabular.xml b/tools/ncbi_blast_plus/blastxml_to_tabular.xml
deleted file mode 100644
index 66bba2c06fc..00000000000
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml
+++ /dev/null
@@ -1,127 +0,0 @@
-
- Convert BLAST XML output to tabular
-
- blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-**What it does**
-
-NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
-formats including tabular and a more detailed XML format. A complex workflow
-may need both the XML and the tabular output - but running BLAST twice is
-slow and wasteful.
-
-This tool takes the BLAST XML output and by default converts it into the
-standard 12 column tabular equivalent:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
- 1 qseqid Query Seq-id (ID of your sequence)
- 2 sseqid Subject Seq-id (ID of the database hit)
- 3 pident Percentage of identical matches
- 4 length Alignment length
- 5 mismatch Number of mismatches
- 6 gapopen Number of gap openings
- 7 qstart Start of alignment in query
- 8 qend End of alignment in query
- 9 sstart Start of alignment in subject (database hit)
- 10 send End of alignment in subject (database hit)
- 11 evalue Expectation value (E-value)
- 12 bitscore Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 22 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name Description
------- ------------- -------------------------------------------
- 13 sallseqid All subject Seq-id(s), separated by a ';'
- 14 score Raw score
- 15 nident Number of identical matches
- 16 positive Number of positive-scoring matches
- 17 gaps Total number of gaps
- 18 ppos Percentage of positive-scoring matches
- 19 qframe Query frame
- 20 sframe Subject frame
- 21 qseq Aligned part of query sequence
- 22 sseq Aligned part of subject sequence
- 23 qlen Query sequence length
- 24 slen Subject sequence length
-====== ============= ===========================================
-
-Beware that the XML file (and thus the conversion) and the tabular output
-direct from BLAST+ may differ in the presence of XXXX masking on regions
-low complexity (columns 21 and 22), and thus also calculated figures like
-the percentage idenity (column 3).
-
-
-
diff --git a/tools/ncbi_blast_plus/hide_stderr.py b/tools/ncbi_blast_plus/hide_stderr.py
deleted file mode 100755
index ebb49d36f29..00000000000
--- a/tools/ncbi_blast_plus/hide_stderr.py
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/env python
-"""A simple script to redirect stderr to stdout when the return code is zero.
-
-See https://bitbucket.org/galaxy/galaxy-central/issue/325/
-
-Currently Galaxy ignores the return code from command line tools (even if it
-is non-zero which by convention indicates an error) and treats any output on
-stderr as an error (even though by convention stderr is used for errors or
-warnings).
-
-This script runs the given command line, capturing all stdout and stderr in
-memory, and gets the return code. For a zero return code, any stderr (which
-should be warnings only) is added to the stdout. That way Galaxy believes
-everything is fine. For a non-zero return code, we output stdout as is, and
-any stderr, plus the return code to ensure there is some output on stderr.
-That way Galaxy treats this as an error.
-
-Once issue 325 is fixed, this script will not be needed.
-"""
-import sys
-import subprocess
-
-#Avoid using shell=True when we call subprocess to ensure if the Python
-#script is killed, so too is the BLAST process.
-try:
- words = []
- for w in sys.argv[1:]:
- if " " in w:
- words.append('"%s"' % w)
- else:
- words.append(w)
- cmd = " ".join(words)
- child = subprocess.Popen(sys.argv[1:],
- stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-except Exception, err:
- sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
- sys.exit(1)
-#Use .communicate as can get deadlocks with .wait(),
-stdout, stderr = child.communicate()
-return_code = child.returncode
-
-if return_code:
- sys.stdout.write(stdout)
- sys.stderr.write(stderr)
- sys.stderr.write("Return error code %i from command:\n" % return_code)
- sys.stderr.write("%s\n" % cmd)
-else:
- sys.stdout.write(stdout)
- sys.stdout.write(stderr)
diff --git a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
deleted file mode 100644
index 6b942380403..00000000000
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
+++ /dev/null
@@ -1,211 +0,0 @@
-
- Search nucleotide database with nucleotide query sequence(s)
-
-
- blastn -version
- hide_stderr.py
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-blastn
--query "$query"
-#if $db_opts.db_opts_selector == "db":
- -db "${db_opts.database.fields.path}"
-#else:
- -subject "$db_opts.subject"
-#end if
--task $blast_type
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
- -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
- -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
-$adv_opts.filter_query
-$adv_opts.strand
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-$adv_opts.ungapped
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-
-
-
-
-
-
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-
-
-
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-
-
-
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-
-
-
-
- blastn
-
-
-
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.
