Mercurial > repos > devteam > ncbi_blast_plus
changeset 32:a52d2d93e595 draft
Update for NCBI BLAST+ 2.14.1
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--- a/test-data/blastn_chimera_vs_three_human_max1.txt Tue Jun 07 12:15:44 2022 +0000 +++ b/test-data/blastn_chimera_vs_three_human_max1.txt Thu Oct 26 12:25:07 2023 +0000 @@ -1,4 +1,4 @@ -BLASTN 2.10.1+ +BLASTN 2.14.1+ Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb @@ -346,7 +346,7 @@ Database: Just 3 human mRNA sequences - Posted date: Sep 9, 2020 11:23 PM + Posted date: Sep 22, 2023 4:36 PM Number of letters in database: 10,732 Number of sequences in database: 3
--- a/test-data/blastn_rhodopsin_vs_three_human.xml Tue Jun 07 12:15:44 2022 +0000 +++ b/test-data/blastn_rhodopsin_vs_three_human.xml Thu Oct 26 12:25:07 2023 +0000 @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastn</BlastOutput_program> - <BlastOutput_version>BLASTN 2.10.1+</BlastOutput_version> + <BlastOutput_version>BLASTN 2.14.1+</BlastOutput_version> <BlastOutput_reference>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.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
--- a/test-data/blastp_four_human_vs_rhodopsin.xml Tue Jun 07 12:15:44 2022 +0000 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Thu Oct 26 12:25:07 2023 +0000 @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastp</BlastOutput_program> - <BlastOutput_version>BLASTP 2.10.1+</BlastOutput_version> + <BlastOutput_version>BLASTP 2.14.1+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, 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.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Q9BS26</BlastOutput_query-ID>
--- a/test-data/blastx_rhodopsin_vs_four_human.xml Tue Jun 07 12:15:44 2022 +0000 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Thu Oct 26 12:25:07 2023 +0000 @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastx</BlastOutput_program> - <BlastOutput_version>BLASTX 2.10.1+</BlastOutput_version> + <BlastOutput_version>BLASTX 2.14.1+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, 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.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
--- a/test-data/tblastn_four_human_vs_rhodopsin.html Tue Jun 07 12:15:44 2022 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Thu Oct 26 12:25:07 2023 +0000 @@ -3,7 +3,7 @@ <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099"> <PRE> -<b>TBLASTN 2.10.1+</b> +<b>TBLASTN 2.14.1+</b> <b><a @@ -89,7 +89,7 @@ gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA <a href=#Subject_1>732</a> 0.0 gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene f... <a href=#Subject_5>711</a> 0.0 -gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodops... <a href=#Subject_4>658</a> 0.0 +gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodops... <a href=#Subject_4>682</a> 0.0 gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complet... <a href=#Subject_2>646</a> 0.0 gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh ... <a href=#Subject_6>626</a> 0.0 gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 2002043... <a href=#Subject_3>229</a> 3e-67 @@ -165,7 +165,7 @@ (RHO) mRNA, partial cds Length=983 - Score = 658 bits (1517), Expect = 0.0, Method: Compositional matrix adjust. + Score = 682 bits (1573), Expect = 0.0, Method: Compositional matrix adjust. Identities = 310/326 (95%), Positives = 322/326 (99%), Gaps = 0/326 (0%) Frame = +1
--- a/test-data/tblastn_four_human_vs_rhodopsin.tabular Tue Jun 07 12:15:44 2022 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin.tabular Thu Oct 26 12:25:07 2023 +0000 @@ -1,6 +1,6 @@ sp|P08100|OPSD_HUMAN gi|57163782|ref|NM_001009242.1| 96.552 348 12 0 1 348 1 1044 0.0 732 sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.391 348 23 0 1 348 1 1044 0.0 711 -sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.092 326 16 0 11 336 1 978 0.0 658 +sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.092 326 16 0 11 336 1 978 0.0 682 sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.795 342 51 1 1 341 42 1067 0.0 646 sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.164 342 60 1 1 341 23 1048 0.0 626 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.243 74 5 0 239 312 3147 3368 1.34e-71 151
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml Tue Jun 07 12:15:44 2022 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin.xml Thu Oct 26 12:25:07 2023 +0000 @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>tblastn</BlastOutput_program> - <BlastOutput_version>TBLASTN 2.10.1+</BlastOutput_version> + <BlastOutput_version>TBLASTN 2.14.1+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, 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.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> @@ -149,8 +149,8 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>658.198</Hsp_bit-score> - <Hsp_score>1517</Hsp_score> + <Hsp_bit-score>682.354</Hsp_bit-score> + <Hsp_score>1573</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>11</Hsp_query-from> <Hsp_query-to>336</Hsp_query-to>
--- a/test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular Tue Jun 07 12:15:44 2022 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular Thu Oct 26 12:25:07 2023 +0000 @@ -1,6 +1,6 @@ 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 GQ290312.1 95.092 326 16 0 11 336 1 978 0.0 682 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
