| Previous changeset 26:2889433c7ae1 (2019-07-20) Next changeset 28:87a7ee4cb36f (2020-09-10) |
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Commit message:
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324" |
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modified:
test-data/four_human_proteins.dbinfo.txt test-data/rhodopsin_nucs.dbinfo.txt test-data/three_human_mRNA.dbinfo.txt tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/blastxml_to_tabular.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml 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_makeprofiledb.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 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml |
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removed:
tools/ncbi_blast_plus/repository_dependencies.xml tools/ncbi_blast_plus/tool_dependencies.xml |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 test-data/four_human_proteins.dbinfo.txt --- a/test-data/four_human_proteins.dbinfo.txt Sat Jul 20 18:36:36 2019 -0400 +++ b/test-data/four_human_proteins.dbinfo.txt Wed Sep 09 15:32:17 2020 +0000 |
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| @@ -1,7 +1,3 @@ Database: Just 4 human proteins 4 sequences; 3,297 total residues -Date: Oct 31, 2017 4:23 PM Longest sequence: 1,382 residues - -Volumes: - /mnt/galaxy/repositories/galaxy_blast/test-data/four_human_proteins_taxid.fasta |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 test-data/rhodopsin_nucs.dbinfo.txt --- a/test-data/rhodopsin_nucs.dbinfo.txt Sat Jul 20 18:36:36 2019 -0400 +++ b/test-data/rhodopsin_nucs.dbinfo.txt Wed Sep 09 15:32:17 2020 +0000 |
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| @@ -1,7 +1,3 @@ Database: Rhodopsin nucleotides 6 sequences; 10,296 total bases -Date: Oct 31, 2017 4:23 PM Longest sequence: 4,301 bases - -Volumes: - /mnt/galaxy/repositories/galaxy_blast/test-data/rhodopsin_nucs.fasta |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 test-data/three_human_mRNA.dbinfo.txt --- a/test-data/three_human_mRNA.dbinfo.txt Sat Jul 20 18:36:36 2019 -0400 +++ b/test-data/three_human_mRNA.dbinfo.txt Wed Sep 09 15:32:17 2020 +0000 |
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| @@ -1,7 +1,3 @@ Database: Just 3 human mRNA sequences 3 sequences; 10,732 total bases -Date: Oct 31, 2017 4:23 PM Longest sequence: 4,796 bases - -Volumes: - /mnt/galaxy/repositories/galaxy_blast/test-data/three_human_mRNA.fasta |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/README.rst Wed Sep 09 15:32:17 2020 +0000 |
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| b'@@ -101,8 +101,10 @@\n \n You can download the NCBI provided databases as tar-balls from here:\n \n-* ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR)\n-* ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD)\n+* ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like\n+ NT and NR)\n+* ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like\n+ CDD)\n \n If using the optional taxonomy columns, you will also need to download the\n NCBI taxonomy files (``taxdb.btd`` and ``taxdb.bti`` from ``taxdb.tar.gz`` on\n@@ -128,59 +130,102 @@\n History\n =======\n \n+The wrappers now follow the Galaxy convention of underlying tool version with\n+a galaxy specific suffix which gets reset to zero with each new BLAST version:\n+\n+============== ===============================================================\n+Version Changes\n+-------------- ---------------------------------------------------------------\n+2.7.1+galaxy0 - Adopted BLAST version with integer Galaxy wrapper suffix.\n+ - Dropped legacy ``repository_dependencies.xml`` and\n+ ``tool_dependencies.xml`` files. Instead assumes conda for\n+ dependency resolution and requires at least Galaxy v16.10\n+ which includes the BLAST datatypes.\n+ - ``blastdbcmd`` wrapper supports multiple locally installed\n+ databases (contribution from Frederic Sapet), or a database\n+ from your Galaxy history.\n+============== ===============================================================\n+\n+Prior releases used a self-contained version number (deliberately kept low to\n+avoid any confusion with the NCBI BLAST version numbers):\n+\n ======= ======================================================================\n Version Changes\n ------- ----------------------------------------------------------------------\n-v0.0.11 - Final revision as part of the Galaxy main repository, and the\n- first release via the Tool Shed\n-v0.0.12 - Implements genetic code option for translation searches.\n- - Changes ``<parallelism>`` to 1000 sequences at a time (to cope with\n- very large sets of queries where BLAST+ can become memory hungry)\n- - Include warning that BLAST+ with subject FASTA gives pairwise\n- e-values\n-v0.0.13 - Use the new error handling options in Galaxy (the previously\n- bundled ``hide_stderr.py`` script is no longer needed).