diff --git a/tools/ncbi_blast_plus/README.rst b/tools/ncbi_blast_plus/README.rst index 41695c0e..3d764aa6 100644 --- a/tools/ncbi_blast_plus/README.rst +++ b/tools/ncbi_blast_plus/README.rst @@ -47,6 +47,7 @@ XML files to your ``tool_conf.xml`` as normal (and do the same in + @@ -143,14 +144,14 @@ v0.0.20 - Added unit tests for BLASTN and TBLASTX. - 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. +v0.0.21 - Use macros to simplify the XML wrappers (by John Chilton). - Added wrapper for dustmasker. - - Enabled masking for makeblastdb. + - 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 macros to simplify the wrappers. +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). @@ -159,16 +160,21 @@ v0.0.22 - More use macros to simplify the wrappers. - Now depends on ``package_blast_plus_2_2_28`` in ToolShed. - Extended tabular output includes 'salltitles' as column 25. v0.1.00 - Now depends on ``package_blast_plus_2_2_29`` in ToolShed. - - Tabular output now includes option to pick specific columns, - including previously unavailable taxonomy columns. - - BLAST XML to tabular tool supports multiple input files. + - Tabular output now includes option to pick specific columns + (based on contribution from Jim Johnson), including previously + unavailable taxonomy columns. + - BLAST XML to tabular tool supports multiple input files + (based on contribution from Jim Johnson). - More detailed descriptions for BLASTN and BLASTP task option. - - Wrappers for segmasker, dustmasker and convert2blastmask. + - Wrappers for segmasker, dustmasker and convert2blastmask + (contribution from Bjoern Gruening). - Supports using maskinfo with makeblastdb wrapper. - 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. ======= ======================================================================