# HG changeset patch
# User peterjc
# Date 1367934751 14400
# Node ID b51633a69a92fd9bd69e7684415a0b0decaa0927
# Parent  6ce8634e20358da563d9fa656833d4ad4e064c1f
Uploaded v0.0.3, add links to Tool Shed in documentation.

Unit test passes locally.

diff -r 6ce8634e2035 -r b51633a69a92 tools/filters/seq_rename.txt
--- a/tools/filters/seq_rename.txt	Mon Apr 22 13:48:03 2013 -0400
+++ b/tools/filters/seq_rename.txt	Tue May 07 09:52:31 2013 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to renamed FASTA, QUAL, FASTQ or SFF sequences
 ==========================================================
 
-This tool is copyright 2011 by Peter Cock, The James Hutton Institute
+This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -11,8 +11,20 @@
 and if there are duplicates in the input sequence file, there will be duplicates
 in the output sequence file.
 
+This tool is available from the Galaxy Tool Shed,
+http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename
+
 See also the sister tools to filter or select sequence files according to IDs
-from column(s) of tabular file.
+from column(s) of tabular file:
+http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
+http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
+
+
+Automated Installation
+======================
+
+This should be straightforward, provided you have installed Biopython 1.54 or later.
+Galaxy should automatically install the Python script, and run the unit tests.
 
 
 Manual Installation
@@ -31,6 +43,11 @@
 
 <tool file="filters/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:
+
+$ ./run_functional_tests.sh -id seq_rename
+
 You will also need to install Biopython 1.54 or later. That's it.
 
 
@@ -41,6 +58,7 @@
 v0.0.2 - Record script version when run from Galaxy.
        - Add unit test.
        - Check for errors using Python script's return code.
+v0.0.3 - Link to Tool Shed added to help text and this documentation.
 
 
 Developers
diff -r 6ce8634e2035 -r b51633a69a92 tools/filters/seq_rename.xml
--- a/tools/filters/seq_rename.xml	Mon Apr 22 13:48:03 2013 -0400
+++ b/tools/filters/seq_rename.xml	Tue May 07 09:52:31 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="seq_rename" name="Rename sequences" version="0.0.2">
+<tool id="seq_rename" name="Rename sequences" version="0.0.3">
 	<description>with ID mapping from a tabular file</description>
 	<version_commmand interpreter="python">seq_rename.py --version</version_commmand>
 	<command interpreter="python">
@@ -64,5 +64,7 @@
 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
 
+This tool is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename
 	</help>
 </tool>