# HG changeset patch # User peterjc # Date 1698323107 0 # Node ID a52d2d93e595a64df07d950c28120eeb1759a273 # Parent 0e3cf9594bb78d58d2f955a8388bd82b3b7b1d6c Update for NCBI BLAST+ 2.14.1 diff -r 0e3cf9594bb7 -r a52d2d93e595 test-data/blastn_chimera_vs_three_human_max1.txt --- 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 diff -r 0e3cf9594bb7 -r a52d2d93e595 test-data/blastn_rhodopsin_vs_three_human.xml --- 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 @@ blastn - BLASTN 2.10.1+ + BLASTN 2.14.1+ 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 0e3cf9594bb7 -r a52d2d93e595 test-data/blastp_four_human_vs_rhodopsin.xml --- 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 @@ blastp - BLASTP 2.10.1+ + BLASTP 2.14.1+ 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 0e3cf9594bb7 -r a52d2d93e595 test-data/blastx_rhodopsin_vs_four_human.xml --- 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 @@ blastx - BLASTX 2.10.1+ + BLASTX 2.14.1+ 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 0e3cf9594bb7 -r a52d2d93e595 test-data/cd00003_and_cd00008.pin Binary file test-data/cd00003_and_cd00008.pin has changed diff -r 0e3cf9594bb7 -r a52d2d93e595 test-data/four_human_proteins.fasta.pin Binary file test-data/four_human_proteins.fasta.pin has changed diff -r 0e3cf9594bb7 -r a52d2d93e595 test-data/four_human_proteins_taxid.fasta.pin Binary file test-data/four_human_proteins_taxid.fasta.pin has changed diff -r 0e3cf9594bb7 -r a52d2d93e595 test-data/rhodopsin_nucs.fasta.nin Binary file test-data/rhodopsin_nucs.fasta.nin has changed diff -r 0e3cf9594bb7 -r a52d2d93e595 test-data/tblastn_four_human_vs_rhodopsin.html --- 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 @@

 
-TBLASTN 2.10.1+
+TBLASTN 2.14.1+
 
 
 732     0.0  
 gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene f...  711     0.0  
-gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodops...  658     0.0  
+gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodops...  682     0.0  
 gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complet...  646     0.0  
 gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh ...  626     0.0  
 gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 2002043...  229     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
 
diff -r 0e3cf9594bb7 -r a52d2d93e595 test-data/tblastn_four_human_vs_rhodopsin.tabular
--- 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
diff -r 0e3cf9594bb7 -r a52d2d93e595 test-data/tblastn_four_human_vs_rhodopsin.xml
--- 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 @@
 
 
   tblastn
-  TBLASTN 2.10.1+
+  TBLASTN 2.14.1+
   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.
   
   Query_1
@@ -149,8 +149,8 @@
   
     
       1
-      658.198
-      1517
+      682.354
+      1573
       0
       11
       336
diff -r 0e3cf9594bb7 -r a52d2d93e595 test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular
--- 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
diff -r 0e3cf9594bb7 -r a52d2d93e595 test-data/tblastn_four_human_vs_rhodopsin_ext.tabular
--- 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
diff -r 0e3cf9594bb7 -r a52d2d93e595 test-data/three_human_mRNA.fasta.nin
Binary file test-data/three_human_mRNA.fasta.nin has changed
diff -r 0e3cf9594bb7 -r a52d2d93e595 tools/ncbi_blast_plus/README.rst
--- 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
diff -r 0e3cf9594bb7 -r a52d2d93e595 tools/ncbi_blast_plus/blastxml_to_tabular.py
--- 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:
diff -r 0e3cf9594bb7 -r a52d2d93e595 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml
--- 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 @@
           
           
         
+        
     
     
 
diff -r 0e3cf9594bb7 -r a52d2d93e595 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
--- 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 @@
             
             
             
-            
+            
             
             
             
diff -r 0e3cf9594bb7 -r a52d2d93e595 tools/ncbi_blast_plus/ncbi_macros.xml
--- 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 @@
 
-    2.10.1
-    2
+    2.14.1
+    0
     16.10
     
         
@@ -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:
diff -r 0e3cf9594bb7 -r a52d2d93e595 tools/ncbi_blast_plus/ncbi_makeblastdb.xml
--- 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 @@
                 
                 
             
             
diff -r 0e3cf9594bb7 -r a52d2d93e595 tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml
--- 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
diff -r 0e3cf9594bb7 -r a52d2d93e595 tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml
--- 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