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changeset 31:13aa389f4eeb draft

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planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 16ef84e19ea373838bbfb921b9ef2cd4b02b8788-dirty
author peterjc
date Mon, 28 May 2018 07:57:56 -0400
parents d724d9af93ee
children 360352490a06
files test-data/blastn_chimera_vs_rhodopsin_db.tabular test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular test-data/blastn_chimera_vs_three_human_max1.txt test-data/blastn_rhodopsin_vs_three_human.xml test-data/blastp_four_human_vs_rhodopsin.tabular test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_ext.tabular test-data/blastx_rhodopsin_vs_four_human.xml test-data/cd00003_and_cd00008.pin test-data/four_human_proteins.dbinfo.txt test-data/four_human_proteins.fasta.pin test-data/four_human_proteins_taxid.fasta.pin test-data/rhodopsin_nucs.dbinfo.txt test-data/rhodopsin_nucs.fasta.nin test-data/tblastn_four_human_vs_rhodopsin.html test-data/tblastn_four_human_vs_rhodopsin.xml test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular test-data/three_human_mRNA.dbinfo.txt test-data/three_human_mRNA.fasta.nin tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml tools/ncbi_blast_plus/ncbi_macros.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml
diffstat 26 files changed, 76 insertions(+), 72 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/blastn_chimera_vs_rhodopsin_db.tabular	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/blastn_chimera_vs_rhodopsin_db.tabular	Mon May 28 07:57:56 2018 -0400
@@ -1,8 +1,8 @@
-chimera	NM_001009242	92.308	1014	78	0	8881	9894	34	1047	0.0	1441
-chimera	GQ290312	91.527	956	81	0	8881	9836	4	959	0.0	1317
-chimera	AB062417	87.586	1015	124	2	8881	9894	34	1047	0.0	1175
-chimera	GQ290303	91.515	330	28	0	8881	9210	4	333	8.28e-130	455
-chimera	GQ290303	91.358	243	19	2	9542	9783	3127	3368	1.46e-92	331
-chimera	GQ290303	94.220	173	10	0	9208	9380	1410	1582	1.50e-72	265
-chimera	GQ290303	92.941	170	12	0	9375	9544	2854	3023	1.51e-67	248
-chimera	GQ290303	95.588	68	3	0	9781	9848	4222	4289	7.43e-26	110
+chimera	NM_001009242.1	92.308	1014	78	0	8881	9894	34	1047	0.0	1441
+chimera	GQ290312.1	91.527	956	81	0	8881	9836	4	959	0.0	1317
+chimera	AB062417.1	87.586	1015	124	2	8881	9894	34	1047	0.0	1175
+chimera	GQ290303.1	91.515	330	28	0	8881	9210	4	333	8.28e-130	455
+chimera	GQ290303.1	91.358	243	19	2	9542	9783	3127	3368	1.46e-92	331
+chimera	GQ290303.1	94.220	173	10	0	9208	9380	1410	1582	1.50e-72	265
+chimera	GQ290303.1	92.941	170	12	0	9375	9544	2854	3023	1.51e-67	248
+chimera	GQ290303.1	95.588	68	3	0	9781	9848	4222	4289	7.43e-26	110
--- a/test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular	Mon May 28 07:57:56 2018 -0400
@@ -1,11 +1,11 @@
 chimera	ENA|AB011145|AB011145.1	100.000	4560	0	0	1	4560	121	4680	0.0	8421
 chimera	ENA|M10051|M10051.1	99.931	4331	3	0	4560	8890	60	4390	0.0	7982
 chimera	ENA|BC112106|BC112106.1	100.000	1093	0	0	8881	9973	121	1213	0.0	2019
-chimera	NM_001009242	92.308	1014	78	0	8881	9894	34	1047	0.0	1441
-chimera	GQ290312	91.527	956	81	0	8881	9836	4	959	0.0	1317
-chimera	AB062417	87.586	1015	124	2	8881	9894	34	1047	0.0	1175
-chimera	GQ290303	91.515	330	28	0	8881	9210	4	333	1.70e-129	455
-chimera	GQ290303	91.358	243	19	2	9542	9783	3127	3368	2.98e-92	331
-chimera	GQ290303	94.220	173	10	0	9208	9380	1410	1582	3.07e-72	265
-chimera	GQ290303	92.941	170	12	0	9375	9544	2854	3023	3.09e-67	248
-chimera	GQ290303	95.588	68	3	0	9781	9848	4222	4289	1.52e-25	110
+chimera	NM_001009242.1	92.308	1014	78	0	8881	9894	34	1047	0.0	1441
+chimera	GQ290312.1	91.527	956	81	0	8881	9836	4	959	0.0	1317
+chimera	AB062417.1	87.586	1015	124	2	8881	9894	34	1047	0.0	1175
+chimera	GQ290303.1	91.515	330	28	0	8881	9210	4	333	1.70e-129	455
+chimera	GQ290303.1	91.358	243	19	2	9542	9783	3127	3368	2.98e-92	331
+chimera	GQ290303.1	94.220	173	10	0	9208	9380	1410	1582	3.07e-72	265
+chimera	GQ290303.1	92.941	170	12	0	9375	9544	2854	3023	3.09e-67	248
+chimera	GQ290303.1	95.588	68	3	0	9781	9848	4222	4289	1.52e-25	110
--- a/test-data/blastn_chimera_vs_three_human_max1.txt	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/blastn_chimera_vs_three_human_max1.txt	Mon May 28 07:57:56 2018 -0400
@@ -1,4 +1,4 @@
-BLASTN 2.5.0+
+BLASTN 2.7.1+
 