-
------
-
-**What it does**
-
-Search a *nucleotide database* using a *nucleotide query*,
-using the NCBI BLAST+ blastn command line tool.
-Algorithms include blastn, megablast, and discontiguous megablast.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
- 1 qseqid Query Seq-id (ID of your sequence)
- 2 sseqid Subject Seq-id (ID of the database hit)
- 3 pident Percentage of identical matches
- 4 length Alignment length
- 5 mismatch Number of mismatches
- 6 gapopen Number of gap openings
- 7 qstart Start of alignment in query
- 8 qend End of alignment in query
- 9 sstart Start of alignment in subject (database hit)
- 10 send End of alignment in subject (database hit)
- 11 evalue Expectation value (E-value)
- 12 bitscore Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name Description
------- ------------- -------------------------------------------
- 13 sallseqid All subject Seq-id(s), separated by a ';'
- 14 score Raw score
- 15 nident Number of identical matches
- 16 positive Number of positive-scoring matches
- 17 gaps Total number of gaps
- 18 ppos Percentage of positive-scoring matches
- 19 qframe Query frame
- 20 sframe Subject frame
- 21 qseq Aligned part of query sequence
- 22 sseq Aligned part of subject sequence
- 23 qlen Query sequence length
- 24 slen Subject sequence length
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
-
-
-
diff --git a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
deleted file mode 100644
index 17dda06e5e1..00000000000
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
+++ /dev/null
@@ -1,278 +0,0 @@
-
- Search protein database with protein query sequence(s)
-
-
- blastp -version
- hide_stderr.py
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-blastp
--query "$query"
-#if $db_opts.db_opts_selector == "db":
- -db "${db_opts.database.fields.path}"
-#else:
- -subject "$db_opts.subject"
-#end if
--task $blast_type
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
- -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
- -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
-$adv_opts.filter_query
--matrix $adv_opts.matrix
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-##Ungapped disabled for now - see comments below
-##$adv_opts.ungapped
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-
-
-
-
-
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-
-
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.
-
------
-
-**What it does**
-
-Search a *protein database* using a *protein query*,
-using the NCBI BLAST+ blastp command line tool.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
- 1 qseqid Query Seq-id (ID of your sequence)
- 2 sseqid Subject Seq-id (ID of the database hit)
- 3 pident Percentage of identical matches
- 4 length Alignment length
- 5 mismatch Number of mismatches
- 6 gapopen Number of gap openings
- 7 qstart Start of alignment in query
- 8 qend End of alignment in query
- 9 sstart Start of alignment in subject (database hit)
- 10 send End of alignment in subject (database hit)
- 11 evalue Expectation value (E-value)
- 12 bitscore Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name Description
------- ------------- -------------------------------------------
- 13 sallseqid All subject Seq-id(s), separated by a ';'
- 14 score Raw score
- 15 nident Number of identical matches
- 16 positive Number of positive-scoring matches
- 17 gaps Total number of gaps
- 18 ppos Percentage of positive-scoring matches
- 19 qframe Query frame
- 20 sframe Subject frame
- 21 qseq Aligned part of query sequence
- 22 sseq Aligned part of subject sequence
- 23 qlen Query sequence length
- 24 slen Subject sequence length
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
-
-Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005.
-
-
-
diff --git a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
deleted file mode 100644
index 487c433ee1b..00000000000
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
+++ /dev/null
@@ -1,242 +0,0 @@
-
- Search protein database with translated nucleotide query sequence(s)
-
-
- blastx -version
- hide_stderr.py
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-blastx
--query "$query"
-#if $db_opts.db_opts_selector == "db":
- -db "${db_opts.database.fields.path}"
-#else:
- -subject "$db_opts.subject"
-#end if
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
- -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
- -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
-$adv_opts.filter_query
-$adv_opts.strand
--matrix $adv_opts.matrix
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-$adv_opts.ungapped
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-
-
-
-
-
-
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-
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-
-
-
-
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.