--- a/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Tue Jun 07 12:15:44 2022 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Thu Oct 26 12:25:07 2023 +0000 @@ -1,6 +1,6 @@ sp|P08100|OPSD_HUMAN gi|57163782|ref|NM_001009242.1| 96.552 348 12 0 1 348 1 1044 0.0 732 gi|57163782|ref|NM_001009242.1| 1689 336 343 0 98.56 0 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 1047 N/A sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.391 348 23 0 1 348 1 1044 0.0 711 gi|18148870|dbj|AB062417.1| 1640 325 337 0 96.84 0 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 1047 N/A -sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.092 326 16 0 11 336 1 978 0.0 658 gi|283855822|gb|GQ290312.1| 1517 310 322 0 98.77 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT 348 983 N/A +sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.092 326 16 0 11 336 1 978 0.0 682 gi|283855822|gb|GQ290312.1| 1573 310 322 0 98.77 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT 348 983 N/A sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.795 342 51 1 1 341 42 1067 0.0 646 gi|2734705|gb|U59921.1|BBU59921 1489 290 320 1 93.57 0 3 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 1574 N/A sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.164 342 60 1 1 341 23 1048 0.0 626 gi|12583664|dbj|AB043817.1| 1444 281 311 1 90.94 0 2 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 1344 N/A sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.243 74 5 0 239 312 3147 3368 1.34e-71 151 gi|283855845|gb|GQ290303.1| 342 69 73 0 98.65 0 3 ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ 348 4301 N/A
--- a/tools/ncbi_blast_plus/README.rst Tue Jun 07 12:15:44 2022 +0000 +++ b/tools/ncbi_blast_plus/README.rst Thu Oct 26 12:25:07 2023 +0000 @@ -136,6 +136,9 @@ ============== =============================================================== Version Changes -------------- --------------------------------------------------------------- +2.14.1+galaxy0 - Updated for NCBI BLAST+ 2.14.1 release. +2.10.1+galaxy3 - Silenced ``deltablast`` warning about using ``-num_threads`` + with ``--subject`` (i.e. FASTA file from your history). 2.10.1+galaxy2 - Fixed ``dc-megablast`` option in ``ncbi_blastn_wrapper.xml`` wrapper from inserting ``-window_size`` twice when executing. 2.10.1+galaxy1 - Add tool `NCBI get species taxids` that wraps NCBI's
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Tue Jun 07 12:15:44 2022 +0000 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Thu Oct 26 12:25:07 2023 +0000 @@ -46,7 +46,7 @@ 25 salltitles All subject titles, separated by '<>' ====== ============= =========================================== -Most of these fields are given explicitly in the XML file, others some like +Most of these fields are given explicitly in the XML file, but 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 @@ -60,13 +60,11 @@ However, check this with "diff -b ..." since BLAST+ sometimes includes an extra space character (probably a bug). """ - from __future__ import print_function import os import re import sys - from optparse import OptionParser if "-v" in sys.argv or "--version" in sys.argv:
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Tue Jun 07 12:15:44 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Thu Oct 26 12:25:07 2023 +0000 @@ -11,8 +11,6 @@ blastdbcmd @DBCMD_OPTS@ -##TODO: What about -ctrl_a and -target_only as advanced options? - #if $id_opts.id_type=="file": -entry_batch '$id_opts.entries' #else: @@ -66,6 +64,7 @@ <option value="original">FASTA with original identifiers</option> <option value="blastid">FASTA with BLAST assigned identifiers</option> </param> + <!-- TODO: What about -ctrl_a and -target_only as advanced options? --> </inputs> <outputs>
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Jun 07 12:15:44 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Oct 26 12:25:07 2023 +0000 @@ -152,7 +152,7 @@ <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" /> <param name="db_opts_selector" value="file" /> <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database value=" /> + <param name="database" value="" /> <param name="evalue_cutoff" value="1e-8"/> <param name="blast_type" value="blastp" /> <param name="out_format" value="6"/>
--- a/tools/ncbi_blast_plus/ncbi_macros.xml Tue Jun 07 12:15:44 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Thu Oct 26 12:25:07 2023 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">2.10.1</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@TOOL_VERSION@">2.14.1</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">16.10</token> <xml name="parallelism"> <!-- If job splitting is enabled, break up the query file into parts --> @@ -655,7 +655,7 @@ -outfmt '6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles' #elif str($output.out_format)=="cols" ##Pick your own columns. Galaxy gives us it comma separated, BLAST+ wants space separated: -##TODO - Can we catch the user picking no columns and raise an error here? +##Can we catch the user picking no columns and raise an error here? #set cols = (str($output.std_cols)+","+str($output.ext_cols)+","+str($output.ids_cols)+","+str($output.misc_cols)+","+str($output.tax_cols)).replace("None", "").replace(",,", ",").replace(",", " ").strip() -outfmt '6 $cols' #else:
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Tue Jun 07 12:15:44 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Oct 26 12:25:07 2023 +0000 @@ -52,7 +52,6 @@ ## -------------------------------------------------------------------- #if $tax.taxselect == 'id': -taxid $tax.taxid -## TODO - Can we use a tabular file for the taxonomy mapping? ## #else if $tax.taxselect == 'map': ## -taxid_map $tax.taxmap #end if @@ -84,6 +83,7 @@ <option value="id">Assign the same Taxonomy ID to all the sequences</option> <!-- <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option> + TODO - Can we use a tabular file for the taxonomy mapping? --> </param> <when value="">
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Tue Jun 07 12:15:44 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Thu Oct 26 12:25:07 2023 +0000 @@ -92,7 +92,7 @@ http://smart.embl-heidelberg.de/ *Tigr* - PSSMs from TIGRFAM database of protein families, see -ftp://ftp.jcvi.org/pub/data/TIGRFAMs/ +ftp://ftp.jcvi.org/data/TIGRFAMs/ *Prk* - PSSms from automatically aligned stable clusters in the Protein Clusters database, see
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Tue Jun 07 12:15:44 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Thu Oct 26 12:25:07 2023 +0000 @@ -90,7 +90,7 @@ http://smart.embl-heidelberg.de/ *Tigr* - PSSMs from TIGRFAM database of protein families, see -ftp://ftp.jcvi.org/pub/data/TIGRFAMs/ +ftp://ftp.jcvi.org/data/TIGRFAMs/ *Prk* - PSSms from automatically aligned stable clusters in the Protein Clusters database, see