 
 Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
@@ -346,7 +346,7 @@
 
 
   Database: Just 3 human mRNA sequences
-    Posted date:  Dec 2, 2016  10:38 AM
+    Posted date:  Oct 31, 2017  4:23 PM
   Number of letters in database: 10,732
   Number of sequences in database:  3
 
--- a/test-data/blastn_rhodopsin_vs_three_human.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/blastn_rhodopsin_vs_three_human.xml	Mon May 28 07:57:56 2018 -0400
@@ -2,7 +2,7 @@
 <!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 2.5.0+</BlastOutput_version>
+  <BlastOutput_version>BLASTN 2.7.1+</BlastOutput_version>
   <BlastOutput_reference>Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), &quot;A greedy algorithm for aligning DNA sequences&quot;, 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.tabular	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/blastp_four_human_vs_rhodopsin.tabular	Mon May 28 07:57:56 2018 -0400
@@ -1,6 +1,6 @@
-P08100	NP_001009242	96.552	348	12	0	1	348	1	348	0.0	701
+P08100	NP_001009242.1	96.552	348	12	0	1	348	1	348	0.0	701
 P08100	0811197A	93.103	348	23	1	1	348	1	347	0.0	673
-P08100	ADB45242	94.817	328	17	0	11	338	1	328	0.0	653
-P08100	ADB45229	94.817	328	17	0	11	338	1	328	0.0	631
-P08100	P56514	84.795	342	51	1	1	341	1	342	0.0	619
-P08100	BAB21486	82.164	342	60	1	1	341	1	342	0.0	599
+P08100	ADB45242.1	94.817	328	17	0	11	338	1	328	0.0	653
+P08100	ADB45229.1	94.817	328	17	0	11	338	1	328	0.0	631
+P08100	P56514.1	84.795	342	51	1	1	341	1	342	0.0	619
+P08100	BAB21486.1	82.164	342	60	1	1	341	1	342	0.0	599
--- a/test-data/blastp_four_human_vs_rhodopsin.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/blastp_four_human_vs_rhodopsin.xml	Mon May 28 07:57:56 2018 -0400
@@ -2,7 +2,7 @@
 <!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 2.5.0+</BlastOutput_version>
+  <BlastOutput_version>BLASTP 2.7.1+</BlastOutput_version>
   <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
   <BlastOutput_db></BlastOutput_db>
   <BlastOutput_query-ID>Q9BS26</BlastOutput_query-ID>
--- a/test-data/blastp_four_human_vs_rhodopsin_ext.tabular	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/blastp_four_human_vs_rhodopsin_ext.tabular	Mon May 28 07:57:56 2018 -0400
@@ -1,6 +1,6 @@
-P08100	NP_001009242	96.552	348	12	0	1	348	1	348	0.0	701	gi|57163783|ref|NP_001009242.1|	1808	336	343	0	98.56	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA	348	348	N/A
+P08100	NP_001009242.1	96.552	348	12	0	1	348	1	348	0.0	701	gi|57163783|ref|NP_001009242.1|	1808	336	343	0	98.56	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA	348	348	N/A
 P08100	0811197A	93.103	348	23	1	1	348	1	347	0.0	673	gi|223523|prf||0811197A	1736	324	336	1	96.55	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA	348	347	N/A
-P08100	ADB45242	94.817	328	17	0	11	338	1	328	0.0	653	gi|283855846|gb|ADB45242.1|	1684	311	321	0	97.87	1	1	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS	VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS	348	328	N/A
