Mercurial > repos > devteam > ncbi_blast_plus
changeset 27:6f8ea4b9a2c4 draft
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
line wrap: on
line diff
--- 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 @@ -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
--- 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 @@ -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
--- 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 @@ -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
--- 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 @@ -101,8 +101,10 @@ You can download the NCBI provided databases as tar-balls from here: -* ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR) -* ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD) +* ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like + NT and NR) +* ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like + CDD) If using the optional taxonomy columns, you will also need to download the NCBI taxonomy files (``taxdb.btd`` and ``taxdb.bti`` from ``taxdb.tar.gz`` on @@ -128,59 +130,102 @@ History ======= +The wrappers now follow the Galaxy convention of underlying tool version with +a galaxy specific suffix which gets reset to zero with each new BLAST version: + +============== =============================================================== +Version Changes +-------------- --------------------------------------------------------------- +2.7.1+galaxy0 - Adopted BLAST version with integer Galaxy wrapper suffix. + - Dropped legacy ``repository_dependencies.xml`` and + ``tool_dependencies.xml`` files. Instead assumes conda for + dependency resolution and requires at least Galaxy v16.10 + which includes the BLAST datatypes. + - ``blastdbcmd`` wrapper supports multiple locally installed + databases (contribution from Frederic Sapet), or a database + from your Galaxy history. +============== =============================================================== + +Prior releases used a self-contained version number (deliberately kept low to +avoid any confusion with the NCBI BLAST version numbers): + ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- -v0.0.11 - Final revision as part of the Galaxy main repository, and the - first release via the Tool Shed -v0.0.12 - Implements genetic code option for translation searches. - - Changes ``<parallelism>`` to 1000 sequences at a time (to cope with - very large sets of queries where BLAST+ can become memory hungry) - - Include warning that BLAST+ with subject FASTA gives pairwise - e-values -v0.0.13 - Use the new error handling options in Galaxy (the previously - bundled ``hide_stderr.py`` script is no longer needed). -v0.0.14 - Support for makeblastdb and blastdbinfo with local BLAST databases - in the history (using work from Edward Kirton), requires v0.0.14 - of the ``blast_datatypes`` repository from the Tool Shed. -v0.0.15 - Stronger warning in help text against searching against subject - FASTA files (better looking e-values than you might be expecting). -v0.0.16 - Added repository_dependencies.xml for automates installation of the - ``blast_datatypes`` repository from the Tool Shed. -v0.0.17 - The BLAST+ search tools now default to extended tabular output - (all too often our users where having to re-run searches just to - get one of the missing columns like query or subject length) -v0.0.18 - Defensive quoting of filenames in case of spaces (where possible, - BLAST+ handling of some multi-file arguments is problematic). -v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new ``blastdb_d.loc`` - for the domain databases they use (e.g. CDD, PFAM or SMART). - - Correct case of exception regular expression (for error handling - fall-back in case the return code is not set properly). - - Clearer naming of output files. -v0.0.20 - Added unit tests for BLASTN and TBLASTX. - - Added percentage identity option to BLASTN. - - Fallback on ElementTree if cElementTree missing in XML to tabular. - - Link to Tool Shed added to help text and this documentation. - - Tweak dependency on ``blast_datatypes`` to also work on Test Tool Shed. - - Dependency on new ``package_blast_plus_2_2_26`` in Tool Shed. - - Adopted standard MIT License. - - Development moved to GitHub, https://github.com/peterjc/galaxy_blast - - Updated citation information (Cock et al. 2013). -v0.0.21 - Use macros to simplify the XML wrappers (by John Chilton). - - Added wrapper for dustmasker. - - Enabled masking for makeblastdb (Nicola