diff tools/align_back_trans/README.rst @ 4:c8469274d136 draft

v0.0.8 Using Biopython 1.67 from Tool Shed or Conda package
author peterjc
date Wed, 10 May 2017 12:05:28 -0400
parents de803005027f
children 2c32e8a8990f
line wrap: on
line diff
--- a/tools/align_back_trans/README.rst	Wed Feb 01 06:55:27 2017 -0500
+++ b/tools/align_back_trans/README.rst	Wed May 10 12:05:28 2017 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to back-translate a protein alignment to nucleotides
 ================================================================
 
-This tool is copyright 2012-2015 by Peter Cock, The James Hutton Institute
+This tool is copyright 2012-2017 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below (MIT licence).
 
@@ -70,6 +70,15 @@
         - Use ``format_source=...`` tag.
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 v0.0.7  - Minor Python code style improvements (internal change only).
+v0.0.8  - Python coding style change to avoid lamba (internal change only).
+        - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
+        - Added two recent NCBI genetic code tables,
+
+          - Table 24, *Pterobranchia* Mitochondrial Code,
+          - Table 25, Candidate Division SR1 and *Gracilibacteria*.
+
+        - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
 ======= ======================================================================
 
 
@@ -86,17 +95,17 @@
 Planemo commands (which requires you have set your Tool Shed access details in
 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
+    $ planemo shed_update -t testtoolshed --check_diff tools/align_back_trans/
     ...
 
 or::
 
-    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
+    $ planemo shed_update -t toolshed --check_diff tools/align_back_trans/
     ...
 
 To just build and check the tar ball, use::
 
-    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/align_back_trans/
+    $ planemo shed_upload --tar_only tools/align_back_trans/
     ...
     $ tar -tzf shed_upload.tar.gz 
     test-data/demo_nucs.fasta