diff tools/seq_rename/README.rst @ 3:e1398f2ba9fe draft default tip

v0.0.8 galaxy_sequence_utils dependency etc

--- a/tools/seq_rename/README.rst	Fri Oct 11 04:39:16 2013 -0400
+++ b/tools/seq_rename/README.rst	Thu Feb 02 11:49:03 2017 -0500
@@ -1,7 +1,7 @@
 Galaxy tool to rename FASTA, QUAL, FASTQ or SFF sequences
 =========================================================
 
-This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -35,20 +35,20 @@
 
 There are just two files to install to use this tool from within Galaxy:
 
-* seq_rename.py (the Python script)
-* seq_rename.xml (the Galaxy tool definition)
+* ``seq_rename.py`` (the Python script)
+* ``seq_rename.xml`` (the Galaxy tool definition)
 
-The suggested location is in a dedicated tools/seq_rename folder.
+The suggested location is in a dedicated ``tools/seq_rename`` folder.
 
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
 tool. One suggested location is in the filters section. Simply add the line::
 
     <tool file="seq_rename/seq_rename.xml" />
 
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder. Then::
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
 
-    $ ./run_functional_tests.sh -id seq_rename
+    $ ./run_tests.sh -id seq_rename
 
 You will also need to install Biopython 1.54 or later. That's it.
 
@@ -70,6 +70,18 @@
         - Updated citation information (Cock et al. 2013).
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
         - Renamed folder and adopted README.rst naming.
+v0.0.5  - Correct automated dependency definition.
+v0.0.6  - Simplified XML to apply input format to output data.
+        - Tool definition now embeds citation information.
+        - If white space is found in the requested tabular field then only
+          the first word is used as the identifier (with a warning to stderr).
+v0.0.7  - Use the ``format_source=...`` tag.
+        - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+        - Capture the tool version via Galaxy (bug fix).
+v0.0.8  - Updated to point at Biopython 1.67 (latest version in Tool Shed).
+        - Explicit dependency on ``galaxy_sequence_utils``.
+        - Python style updates (internal change only).
 ======= ======================================================================
 
 
@@ -82,21 +94,30 @@
 Development has now moved to a dedicated GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+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/seq_rename/
+    ...
+
+or::
 
-    $ tar -czf seq_rename.tar.gz tools/seq_rename/README.rst tools/seq_rename/seq_rename.* tools/seq_rename/repository_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.rename.tabular test-data/four_human_proteins.rename.fasta
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_rename/
+    ...
+
+To just build and check the tar ball, use::
 
-Check this worked::
-
-    $ tar -tzf seq_rename.tar.gz
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/seq_rename/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/four_human_proteins.fasta
+    test-data/four_human_proteins.rename.fasta
+    test-data/four_human_proteins.rename.tabular
     tools/seq_rename/README.rst
     tools/seq_rename/seq_rename.py
     tools/seq_rename/seq_rename.xml
-    tools/seq_rename/repository_dependencies.xml
-    test-data/four_human_proteins.fasta
-    test-data/four_human_proteins.rename.tabular
-    test-data/four_human_proteins.rename.fasta
+    tools/seq_rename/tool_dependencies.xml
 
 
 Licence (MIT)