Soranzo). - - Requires ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` datatypes, - defined in ``blast_datatypes`` v0.0.17 on Galaxy ToolShed. - - Tests updated for BLAST+ 2.2.27 instead of BLAST+ 2.2.26. - - Now depends on ``package_blast_plus_2_2_27`` in ToolShed. -v0.0.22 - More use of macros to simplify the wrappers. - - Set number of threads via ``$GALAXY_SLOTS`` environment variable. - - More descriptive default output names. - - Tests require updated BLAST DB definitions (``blast_datatypes`` v0.0.18). - - Pre-check for duplicate identifiers in ``makeblastdb`` wrapper. - - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27. - - Now depends on ``package_blast_plus_2_2_28`` in ToolShed. - - Extended tabular output includes 'salltitles' as column 25. +v0.3.3 - Fixed ``tool_dependencies.xml`` to use BLAST+ 2.7.1 (useful only for + older Galaxy instances - we recommend conda for dependencies now). +v0.3.2 - Fixed incomplete ``@CLI_OPTIONS@`` macro in the help text for the + ``tblastn`` and ``blastdbcmd`` wrappers. +v0.3.1 - Clarify help text for max hits option, confusing as depending on the + output format it must be mapped to different command line arguments. + - Extend gzipped query support to all the command line tools. + - Workaround for gzipped support under Galaxy release 16.01 or older. +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. + - Accept gzipped FASTA inputs for subject files, queries to ``blastn`` + and input to ``makeblastdb`` (contribution from Anton Nekrutenko). +v0.2.02 - Document the BLAST+ 2.5.0 change in the standard 12 column output + from ``qseqid,sseqid,...`` to ``qacc,sacc,...`` instead. + - Support for per-matrix recommended gaps settings (``-gapopen`` and + ``-gapextend``, contribution from Caleb Easterly and Jim Johnson). + - Support for ``-window_size``, ``-threshold``, ``-comp_based_stats`` + and revising ``-word_size`` to avoid using zero to mean default + (contribution from Caleb Easterly). +v0.2.01 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). + - Show BLAST command line argument corresponding to each tool + parameter (contribution from Nicola Soranzo). + - Add ``-max_hsps`` option (contribution from Nicola Soranzo). + - Add ``-use_sw_tback`` option for BLASTP (Nicola Soranzo). +v0.2.00 - Updated for NCBI BLAST+ 2.5.0, where GI numbers are less visible, + tabular output changes with `-parse_deflines`, and percentage + identifies are now given to 3dp rather than 2dp. + - Depends on ``package_blast_plus_2_5_0`` in ToolShed, or BioConda. + - ``blastxml_to_tabular`` now also gives percentage idenity to 3dp. + - Removed never-used binary and Python module dependency declarations + (internal change only). +v0.1.08 - Allow searching against multiple locally installed databases + (contribution from Gildas Le Corguillé and Emma Prudent). + - Minor XML and Python style changes (internal change only). + - Set ``allow_duplicate_entries="False"`` in sample configuration file + ``tool_data_table_conf.xml``. + - Fix identifers with pipes in ``blastdbcmd`` wrapper (Devon Ryan). +v0.1.07 - Re-enabled some ``*.loc`` file tests (these had not been supported + on the Tool Shed test framework, but that is not currently in use). + - Fixed macro problem with version field in blastxml_to_tabular.xml + (contribution from Bjoern Gruening and Daniel Blankenberg). +v0.1.06 - Now depends on ``package_blast_plus_2_2_31`` in ToolShed. + - Tests updated for BLAST+ 2.2.31 instead of BLAST+ 2.2.30. +v0.1.05 - Define ``parallelism`` tag via a macro (internal change only). + - Define wrapper versions via a macro (internal change only). + - Update citation information now GigaScience paper is out. +v0.1.04 - Fixed regression using BLAST databases from the history. Currently + Galaxy inputs must still use ``.extra_files_path`` rather than the + more consise ``.extra_files`` available for output files (Issue #69) +v0.1.03 - Reorder XML elements (internal change only). + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). +v0.1.02 - Now depends on ``package_blast_plus_2_2_30`` in ToolShed. + - Tests updated for BLAST+ 2.2.30 instead of BLAST+ 2.2.29. + - New tasks ``blastp-fast``, ``blastx-fast`` and ``tblastn-fast``. + - New minimum query HSP coverage option, ``-qcov_hsp_perc``. + - Removed ``-word_size`` from RPS-BLAST and RPS-TBLASTN wrappers, this + is set during database construction and should not have been offered + as a command line option in releases prior to BLAST+ 2.2.30. + - BLAST database ``blastdb*.loc`` files now accessed via the XML + table definitions in Galaxy's ``tool_data_table_conf.xml`` file, + setup via ``tool-data/tool_data_table_conf.xml.sample`` + - Replace ``.extra_files_path`` with ``.files_path`` (internal change, + thanks to Bjoern Gruening and John Chilton). + - Added *"NCBI BLAST+ integrated into Galaxy"* preprint citation. +v0.1.01 - Requires ``blastdbd`` datatype (``blast_datatypes`` v0.0.19). + - Wrapper for makeprofiledb added to create protein domain databases + (based on contribution from Bjoern Gruening). + - The RPS-BLAST and RPS-TBLASTN wrappers support using a protein + domain database from the user's history. + - Tool definitions now embed citation information (by John Chilton). + - BLAST tools support GI and SeqID filters (added by Bjoern Gruening). v0.1.00 - Now depends on ``package_blast_plus_2_2_29`` in ToolShed. - Tabular output now includes option to pick specific columns (based on contribution from Jim Johnson), including previously @@ -194,80 +239,55 @@ - Supports setting a taxonomy ID in ``makeblastdb`` wrapper. - Subtle changes like new conditional settings will require some old workflows be updated to cope. -v0.1.01 - Requires ``blastdbd`` datatype (``blast_datatypes`` v0.0.19). - - Wrapper for makeprofiledb added to create protein domain databases - (based on contribution from Bjoern Gruening). - - The RPS-BLAST and RPS-TBLASTN wrappers support using a protein - domain database from the user's history. - - Tool definitions now embed citation information (by John Chilton). - - BLAST tools support GI and SeqID filters (added by Bjoern Gruening). -v0.1.02 - Now depends on ``package_blast_plus_2_2_30`` in ToolShed. - - Tests updated for BLAST+ 2.2.30 instead of BLAST+ 2.2.29. - - New tasks ``blastp-fast``, ``blastx-fast`` and ``tblastn-fast``. - - New minimum query HSP coverage option, ``-qcov_hsp_perc``. - - Removed ``-word_size`` from RPS-BLAST and RPS-TBLASTN wrappers, this - is set during database construction and should not have been offered - as a command line option in releases prior to BLAST+ 2.2.30. - - BLAST database ``blastdb*.loc`` files now accessed via the XML - table definitions in Galaxy's ``tool_data_table_conf.xml`` file, - setup via ``tool-data/tool_data_table_conf.xml.sample`` - - Replace ``.extra_files_path`` with ``.files_path`` (internal change, - thanks to Bjoern Gruening and John Chilton). - - Added *"NCBI BLAST+ integrated into Galaxy"* preprint citation. -v0.1.03 - Reorder XML elements (internal change only). - - Planemo for Tool Shed upload (``.shed.yml``, internal change only). -v0.1.04 - Fixed regression using BLAST databases from the history. Currently - Galaxy inputs must still use ``.extra_files_path`` rather than the - more consise ``.extra_files`` available for output files (Issue #69) -v0.1.05 - Define ``parallelism`` tag via a macro (internal change only). - - Define wrapper versions via a macro (internal change only). - - Update citation information now GigaScience paper is out. -v0.1.06 - Now depends on ``package_blast_plus_2_2_31`` in ToolShed. - - Tests updated for BLAST+ 2.2.31 instead of BLAST+ 2.2.30. -v0.1.07 - Re-enabled some ``*.loc`` file tests (these had not been supported - on the Tool Shed test framework, but that is not currently in use). - - Fixed macro problem with version field in blastxml_to_tabular.xml - (contribution from Bjoern Gruening and Daniel Blankenberg). -v0.1.08 - Allow searching against multiple locally installed databases - (contribution from Gildas Le Corguillé and Emma Prudent). - - Minor XML and Python style changes (internal change only). - - Set ``allow_duplicate_entries="False"`` in sample configuration file - ``tool_data_table_conf.xml``. - - Fix identifers with pipes in ``blastdbcmd`` wrapper (Devon Ryan). -v0.2.00 - Updated for NCBI BLAST+ 2.5.0, where GI numbers are less visible, - tabular output changes with `-parse_deflines`, and percentage - identifies are now given to 3dp rather than 2dp. - - Depends on ``package_blast_plus_2_5_0`` in ToolShed, or BioConda. - - ``blastxml_to_tabular`` now also gives percentage idenity to 3dp. - - Removed never-used binary and Python module dependency declarations - (internal change only). -v0.2.01 - Use ``<command detect_errors="aggressive">`` (internal change only). - - Single quote command line arguments (internal change only). - - Show BLAST command line argument corresponding to each tool - parameter (contribution from Nicola Soranzo). - - Add ``-max_hsps`` option (contribution from Nicola Soranzo). - - Add ``-use_sw_tback`` option for BLASTP (Nicola Soranzo). -v0.2.02 - Document the BLAST+ 2.5.0 change in the standard 12 column output - from ``qseqid,sseqid,...