diff tools/samtools_idxstats/README.rst @ 1:8945bad80f4a draft

v0.0.4; internal changes for packaging

--- a/tools/samtools_idxstats/README.rst	Wed Nov 20 12:27:33 2013 -0500
+++ b/tools/samtools_idxstats/README.rst	Wed May 13 10:35:50 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy wrapper for samtools idxstats
 ====================================
 
-This wrapper is copyright 2013 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2013-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -26,19 +26,19 @@
 To install the wrapper copy or move the following files under the Galaxy tools
 folder, e.g. in a ``tools/samtools_idxstats`` folder:
 
-* samtools_idxstats.xml (the Galaxy tool definition)
-* samtools_idxstats.py (the Python wrapper script)
-* README.rst (this file)
+* ``samtools_idxstats.xml`` (the Galaxy tool definition)
+* ``samtools_idxstats.py`` (the Python wrapper script)
+* ``README.rst`` (this file)
 
 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
 the tool. Just add the line, perhaps under the NGS tools section::
 
   <tool file="samtools_idxstats/samtools_idxstats.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 samtools_idxstats
+    $ ./run_tests.sh -id samtools_idxstats
 
 That's it.
 
@@ -50,29 +50,43 @@
 Version Changes
 ------- ----------------------------------------------------------------------
 v0.0.1  - Initial public release
+v0.0.2  - Use quoted filenames when calling samtools (in case of spaces etc)
+v0.0.3  - Embed samtools citation in tool XML.
+v0.0.4  - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
 Developers
 ==========
 
-Development is one this GitHub repository:
+Development is on this GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
 
-    $ tar -czf samtools_idxstats.tar.gz tools/samtools_idxstats/README.rst tools/samtools_idxstats/samtools_idxstats.xml tools/samtools_idxstats/samtools_idxstats.py tools/samtools_idxstats/tool_dependencies.xml test-data/ex1.bam test-data/ex1.idxstats.tabular
+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_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/
+    ...
 
-Check this worked::
+or::
+
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/
+    ...
 
-    $ tar -tzf samtools_idxstats.tar.gz
-    tools/samtools_idxstats/README.rst
-    tools/samtools_idxstats/samtools_idxstats.xml
-    tools/samtools_idxstats/samtools_idxstats.py
-    tools/samtools_idxstats/tool_dependencies.xml
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/samtools_idxstats/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
     test-data/ex1.bam
     test-data/ex1.idxstats.tabular
+    tools/samtools_idxstats/README.rst
+    tools/samtools_idxstats/samtools_idxstats.py
+    tools/samtools_idxstats/samtools_idxstats.xml
+    tools/samtools_idxstats/tool_dependencies.xml
 
 
 Licence (MIT)