-P08100	ADB45229	94.817	328	17	0	11	338	1	328	0.0	631	gi|283855823|gb|ADB45229.1|	1627	311	323	0	98.48	1	1	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS	VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS	348	328	N/A
-P08100	P56514	84.795	342	51	1	1	341	1	342	0.0	619	gi|3024260|sp|P56514.1|OPSD_BUFBU	1595	290	322	1	94.15	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE	MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE	348	354	N/A
-P08100	BAB21486	82.164	342	60	1	1	341	1	342	0.0	599	gi|12583665|dbj|BAB21486.1|	1544	281	314	1	91.81	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE	MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE	348	354	N/A
+P08100	ADB45242.1	94.817	328	17	0	11	338	1	328	0.0	653	gi|283855846|gb|ADB45242.1|	1684	311	321	0	97.87	1	1	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS	VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS	348	328	N/A
+P08100	ADB45229.1	94.817	328	17	0	11	338	1	328	0.0	631	gi|283855823|gb|ADB45229.1|	1627	311	323	0	98.48	1	1	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS	VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS	348	328	N/A
+P08100	P56514.1	84.795	342	51	1	1	341	1	342	0.0	619	gi|3024260|sp|P56514.1|OPSD_BUFBU	1595	290	322	1	94.15	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE	MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE	348	354	N/A
+P08100	BAB21486.1	82.164	342	60	1	1	341	1	342	0.0	599	gi|12583665|dbj|BAB21486.1|	1544	281	314	1	91.81	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE	MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE	348	354	N/A
--- a/test-data/blastx_rhodopsin_vs_four_human.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/blastx_rhodopsin_vs_four_human.xml	Mon May 28 07:57:56 2018 -0400
@@ -2,7 +2,7 @@
 <!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 2.5.0+</BlastOutput_version>
+  <BlastOutput_version>BLASTX 2.7.1+</BlastOutput_version>
   <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
   <BlastOutput_db></BlastOutput_db>
   <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
Binary file test-data/cd00003_and_cd00008.pin has changed
--- a/test-data/four_human_proteins.dbinfo.txt	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/four_human_proteins.dbinfo.txt	Mon May 28 07:57:56 2018 -0400
@@ -1,7 +1,7 @@
 Database: Just 4 human proteins
 	4 sequences; 3,297 total residues
 
-Date: Dec 2, 2016  10:38 AM	Longest sequence: 1,382 residues
+Date: Oct 31, 2017  4:23 PM	Longest sequence: 1,382 residues
 
 Volumes:
-	/mnt/shared/users/pc40583/repositories/galaxy_blast/test-data/four_human_proteins_taxid.fasta
+	/mnt/galaxy/repositories/galaxy_blast/test-data/four_human_proteins_taxid.fasta
Binary file test-data/four_human_proteins.fasta.pin has changed
Binary file test-data/four_human_proteins_taxid.fasta.pin has changed
--- a/test-data/rhodopsin_nucs.dbinfo.txt	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/rhodopsin_nucs.dbinfo.txt	Mon May 28 07:57:56 2018 -0400
@@ -1,7 +1,7 @@
 Database: Rhodopsin nucleotides
 	6 sequences; 10,296 total bases
 
