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Changeset 48:25f86a96c4c9 (2020-09-08)

Previous changeset 47:00330a63ffcf (2020-08-21) Next changeset 49:17f84d08f5a6 (2020-09-08)

Commit message:
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8b5b3a72e5714b12142d0f863729f56964691244-dirty"

modified:
tools/ncbi_blast_plus/README.rst

diff -r 00330a63ffcf -r 25f86a96c4c9 tools/ncbi_blast_plus/README.rst
--- a/tools/ncbi_blast_plus/README.rst Fri Aug 21 12:44:41 2020 +0000
+++ b/tools/ncbi_blast_plus/README.rst Tue Sep 08 16:38:13 2020 +0000

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@@ -131,56 +133,80 @@\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- - Tweak dependency on ``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-v0.0.21 - 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-v0.0.22 - 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`` v0.0.18).\n- - Pre-check for duplicate identifiers in ``makeblastdb`` wrapper.\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"