\n-v0.0.14 - Support for makeblastdb and blastdbinfo with local BLAST databases\n- in the history (using work from Edward Kirton), requires v0.0.14\n- of the ``blast_datatypes`` repository from the Tool Shed.\n-v0.0.15 - Stronger warning in help text against searching against subject\n- FASTA files (better looking e-values than you might be expecting).\n-v0.0.16 - Added repository_dependencies.xml for automates installation of the\n- ``blast_datatypes`` repository from the Tool Shed.\n-v0.0.17 - The BLAST+ search tools now default to extended tabular output\n- (all too often our users where having to re-run searches just to\n- get one of the missing columns like query or subject length)\n-v0.0.18 - Defensive quoting of filenames in case of spaces (where possible,\n- BLAST+ handling of some multi-file arguments is problematic).\n-v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new ``blastdb_d.loc``\n- for the domain databases they use (e.g. CDD, PFAM or SMART).\n- - Correct case of exception regular expression (for error handling\n- fall-back in case the return code is not set properly).\n- - Clearer naming of output files.\n-v0.0.20 - Added unit tests for BLASTN and TBLASTX.\n- - Added percentage identity option to BLASTN.\n- - Fallback on ElementTree if cElementTree missing in XML to tabular.\n- - Link to Tool Shed added to help text and this documentation.\n- '..b"nd input to ``makeblastdb`` (contribution from Anton Nekrutenko).\n-v0.3.1 - Clarify help text for max hits option, confusing as depending on the\n- output format it must be mapped to different command line arguments.\n- - Extend gzipped query support to all the command line tools.\n- - Workaround for gzipped support under Galaxy release 16.01 or older.\n-v0.3.2 - Fixed incomplete ``@CLI_OPTIONS@`` macro in the help text for the\n- ``tblastn`` and ``blastdbcmd`` wrappers.\n-v0.3.3 - Fixed ``tool_dependencies.xml`` to use BLAST+ 2.7.1 (useful only for\n- older Galaxy instances - we recommend conda for dependencies now).\n+v0.0.21 - Use macros to simplify the XML wrappers (by John Chilton).\n+ - Added wrapper for dustmasker.\n+ - Enabled masking for makeblastdb (Nicola Soranzo).\n+ - Requires ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` datatypes,\n+ defined in ``blast_datatypes`` v0.0.17 on Galaxy ToolShed.\n+ - Tests updated for BLAST+ 2.2.27 instead of BLAST+ 2.2.26.\n+ - Now depends on ``package_blast_plus_2_2_27`` in ToolShed.\n+v0.0.20 - Added unit tests for BLASTN and TBLASTX.\n+ - Added percentage identity option to BLASTN.\n+ - Fallback on ElementTree if cElementTree missing in XML to tabular.\n+ - Link to Tool Shed added to help text and this documentation.\n+ - Tweak ``blast_datatypes`` to also work on Test Tool Shed.\n+ - Dependency on new ``package_blast_plus_2_2_26`` in Tool Shed.\n+ - Adopted standard MIT License.\n+ - Development moved to GitHub, https://github.com/peterjc/galaxy_blast\n+ - Updated citation information (Cock et al. 2013).\n+v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new ``blastdb_d.loc``\n+ for the domain databases they use (e.g. CDD, PFAM or SMART).\n+ - Correct case of exception regular expression (for error handling\n+ fall-back in case the return code is not set properly).\n+ - Clearer naming of output files.\n+v0.0.17 - The BLAST+ search tools now default to extended tabular output\n+ (all too often our users where having to re-run searches just to\n+ get one of the missing columns like query or subject length)\n+v0.0.16 - Added repository_dependencies.xml for automates installation of the\n+ ``blast_datatypes`` repository from the Tool Shed.\n+v0.0.15 - Stronger warning in help text against searching against subject\n+ FASTA files (better looking e-values than you might be expecting).\n+v0.0.14 - Support for makeblastdb and blastdbinfo with local BLAST databases\n+ in the history (using work from Edward Kirton), requires v0.0.14\n+ of the ``blast_datatypes`` repository from the Tool Shed.\n+v0.0.13 - Use the new error handling options in Galaxy (the previously\n+ bundled ``hide_stderr.py`` script is no longer needed).\n+v0.0.12 - Implements genetic code option for translation searches.\n+ - Changes ``<parallelism>`` to 1000 sequences at a time (to cope with\n+ very large sets of queries where BLAST+ can become memory hungry)\n+ - Include warning that BLAST+ with subject FASTA gives pairwise\n+ e-values\n+v0.0.11 - Final revision as part of the Galaxy main repository, and the\n+ first release via the Tool Shed\n+v0.0.22 - More use of macros to simplify the wrappers.\n+ - Set number of threads via ``$GALAXY_SLOTS`` environment variable.