diff tools/blast_rbh/README.rst @ 5:8f4500f6f2aa draft

Refactored to use more than one Python file (internal change only).

--- a/tools/blast_rbh/README.rst	Wed Apr 19 07:44:47 2017 -0400
+++ b/tools/blast_rbh/README.rst	Tue Dec 06 15:53:36 2022 +0000
@@ -24,13 +24,13 @@
 NCBI BLAST+ integrated into Galaxy.
 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
 *GigaScience* 2015, 4:39
-DOI: http://dx.doi.org/10.1186/s13742-015-0080-7
+https://doi.org/10.1186/s13742-015-0080-7
 
 You should also cite the NCBI BLAST+ tools:
 
 BLAST+: architecture and applications.
 C. Camacho et al. *BMC Bioinformatics* 2009, 10:421.
-DOI: http://dx.doi.org/10.1186/1471-2105-10-421
+https://doi.org/10.1186/1471-2105-10-421
 
 
 Automated Installation
@@ -43,9 +43,10 @@
 Manual Installation
 ===================
 
-There are just two files to install:
+There are just three files to install:
 
 - ``blast_rbh.py`` (the Python script)
+- ``best_hits.py`` (helper script, put in same directory)
 - ``blast_rbh.xml`` (the Galaxy tool definition)
 
 The suggested location is in a ``tools/blast_rbh/`` folder. You will then
@@ -91,6 +92,9 @@
 v0.1.11 - Updated to depend on NCBI BLAST+ 2.5.0 via ToolShed or BioConda.
         - Update Biopython dependency.
         - Tweak Python script to work under Python 2 or Python 3.
+v0.1.12 - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
+v0.2.0  - Refactored to use more than one Python file (internal change only).
 ======= ======================================================================
 
 
@@ -116,7 +120,7 @@
 
     $ planemo shed_upload --tar_only tools/blast_rbh/
     ...
-    $ tar -tzf shed_upload.tar.gz 
+    $ tar -tzf shed_upload.tar.gz
     test-data/four_human_proteins.fasta
     test-data/k12_edited_proteins.fasta
     test-data/k12_ten_proteins.fasta