-Date: Dec 2, 2016  10:38 AM	Longest sequence: 4,301 bases
+Date: Oct 31, 2017  4:23 PM	Longest sequence: 4,301 bases
 
 Volumes:
-	/mnt/shared/users/pc40583/repositories/galaxy_blast/test-data/rhodopsin_nucs.fasta
+	/mnt/galaxy/repositories/galaxy_blast/test-data/rhodopsin_nucs.fasta
Binary file test-data/rhodopsin_nucs.fasta.nin has changed
--- a/test-data/tblastn_four_human_vs_rhodopsin.html	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin.html	Mon May 28 07:57:56 2018 -0400
@@ -1,9 +1,9 @@
 <HTML>
-<TITLE>BLAST Search Results</TITLE>
+<HEAD><TITLE>BLAST Search Results</TITLE></HEAD>
 <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
 <PRE>
 
-<b>TBLASTN 2.5.0+</b>
+<b>TBLASTN 2.7.1+</b>
 
 
 <b><a
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin.xml	Mon May 28 07:57:56 2018 -0400
@@ -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 2.5.0+</BlastOutput_version>
+  <BlastOutput_version>TBLASTN 2.7.1+</BlastOutput_version>
   <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, 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_deflines.tabular	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular	Mon May 28 07:57:56 2018 -0400
@@ -1,10 +1,10 @@
-P08100	NM_001009242	96.552	348	12	0	1	348	1	1044	0.0	732
-P08100	AB062417	93.391	348	23	0	1	348	1	1044	0.0	711
-P08100	GQ290312	95.092	326	16	0	11	336	1	978	0.0	658
-P08100	U59921	84.795	342	51	1	1	341	42	1067	0.0	646
-P08100	AB043817	82.164	342	60	1	1	341	23	1048	0.0	626
-P08100	GQ290303	93.243	74	5	0	239	312	3147	3368	1.34e-71	151
-P08100	GQ290303	91.525	59	5	0	177	235	2855	3031	1.34e-71	126
-P08100	GQ290303	96.396	111	4	0	11	121	1	333	3.31e-67	229
-P08100	GQ290303	93.220	59	4	0	119	177	1404	1580	2.31e-32	122
-P08100	GQ290303	88.462	26	3	0	312	337	4222	4299	3.61e-12	57.7
+P08100	NM_001009242.1	96.552	348	12	0	1	348	1	1044	0.0	732
+P08100	AB062417.1	93.391	348	23	0	1	348	1	1044	0.0	711
+P08100	GQ290312.1	95.092	326	16	0	11	336	1	978	0.0	658
+P08100	U59921.1	84.795	342	51	1	1	341	42	1067	0.0	646
+P08100	AB043817.1	82.164	342	60	1	1	341	23	1048	0.0	626
+P08100	GQ290303.1	93.243	74	5	0	239	312	3147	3368	1.34e-71	151
+P08100	GQ290303.1	91.525	59	5	0	177	235	2855	3031	1.34e-71	126
+P08100	GQ290303.1	96.396	111	4	0	11	121	1	333	3.31e-67	229
+P08100	GQ290303.1	93.220	59	4	0	119	177	1404	1580	2.31e-32	122
+P08100	GQ290303.1	88.462	26	3	0	312	337	4222	4299	3.61e-12	57.7
--- a/test-data/three_human_mRNA.dbinfo.txt	Mon Oct 30 11:49:17 2017 -0400
+++ b/test-data/three_human_mRNA.dbinfo.txt	Mon May 28 07:57:56 2018 -0400
@@ -1,7 +1,7 @@
 Database: Just 3 human mRNA sequences
 	3 sequences; 10,732 total bases
 
-Date: Dec 2, 2016  10:38 AM	Longest sequence: 4,796 bases
+Date: Oct 31, 2017  4:23 PM	Longest sequence: 4,796 bases
 