\n+ - More descriptive default output names.\n+ - Tests require updated BLAST DB definitions (``blast_datatypes``\n+ v0.0.18).\n+ - Pre-check for duplicate identifiers in ``makeblastdb`` wrapper.\n+ - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27.\n+ - Now depends on ``package_blast_plus_2_2_28`` in ToolShed.\n+ - Extended tabular output includes 'salltitles' as column 25.\n ======= ======================================================================\n \n \n" |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/blastxml_to_tabular.xml --- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Wed Sep 09 15:32:17 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="@WRAPPER_VERSION@"> +<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Convert BLAST XML output to tabular</description> <macros> <import>ncbi_macros.xml</import> |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Wed Sep 09 15:32:17 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="@WRAPPER_VERSION@"> +<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Show BLAST database information from blastdbcmd</description> <macros> <token name="@BINARY@">blastdbcmd</token> @@ -6,29 +6,36 @@ </macros> <expand macro="preamble" /> <command detect_errors="aggressive"> -blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" +blastdbcmd +@DBCMD_OPTS@ +-info -out "$info" </command> <inputs> <expand macro="input_conditional_choose_db_type" /> </inputs> <outputs> - <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> + <data name="info" format="txt" label="@ON_DBCMD_OPTS@ info" /> </outputs> <tests> <test> <param name="db_opts|db_type" value="prot" /> - <param name="db_opts|database" value="four_human_proteins" /> - <output name="info" file="four_human_proteins.dbinfo.txt" ftype="txt" lines_diff="4" /> + <param name="db_opts|db_origin|database" value="four_human_proteins" /> + <output name="info" file="four_human_proteins.dbinfo.txt" ftype="txt" compare="contains" /> </test> <test> <param name="db_opts|db_type" value="nucl" /> - <param name="db_opts|database" value="three_human_mRNA" /> - <output name="info" file="three_human_mRNA.dbinfo.txt" ftype="txt" lines_diff="4" /> + <param name="db_opts|db_origin|database" value="three_human_mRNA" /> + <output name="info" file="three_human_mRNA.dbinfo.txt" ftype="txt" compare="contains" /> </test> <test> <param name="db_opts|db_type" value="nucl" /> - <param name="db_opts|database" value="rhodopsin_nucs" /> - <output name="info" file="rhodopsin_nucs.dbinfo.txt" ftype="txt" lines_diff="4" /> + <param name="db_opts|db_origin|database" value="rhodopsin_nucs" /> + <output name="info" file="rhodopsin_nucs.dbinfo.txt" ftype="txt" compare="contains" /> + </test> + <test> + <param name="db_opts|db_type" value="nucl" /> + <param name="db_opts|db_origin|database" value="three_human_mRNA,rhodopsin_nucs" /> + <output name="info" file="three_human_mRNA_and_rhodopsin_nucs.dbinfo.txt" ftype="txt" compare="contains" /> </test> </tests> <help> |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Sep 09 15:32:17 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="@WRAPPER_VERSION@"> +<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Extract sequence(s) from BLAST database</description> <macros> <token name="@BINARY@">blastdbcmd</token> @@ -8,7 +8,8 @@ <command detect_errors="aggressive" strict="true"> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces -blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path.replace(',',' ')}" +blastdbcmd +@DBCMD_OPTS@ ##TODO: What about -ctrl_a and -target_only as advanced options? @@ -67,12 +68,15 @@ </param> </inputs> <outputs> - <data name="seq" format="fasta" label="Sequences from ${db_opts.database.fields.name}" /> + + <data name="seq" format="fasta" label="Sequences from blastdbcmd @ON_DBCMD_OPTS@"> + </data> </outputs> <tests> <test> <param name="db_opts|db_type" value="prot" /> - <param name="db_opts|database" value="four_human_proteins" /> + <param name="db_opts|db_origin|database" value="four_human_proteins" /> + <param name="db_opts|db_origin|db_origin_selector" value="db" /> <param name="id_opts|id_type" value="prompt" /> <param name="id_opts|entries" value="all" /> <param name="outfmt" value="original" /> @@ -81,7 +85,7 @@ <test> <!-- This used to recover the original FASTA file, but had GI numbers --> <param name="db_opts|db_type" value="nucl" /> - <param name="db_opts|database" value="rhodopsin_nucs" /> + <param name="db_opts|db_origin|database" value="rhodopsin_nucs" /> <param name="id_opts|id_type" value="prompt" /> <param name="id_opts|entries" value="all" /> <param name="outfmt" value="original" /> @@ -90,7 +94,7 @@ <test> <!