diff tools/seq_primer_clip/README.rst @ 4:9b074c1db68e draft

v0.0.14 galaxy_sequence_utils dependency etc
author peterjc
date Thu, 02 Feb 2017 11:52:37 -0500
parents 708ce1e5ac94
children 530c8d6fedd8
line wrap: on
line diff
--- a/tools/seq_primer_clip/README.rst	Thu Nov 21 10:47:23 2013 -0500
+++ b/tools/seq_primer_clip/README.rst	Thu Feb 02 11:52:37 2017 -0500
@@ -1,7 +1,7 @@
 Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads
-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 (MIT licence).
@@ -23,18 +23,19 @@
 There are just two files to install:
-* seq_primer_clip.py (the Python script)
-* seq_primer_clip.xml (the Galaxy tool definition)
+* ``seq_primer_clip.py`` (the Python script)
+* ``seq_primer_clip.xml`` (the Galaxy tool definition)
-The suggested location is a new tools/seq_primer_clip folder. You will also
-need to modify the tools_conf.xml file to tell Galaxy to offer the tool::
+The suggested location is a new ``tools/seq_primer_clip/`` folder. You will
+also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
   <tool file="seq_primer_clip/seq_primer_clip.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_primer_clip
+    $ ./run_tests.sh -id seq_primer_clip
 You will also need to install Biopython 1.54 or later. That's it.
@@ -62,6 +63,14 @@
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
         - Renamed folder and adopted README.rst naming.
 v0.0.11 - Correct automated dependency definition.
+v0.0.12 - Simplified XML to apply input format to output data.
+        - Tool definition now embeds citation information.
+v0.0.13 - Use ``format_source=...`` tag.
+        - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+        - Fixed input file help text.
+v0.0.14 - Updated to point at Biopython 1.67 (latest version in Tool Shed).
+        - Explicit dependency on ``galaxy_sequence_utils``.
 ======= ======================================================================
@@ -75,19 +84,24 @@
 Development has now moved to a dedicated GitHub repository:
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
-    $ tar -czf seq_primer_clip.tar.gz tools/seq_primer_clip/README.rst tools/seq_primer_clip/seq_primer_clip.* tools/seq_primer_clip/tool_dependencies.xml test-data/dop_primers.fasta test-data/MID4_GLZRM4E04_rnd30*
+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)::
-Check this worked::
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/
+    ...
-    $ tar -tzf seq_primer_clip.tar.gz
-    tools/seq_primer_clip/README.rst
-    tools/seq_primer_clip/seq_primer_clip.xml
-    tools/seq_primer_clip/seq_primer_clip.py
-    tools/seq_primer_clip/tool_dependencies.xml
-    test-data/dop_primers.fasta
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/
+    ...
+To just build and check the tar ball, use::
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/seq_primer_clip/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
@@ -97,6 +111,11 @@
+    test-data/dop_primers.fasta
+    tools/seq_primer_clip/README.rst
+    tools/seq_primer_clip/seq_primer_clip.py
+    tools/seq_primer_clip/seq_primer_clip.xml
+    tools/seq_primer_clip/tool_dependencies.xml
 Licence (MIT)