 Volumes:
-	/mnt/shared/users/pc40583/repositories/galaxy_blast/test-data/three_human_mRNA.fasta
+	/mnt/galaxy/repositories/galaxy_blast/test-data/three_human_mRNA.fasta
Binary file test-data/three_human_mRNA.fasta.nin has changed
--- a/tools/ncbi_blast_plus/README.rst	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/README.rst	Mon May 28 07:57:56 2018 -0400
@@ -255,6 +255,10 @@
         - Support for ``-window_size``, ``-threshold``, ``-comp_based_stats``
           and revising ``-word_size`` to avoid using zero to mean  default
           (contribution from Caleb Easterly).
+v0.3.0  - Updated for NCBI BLAST+ 2.7.1,
+        - Depends on BioConda or legacy ToolShed ``package_blast_plus_2_7_1``.
+        - Document the BLAST+ 2.6.0 change in the standard 12 column output
+          from ``qacc,sacc,...`` to ``qaccver,saccver,...`` instead.
 ======= ======================================================================
 
 
--- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Mon May 28 07:57:56 2018 -0400
@@ -86,7 +86,7 @@
 More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_.
 
 .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/
-.. _DUST: http://www.ncbi.nlm.nih.gov/pubmed/16796549
+.. _DUST: https://www.ncbi.nlm.nih.gov/pubmed/16796549
 
 **References**
 
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Mon May 28 07:57:56 2018 -0400
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">0.2.02</token>
+    <token name="@WRAPPER_VERSION@">0.3.0</token>
     <xml name="parallelism">
         <!-- If job splitting is enabled, break up the query file into parts -->
         <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" />
@@ -7,7 +7,7 @@
 
     <xml name="preamble">
         <requirements>
-            <requirement type="package" version="2.5.0">blast</requirement>
+            <requirement type="package" version="2.7.1">blast</requirement>
         </requirements>
         <version_command>@BINARY@ -version</version_command>
     </xml>
@@ -288,7 +288,7 @@
 
     <xml name="input_query_gencode">
         <param argument="-query_gencode" type="select" label="Query genetic code">
-            <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
+            <!-- See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
             <option value="1" selected="true">1. Standard</option>
             <option value="2">2. Vertebrate Mitochondrial</option>
             <option value="3">3. Yeast Mitochondrial</option>
@@ -312,7 +312,7 @@
 
     <xml name="input_db_gencode">
         <param argument="-db_gencode" type="select" label="Database/subject genetic code">
-            <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
+            <!-- See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
             <option value="1" selected="true">1. Standard</option>
             <option value="2">2. Vertebrate Mitochondrial</option>
             <option value="3">3. Yeast Mitochondrial</option>
@@ -678,8 +678,8 @@
 ====== ========= ============================================
 Column NCBI name Description
 ------ --------- --------------------------------------------
-     1 qacc      Query accession
-     2 sacc      Subject accession (database hit)
+     1 qaccver   Query accession dot version
+     2 saccver   Subject accession dot version (database hit)
      3 pident    Percentage of identical matches
      4 length    Alignment length
      5 mismatch  Number of mismatches
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Mon May 28 07:57:56 2018 -0400
@@ -110,7 +110,7 @@
             <param name="hash_index" value="true" />
             <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp">
                 <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" />
-                <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" />
+                <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" compare="sim_size" delta="0" />
                 <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" />
                 <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" />
                 <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" />
@@ -129,7 +129,7 @@
             <param name="taxid" value="9606" />
             <output name="outfile" compare="contains" file="four_human_proteins_taxid.fasta.log.txt" ftype="blastdbp">
                 <extra_files type="file" value="four_human_proteins_taxid.fasta.phr" name="blastdb.phr" />
-                <extra_files type="file" value="four_human_proteins_taxid.fasta.pin" name="blastdb.pin" lines_diff="2" />
+                <extra_files type="file" value="four_human_proteins_taxid.fasta.pin" name="blastdb.pin" compare="sim_size" delta="0" />
                 <extra_files type="file" value="four_human_proteins_taxid.fasta.psq" name="blastdb.psq" />
                 <extra_files type="file" value="four_human_proteins_taxid.fasta.pog" name="blastdb.pog" />
                 <extra_files type="file" value="four_human_proteins_taxid.fasta.phd" name="blastdb.phd" />
@@ -147,7 +147,7 @@
             <param name="mask_data_file" value="segmasker_four_human.maskinfo-asn1" ftype="maskinfo-asn1" />
             <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp">
                 <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" />
-                <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" />
+                <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" compare="sim_size" delta="0" />
                 <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" />
                 <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" />
                 <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" />
@@ -166,7 +166,7 @@
             <param name="taxid" value="9606" />
             <output name="outfile" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn">
                 <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" />
-                <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" lines_diff="2" />
+                <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" compare="sim_size" delta="8" />
                 <extra_files type="file" value="three_human_mRNA.fasta.nsq" name="blastdb.nsq" />
                 <extra_files type="file" value="three_human_mRNA.fasta.nog" name="blastdb.nog" />
                 <extra_files type="file" value="three_human_mRNA.fasta.nhd" name="blastdb.nhd" />
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Mon May 28 07:57:56 2018 -0400
@@ -75,15 +75,15 @@
 (PSSMs) and are available for a number of domain collections including:
 
