Mercurial > repos > devteam > ncbi_blast_plus
changeset 53:061c2abccfea draft
"Updated to 2.10.1+galaxy0"
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--- a/test-data/blastn_chimera_vs_three_human_max1.txt Thu Sep 10 10:32:26 2020 +0000 +++ b/test-data/blastn_chimera_vs_three_human_max1.txt Thu Sep 10 13:21:55 2020 +0000 @@ -1,4 +1,4 @@ -BLASTN 2.9.0+ +BLASTN 2.10.1+ Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb @@ -15,10 +15,10 @@ Query= chimera chunks of AB011145 plus M10051 plus BC112106 Length=9973 - Score E -Sequences producing significant alignments: (Bits) Value + Score E +Sequences producing significant alignments: (Bits) Value -ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, p... 8421 0.0 +ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, p... 8421 0.0 >ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, @@ -346,7 +346,7 @@ Database: Just 3 human mRNA sequences - Posted date: Apr 23, 2020 3:16 PM + Posted date: Sep 9, 2020 11:23 PM Number of letters in database: 10,732 Number of sequences in database: 3
--- a/test-data/blastn_rhodopsin_vs_three_human.xml Thu Sep 10 10:32:26 2020 +0000 +++ b/test-data/blastn_rhodopsin_vs_three_human.xml Thu Sep 10 13:21:55 2020 +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 2.9.0+</BlastOutput_version> + <BlastOutput_version>BLASTN 2.10.1+</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 Thu Sep 10 10:32:26 2020 +0000 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Thu Sep 10 13:21:55 2020 +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 2.9.0+</BlastOutput_version> + <BlastOutput_version>BLASTP 2.10.1+</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 Thu Sep 10 10:32:26 2020 +0000 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Thu Sep 10 13:21:55 2020 +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 2.9.0+</BlastOutput_version> + <BlastOutput_version>BLASTX 2.10.1+</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 Thu Sep 10 10:32:26 2020 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Thu Sep 10 13:21:55 2020 +0000 @@ -3,7 +3,7 @@ <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099"> <PRE> -<b>TBLASTN 2.9.0+</b> +<b>TBLASTN 2.10.1+</b> <b><a @@ -84,15 +84,15 @@ <b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 Length=348 - Score E -Sequences producing significant alignments: (Bits) Value + Score E +Sequences producing significant alignments: (Bits) Value -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|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 +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|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 ><a name=Subject_1></a> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO),
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml Thu Sep 10 10:32:26 2020 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin.xml Thu Sep 10 13:21:55 2020 +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 2.9.0+</BlastOutput_version> + <BlastOutput_version>TBLASTN 2.10.1+</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/tools/ncbi_blast_plus/README.rst Thu Sep 10 10:32:26 2020 +0000 +++ b/tools/ncbi_blast_plus/README.rst Thu Sep 10 13:21:55 2020 +0000 @@ -136,6 +136,13 @@ ============== =============================================================== Version Changes -------------- --------------------------------------------------------------- +2.10.1+galaxy0 - Updated for NCBI BLAST+ 2.10.1 release. + - Supports locally installed v4 or v5 format BLAST databases + (listed in the ``blastdb*.loc`` files). + - ``makeblastdb`` and ``makeprofiledb`` still produce v4 format + databases (pending updates to the Galaxy datatypes for v5). + - Minimum word size for ``blastn`` now 4 (update from Anthony + Bretaudeau). 2.9.0+galaxy0 - Updated for NCBI BLAST+ 2.9.0 release (contribution from Anthony Bretaudeau). 2.7.1+galaxy0 - Adopted BLAST version with integer Galaxy wrapper suffix.
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Sep 10 10:32:26 2020 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Sep 10 13:21:55 2020 +0000 @@ -61,7 +61,7 @@ <expand macro="input_strand" /> <expand macro="input_max_hits" /> <param name="identity_cutoff" argument="-perc_identity" type="float" min="0" max="100" value="0" label="Percent identity cutoff" help="Use zero for no cutoff" /> - <expand macro="input_word_size" /> + <expand macro="input_word_size_blastn" /> <param argument="-ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> <expand macro="input_parse_deflines" /> <expand macro="advanced_optional_id_files" />
--- a/tools/ncbi_blast_plus/ncbi_macros.xml Thu Sep 10 10:32:26 2020 +0000 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Thu Sep 10 13:21:55 2020 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">2.9.0</token> + <token name="@TOOL_VERSION@">2.10.1</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">16.10</token> <xml name="parallelism"> @@ -493,6 +493,12 @@ help="Leave blank for default, otherwise minimum 2" /> </xml> + <xml name="input_word_size_blastn"> + <param argument="-word_size" type="integer" min="4" optional="true" + label="Word size for wordfinder algorithm" + help="Leave blank for default, otherwise minimum 4" /> + </xml> + <xml name="input_strand"> <param argument="-strand" type="select" label="Query strand(s) to search against database/subject"> <option value="-strand both">Both</option>
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Sep 10 10:32:26 2020 +0000 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Sep 10 13:21:55 2020 +0000 @@ -24,6 +24,7 @@ #end if #end for | makeblastdb -out '${os.path.join($outfile.files_path, "blastdb")}' +-blastdb_version 4 $parse_seqids $hash_index -in -
--- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Thu Sep 10 10:32:26 2020 +0000 +++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Thu Sep 10 13:21:55 2020 +0000 @@ -8,7 +8,9 @@ <command detect_errors="aggressive" strict="true"> ##Unlike makeblastdb, makeprofiledb needs directory to exist already: mkdir -p $outfile.files_path && -makeprofiledb -out '${os.path.join($outfile.files_path, "blastdb")}' +makeprofiledb +-blastdb_version 4 +-out '${os.path.join($outfile.files_path, "blastdb")}' ##We turn $input_file into $infiles with a configfile entry defined below -in '$infiles'