`` to ``qacc,sacc,...`` instead. - - Support for per-matrix recommended gaps settings (``-gapopen`` and - ``-gapextend``, contribution from Caleb Easterly and Jim Johnson). - - 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. - - Accept gzipped FASTA inputs for subject files, queries to ``blastn`` - and input to ``makeblastdb`` (contribution from Anton Nekrutenko). -v0.3.1 - Clarify help text for max hits option, confusing as depending on the - output format it must be mapped to different command line arguments. - - Extend gzipped query support to all the command line tools. - - Workaround for gzipped support under Galaxy release 16.01 or older. -v0.3.2 - Fixed incomplete ``@CLI_OPTIONS@`` macro in the help text for the - ``tblastn`` and ``blastdbcmd`` wrappers. -v0.3.3 - Fixed ``tool_dependencies.xml`` to use BLAST+ 2.7.1 (useful only for - older Galaxy instances - we recommend conda for dependencies now). +v0.0.21 - Use macros to simplify the XML wrappers (by John Chilton). + - Added wrapper for dustmasker. + - Enabled masking for makeblastdb (Nicola Soranzo). + - Requires ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` datatypes, + defined in ``blast_datatypes`` v0.0.17 on Galaxy ToolShed. + - Tests updated for BLAST+ 2.2.27 instead of BLAST+ 2.2.26. + - Now depends on ``package_blast_plus_2_2_27`` in ToolShed. +v0.0.20 - Added unit tests for BLASTN and TBLASTX. + - Added percentage identity option to BLASTN. + - Fallback on ElementTree if cElementTree missing in XML to tabular. + - Link to Tool Shed added to help text and this documentation. + - Tweak ``blast_datatypes`` to also work on Test Tool Shed. + - Dependency on new ``package_blast_plus_2_2_26`` in Tool Shed. + - Adopted standard MIT License. + - Development moved to GitHub, https://github.com/peterjc/galaxy_blast + - Updated citation information (Cock et al. 2013). +v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new ``blastdb_d.loc`` + for the domain databases they use (e.g. CDD, PFAM or SMART). + - Correct case of exception regular expression (for error handling + fall-back in case the return code is not set properly). + - Clearer naming of output files. +v0.0.17 - The BLAST+ search tools now default to extended tabular output + (all too often our users where having to re-run searches just to + get one of the missing columns like query or subject length) +v0.0.16 - Added repository_dependencies.xml for automates installation of the + ``blast_datatypes`` repository from the Tool Shed. +v0.0.15 - Stronger warning in help text against searching against subject + FASTA files (better looking e-values than you might be expecting). +v0.0.14 - Support for makeblastdb and blastdbinfo with local BLAST databases + in the history (using work from Edward Kirton), requires v0.0.14 + of the ``blast_datatypes`` repository from the Tool Shed. +v0.0.13 - Use the new error handling options in Galaxy (the previously + bundled ``hide_stderr.py`` script is no longer needed). +v0.0.12 - Implements genetic code option for translation searches. + - Changes ``<parallelism>`` to 1000 sequences at a time (to cope with + very large sets of queries where BLAST+ can become memory hungry) + - Include warning that BLAST+ with subject FASTA gives pairwise + e-values +v0.0.11 - Final revision as part of the Galaxy main repository, and the + first release via the Tool Shed +v0.0.22 - More use of macros to simplify the wrappers. + - Set number of threads via ``$GALAXY_SLOTS`` environment variable. + - More descriptive default output names. + - Tests require updated BLAST DB definitions (``blast_datatypes`` + v0.0.18). + - Pre-check for duplicate identifiers in ``makeblastdb`` wrapper. + - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27. + - Now depends on ``package_blast_plus_2_2_28`` in ToolShed. + - Extended tabular output includes 'salltitles' as column 25. ======= ======================================================================
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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" />
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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
--- 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 @@ -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