diff tools/samtools_depad/README.rst @ 1:01f8967ce1e0 draft

v0.0.3; internal changes to help packaging with planemo

--- a/tools/samtools_depad/README.rst	Fri Nov 21 06:37:20 2014 -0500
+++ b/tools/samtools_depad/README.rst	Wed May 13 10:15:02 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy wrapper for samtools depad
 =================================
 
-This wrapper is copyright 2014 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2014-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -21,7 +21,7 @@
 Manual Installation
 ===================
 
-This expects samtools to be on the $PATH, and was tested using v0.1.19.
+This expects samtools to be on the ``$PATH``, and was tested using v0.1.19.
 
 To install the wrapper copy or move the following files under the Galaxy tools
 folder, e.g. in a ``tools/samtools_depad`` folder:
@@ -35,10 +35,10 @@
 
   <tool file="samtools_depad/samtools_depad.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_depad
+    $ ./run_tests.sh -id samtools_depad
 
 That's it.
 
@@ -49,7 +49,11 @@
 ======= ======================================================================
 Version Changes
 ------- ----------------------------------------------------------------------
-v0.0.1  - Initial public release
+v0.0.1  - Initial public release.
+v0.0.2  - Embed samtools citation in the tool XML.
+        - Removed unused imports from Python wrapper script.
+v0.0.3  - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -59,22 +63,31 @@
 Development is on this GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad
 
-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)::
 
-    $ tar -czf samtools_depad.tar.gz tools/samtools_depad/README.rst tools/samtools_depad/samtools_depad.xml tools/samtools_depad/samtools_depad.py tools/samtools_depad/tool_dependencies.xml test-data/sam_spec_padded.fasta test-data/sam_spec_padded.sam test-data/sam_spec_padded.bam test-data/sam_spec_padded.depad.bam
+    $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_depad/
+    ...
+
+or::
 
-Check this worked::
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_depad/
+    ...
+
+To just build and check the tar ball, use::
 
-    $ tar -tzf samtools_depad.tar.gz
-    tools/samtools_depad/README.rst
-    tools/samtools_depad/samtools_depad.xml
-    tools/samtools_depad/samtools_depad.py
-    tools/samtools_depad/tool_dependencies.xml
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/samtools_depad/
+    ...
+    $ tar -tzf shed_upload.tar.gz
+    test-data/sam_spec_padded.bam
+    test-data/sam_spec_padded.depad.bam
     test-data/sam_spec_padded.fasta
     test-data/sam_spec_padded.sam
-    test-data/sam_spec_padded.bam
-    test-data/sam_spec_padded.depad.bam
+    tools/samtools_depad/README.rst
+    tools/samtools_depad/samtools_depad.py
+    tools/samtools_depad/samtools_depad.xml
+    tools/samtools_depad/tool_dependencies.xml
 
 
 Licence (MIT)