diff tools/ncbi_blast_plus/README.rst @ 25:e25d3acf6e68 draft

v0.3.1 completed gzip support

--- a/tools/ncbi_blast_plus/README.rst	Mon Jul 09 10:08:16 2018 -0400
+++ b/tools/ncbi_blast_plus/README.rst	Tue Oct 23 08:48:19 2018 -0400
@@ -213,7 +213,7 @@
           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.
+        - 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
@@ -252,13 +252,18 @@
         - 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
+          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 (contribution from Anton Nekrutenko).
+        - 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.
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