-- This uses various start end frame combinations but all recover full sequence --> <param name="db_opts|db_type" value="nucl" /> - <param name="db_opts|database" value="rhodopsin_nucs" /> + <param name="db_opts|db_origin|database" value="rhodopsin_nucs" /> <param name="id_opts|id_type" value="file" /> <param name="id_opts|entries" value="rhodopsin_nucs.blastdbcmd.txt" ftype="txt" /> <param name="outfmt" value="original" /> @@ -98,7 +102,7 @@ </test> <test> <param name="db_opts|db_type" value="nucl" /> - <param name="db_opts|database" value="rhodopsin_nucs" /> + <param name="db_opts|db_origin|database" value="rhodopsin_nucs" /> <param name="id_opts|id_type" value="prompt" /> <param name="id_opts|entries" value="U59921.1" /> <param name="outfmt" value="original" /> @@ -106,7 +110,8 @@ </test> <test> <param name="db_opts|db_type" value="nucl" /> - <param name="db_opts|database" value="rhodopsin_nucs" /> + <!-- look in two databases for this entry --> + <param name="db_opts|db_origin|database" value="rhodopsin_nucs,three_human_mRNA" /> <param name="id_opts|id_type" value="prompt" /> <param name="id_opts|entries" value="gi|2734705|gb|U59921.1|BBU59921" /> <param name="outfmt" value="original" /> |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Sep 09 15:32:17 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="@WRAPPER_VERSION@"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Search nucleotide database with nucleotide query sequence(s)</description> <macros> <token name="@BINARY@">blastn</token> |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Sep 09 15:32:17 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="@WRAPPER_VERSION@"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Search protein database with protein query sequence(s)</description> <macros> <token name="@BINARY@">blastp</token> |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Sep 09 15:32:17 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="@WRAPPER_VERSION@"> +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Search protein database with translated nucleotide query sequence(s)</description> <macros> <token name="@BINARY@">blastx</token> |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Wed Sep 09 15:32:17 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="@WRAPPER_VERSION@"> +<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb</description> <macros> <token name="@BINARY@">convert2blastmask</token> |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Wed Sep 09 15:32:17 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="@WRAPPER_VERSION@"> +<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo --> <description>masks low complexity regions</description> <macros> |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Wed Sep 09 15:32:17 2020 +0000 |
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| @@ -1,5 +1,7 @@ <macros> - <token name="@WRAPPER_VERSION@">0.3.3</token> + <token name="@TOOL_VERSION@">2.7.1</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 --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> @@ -7,7 +9,7 @@ <xml name="preamble"> <requirements> - <requirement type="package" version="2.7.1">blast</requirement> + <requirement type="package" version="@TOOL_VERSION@">blast</requirement> </requirements> <version_command>@BINARY@ -version</version_command> </xml> @@ -426,14 +428,40 @@ <option value="prot">Protein</option> </param> <when value="nucl"> - <param name="database" argument="-db" type="select" multiple="true" label="Nucleotide BLAST database"> - <options from_data_table="blastdb" /> - </param> + <conditional name="db_origin"> + <param name="db_origin_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="true">Locally installed BLAST database</option> + <option value="histdb">BLAST database from your history</option> + </param> + <when value="db"> + <param name="database" argument="-db" type="select" multiple="true" label="Nucleotide BLAST database"> + <options from_data_table="blastdb" /> + </param> + <param name="histdb" type="hidden" value="" /> + </when> + <when value="histdb"> + <param name="database" type="hidden" value="" /> + <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> + </when> + </conditional> </when> <when value="prot"> - <param name="database" argument="-db" type="select" multiple="true" label="Protein BLAST database"> - <options from_data_table="blastdb_p" /> - </param> + <conditional name="db_origin"> + <param name="db_origin_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="true">Locally installed BLAST database</option> + <option value="histdb">BLAST database from your history</option> + </param> + <when value="db"> + <param name="database" argument="-db" type="select" multiple="true" label="Protein BLAST database"> + <options from_data_table="blastdb_p" /> + </param> + <param name="histdb" type="hidden" value="" /> + </when> + <when value="histdb"> + <param name="database" type="hidden" value="" /> + <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> + </when> + </conditional> </when> </conditional> </xml> @@ -574,6 +602,17 @@ #end if ]]></token> + <!