-
------
-
-**What it does**
-
-Search a *protein database* using a *translated nucleotide query*,
-using the NCBI BLAST+ blastx command line tool.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
- 1 qseqid Query Seq-id (ID of your sequence)
- 2 sseqid Subject Seq-id (ID of the database hit)
- 3 pident Percentage of identical matches
- 4 length Alignment length
- 5 mismatch Number of mismatches
- 6 gapopen Number of gap openings
- 7 qstart Start of alignment in query
- 8 qend End of alignment in query
- 9 sstart Start of alignment in subject (database hit)
- 10 send End of alignment in subject (database hit)
- 11 evalue Expectation value (E-value)
- 12 bitscore Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name Description
------- ------------- -------------------------------------------
- 13 sallseqid All subject Seq-id(s), separated by a ';'
- 14 score Raw score
- 15 nident Number of identical matches
- 16 positive Number of positive-scoring matches
- 17 gaps Total number of gaps
- 18 ppos Percentage of positive-scoring matches
- 19 qframe Query frame
- 20 sframe Subject frame
- 21 qseq Aligned part of query sequence
- 22 sseq Aligned part of subject sequence
- 23 qlen Query sequence length
- 24 slen Subject sequence length
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
-
-
-
diff --git a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
deleted file mode 100644
index 73cead395d8..00000000000
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
+++ /dev/null
@@ -1,288 +0,0 @@
-
- Search translated nucleotide database with protein query sequence(s)
-
-
- tblastn -version
- hide_stderr.py
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-tblastn
--query "$query"
-#if $db_opts.db_opts_selector == "db":
- -db "${db_opts.database.fields.path}"
-#else:
- -subject "$db_opts.subject"
-#end if
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
- -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
- -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
-$adv_opts.filter_query
--matrix $adv_opts.matrix
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-##Ungapped disabled for now - see comments below
-##$adv_opts.ungapped
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-
-
-
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-
-
-
-
-
-
-
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.
-
------
-
-**What it does**
-
-Search a *translated nucleotide database* using a *protein query*,
-using the NCBI BLAST+ tblastn command line tool.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
- 1 qseqid Query Seq-id (ID of your sequence)
- 2 sseqid Subject Seq-id (ID of the database hit)
- 3 pident Percentage of identical matches
- 4 length Alignment length
- 5 mismatch Number of mismatches
- 6 gapopen Number of gap openings
- 7 qstart Start of alignment in query
- 8 qend End of alignment in query
- 9 sstart Start of alignment in subject (database hit)
- 10 send End of alignment in subject (database hit)
- 11 evalue Expectation value (E-value)
- 12 bitscore Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name Description
------- ------------- -------------------------------------------
- 13 sallseqid All subject Seq-id(s), separated by a ';'
- 14 score Raw score
- 15 nident Number of identical matches
- 16 positive Number of positive-scoring matches
- 17 gaps Total number of gaps
- 18 ppos Percentage of positive-scoring matches
- 19 qframe Query frame
- 20 sframe Subject frame
- 21 qseq Aligned part of query sequence
- 22 sseq Aligned part of subject sequence
- 23 qlen Query sequence length
- 24 slen Subject sequence length
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
-
-
-
diff --git a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
deleted file mode 100644
index bb96f972a9c..00000000000
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
+++ /dev/null
@@ -1,208 +0,0 @@
-
- Search translated nucleotide database with translated nucleotide query sequence(s)
-
-
- tblastx -version
- hide_stderr.py
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-tblastx
--query "$query"
-#if $db_opts.db_opts_selector == "db":
- -db "${db_opts.database.fields.path}"
-#else:
- -subject "$db_opts.subject"
-#end if
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
- -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
- -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
-$adv_opts.filter_query
-$adv_opts.strand
--matrix $adv_opts.matrix
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-
-
-
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-
-
-
- tblastx
-
-
-
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.
-
------
-
-**What it does**
-
-Search a *translated nucleotide database* using a *protein query*,
-using the NCBI BLAST+ tblastx command line tool.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
- 1 qseqid Query Seq-id (ID of your sequence)
- 2 sseqid Subject Seq-id (ID of the database hit)
- 3 pident Percentage of identical matches
- 4 length Alignment length
- 5 mismatch Number of mismatches
- 6 gapopen Number of gap openings
- 7 qstart Start of alignment in query
- 8 qend End of alignment in query
- 9 sstart Start of alignment in subject (database hit)
- 10 send End of alignment in subject (database hit)
- 11 evalue Expectation value (E-value)
- 12 bitscore Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name Description
------- ------------- -------------------------------------------
- 13 sallseqid All subject Seq-id(s), separated by a ';'
- 14 score Raw score
- 15 nident Number of identical matches
- 16 positive Number of positive-scoring matches
- 17 gaps Total number of gaps
- 18 ppos Percentage of positive-scoring matches
- 19 qframe Query frame
- 20 sframe Subject frame
- 21 qseq Aligned part of query sequence
- 22 sseq Aligned part of subject sequence
- 23 qlen Query sequence length
- 24 slen Subject sequence length
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
-
-
-