 *CDD* - NCBI curarated meta-collection of domains, see
-http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains
+https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains
 
 *Kog* - PSSMs from automatically aligned sequences and sequence
 fragments classified in the KOGs resource, the eukaryotic
-counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/
+counterpart to COGs, see https://www.ncbi.nlm.nih.gov/COG/
 
 *Cog* - PSSMs from automatically aligned sequences and sequence
 fragments classified in the COGs resource, which focuses primarily
-on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/
+on prokaryotes, see https://www.ncbi.nlm.nih.gov/COG/
 
 *Pfam* - PSSMs from Pfam-A seed alignment database, see
 http://xfam.org/
@@ -92,11 +92,11 @@
 http://smart.embl-heidelberg.de/
 
 *Tigr* - PSSMs from TIGRFAM database of protein families, see
-http://www.jcvi.org/cms/research/projects/tigrfams/overview/
+ftp://ftp.jcvi.org/pub/data/TIGRFAMs/
 
 *Prk* - PSSms from automatically aligned stable clusters in the
 Protein Clusters database, see
-http://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&amp;db=proteinclusters
+https://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&amp;db=proteinclusters
 
 The exact list of domain databases offered will depend on how your
 local Galaxy has been configured.
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Mon May 28 07:57:56 2018 -0400
@@ -73,15 +73,15 @@
 (PSSMs) and are available for a number of domain collections including:
 
 *CDD* - NCBI curarated meta-collection of domains, see
-http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains
+https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains
 
 *Kog* - PSSMs from automatically aligned sequences and sequence
 fragments classified in the KOGs resource, the eukaryotic
-counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/
+counterpart to COGs, see https://www.ncbi.nlm.nih.gov/COG/
 
 *Cog* - PSSMs from automatically aligned sequences and sequence
 fragments classified in the COGs resource, which focuses primarily
-on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/
+on prokaryotes, see https://www.ncbi.nlm.nih.gov/COG/
 
 *Pfam* - PSSMs from Pfam-A seed alignment database, see
 http://xfam.org/
@@ -90,11 +90,11 @@
 http://smart.embl-heidelberg.de/
 
 *Tigr* - PSSMs from TIGRFAM database of protein families, see
-http://www.jcvi.org/cms/research/projects/tigrfams/overview/
+ftp://ftp.jcvi.org/pub/data/TIGRFAMs/
 
 *Prk* - PSSms from automatically aligned stable clusters in the
 Protein Clusters database, see
-http://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&amp;db=proteinclusters
+https://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&amp;db=proteinclusters
 
 The exact list of domain databases offered will depend on how your
 local Galaxy has been configured.
--- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Mon Oct 30 11:49:17 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Mon May 28 07:57:56 2018 -0400
@@ -88,7 +88,7 @@
 More information about segmasker can be found in the `BLAST Command Line Applications User Manual`_.
 
 .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/
-.. _SEG: http://www.ncbi.nlm.nih.gov/pubmed/8743706
+.. _SEG: https://www.ncbi.nlm.nih.gov/pubmed/8743706
 
 **References**