-- Implement -dbtype and -db command line options (in blastdbcmd) --> + <token name="@DBCMD_OPTS@"><![CDATA[ +-dbtype "$db_opts.db_type" +#if $db_opts.db_origin.db_origin_selector=="db": + -db "${db_opts.db_origin.database.fields.path.replace(',',' ')}" +#else if $db_opts.db_origin.db_origin_selector=="histdb": + -db '${os.path.join($db_opts.db_origin.histdb.extra_files_path, "blastdb")}' +#end if + ]]></token> + + <!-- Implement -db ... / -subject ... command line options --> <token name="@BLAST_DB_SUBJECT@"><![CDATA[ #if $db_opts.db_opts_selector == "db": -db '${" ".join(str($db_opts.database.fields.path).split(","))}' @@ -699,6 +738,15 @@ #end if ]]></token> + <!-- @ON_DBCMD_OPTS@ is for use with @DBCMD_OPTS@ --> + <token name="@ON_DBCMD_OPTS@"><![CDATA[ +#if str($db_opts.db_origin.db_origin_selector)=="db" +'${db_opts.db_origin.database}' +#else +'${db_opts.db_origin.histdb.name}' +#end if +]]></token> + <token name="@REFERENCES@"><![CDATA[ Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015). NCBI BLAST+ integrated into Galaxy. *GigaScience* 4:39 |
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| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Sep 09 15:32:17 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="@WRAPPER_VERSION@"> +<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Make BLAST database</description> <macros> <token name="@BINARY@">makeblastdb</token> |
| b |
| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_makeprofiledb.xml --- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Wed Sep 09 15:32:17 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="@WRAPPER_VERSION@"> +<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Make profile database</description> <macros> <token name="@BINARY@">makeprofiledb</token> |
| b |
| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Wed Sep 09 15:32:17 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="@WRAPPER_VERSION@"> +<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Search protein domain database (PSSMs) with protein query sequence(s)</description> <macros> <token name="@BINARY@">deltablast</token> |
| b |
| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Wed Sep 09 15:32:17 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="@WRAPPER_VERSION@"> +<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description> <macros> <token name="@BINARY@">rpstblastn</token> |
| b |
| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Wed Sep 09 15:32:17 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="@WRAPPER_VERSION@"> +<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>low-complexity regions in protein sequences</description> <macros> <token name="@BINARY@">segmasker</token> |
| b |
| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Sep 09 15:32:17 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="@WRAPPER_VERSION@"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Search translated nucleotide database with protein query sequence(s)</description> <macros> <token name="@BINARY@">tblastn</token> @@ -146,7 +146,7 @@ <param name="max_hits" value="0" /> <param name="word_size" value="" /> <param name="parse_deflines" value="false" /> - <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" lines_diff="8" /> + <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" lines_diff="10" /> </test> </tests> <help> |
| b |
| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Sep 09 15:32:17 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="@WRAPPER_VERSION@"> +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> <macros> <token name="@BINARY@">tblastx</token> |
| b |
| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/repository_dependencies.xml --- a/tools/ncbi_blast_plus/repository_dependencies.xml Sat Jul 20 18:36:36 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -<?xml version="1.0" ?> -<repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> - <repository changeset_revision="01b38f20197e" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu"/> -</repositories> \ No newline at end of file |
| b |
| diff -r 2889433c7ae1 -r 6f8ea4b9a2c4 tools/ncbi_blast_plus/tool_dependencies.xml --- a/tools/ncbi_blast_plus/tool_dependencies.xml Sat Jul 20 18:36:36 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0" ?> -<tool_dependency> - <package name="blast" version="2.7.1"> - <repository changeset_revision="2e9109a8924f" name="package_blast_plus_2_7_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/> - </package> -</tool_dependency> \ No newline at end of file |