--- a/tools/fastq/fastq_paired_unpaired.py	Tue Apr 30 14:08:37 2013 -0400
+++ b/tools/fastq/fastq_paired_unpaired.py	Wed Sep 18 06:13:27 2013 -0400
@@ -9,10 +9,10 @@
 Note that the FASTQ variant is unimportant (Sanger, Solexa, Illumina, or even
 Color Space should all work equally well).
 
-This script is copyright 2010-2011 by Peter Cock, The James Hutton Institute
+This script is copyright 2010-2013 by Peter Cock, The James Hutton Institute
 (formerly SCRI), Scotland, UK. All rights reserved.
 
-See accompanying text file for licence details (MIT/BSD style).
+See accompanying text file for licence details (MIT license).
 """
 import os
 import sys
@@ -20,7 +20,7 @@
 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print "Version 0.0.6"
+    print "Version 0.0.8"
     sys.exit(0)
 
 def stop_err(msg, err=1):

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/fastq/fastq_paired_unpaired.rst	Wed Sep 18 06:13:27 2013 -0400
@@ -0,0 +1,113 @@
+Galaxy tool to divide FASTQ files into paired and unpaired reads
+================================================================
+
+This tool is copyright 2010-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below (MIT licence).
+
+This tool is a short Python script which divides a FASTQ file into paired
+reads, and single or orphan reads. You can have separate files for the
+forward/reverse reads, or have them interleaved in a single file.
+
+Note that the FASTQ variant is unimportant (Sanger, Solexa, Illumina, or even
+Color Space should all work equally well).
+
+This tool is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and install
+the tool from the Galaxy Tool Shed, and run the unit tests
+
+
+Manual Installation
+===================
+
+There are just two files to install:
+
+* fastq_paired_unpaired.py (the Python script)
+* fastq_paired_unpaired.xml (the Galaxy tool definition)
+
+The suggested location is in the Galaxy folder tools/fastq next to other FASTQ
+tools provided with Galaxy.
+
+You will also need to modify the tools_conf.xml file to tell Galaxy to offer
+the tool. One suggested location is next to the fastq_filter.xml entry. Simply
+add the line::
+
+    <tool file="fastq/fastq_paired_unpaired.xml" />
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version, using Biopython
+v0.0.2  - Help text; cope with multiple pairs per template
+v0.0.3  - Galaxy XML wrappers added
+v0.0.4  - Use Galaxy library to handle FASTQ files (avoid Biopython dependency)
+v0.0.5  - Handle Illumina 1.8 style pair names
+v0.0.6  - Record script version when run from Galaxy
+        - Added unit test (FASTQ file using Sanger naming)
+v0.0.7  - Link to Tool Shed added to help text and this documentation.
+v0.0.8  - Use reStructuredText for this README file.
+        - Adopt standard MIT License.
+        - Updated citation information (Cock et al. 2013).
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and other tools for filtering FASTA, FASTQ and SFF files were
+initially developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
+
+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::
+
+    $ tar -czf fastq_paired_unpaired.tar.gz tools/fastq/fastq_paired_unpaired.* test-data/sanger-pairs-*.fastq
+
+Check this worked::
+
+    $ tar -tzf fastq_paired_unpaired.tar.gz
+    tools/fastq/fastq_paired_unpaired.py
+    tools/fastq/fastq_paired_unpaired.rst
+    tools/fastq/fastq_paired_unpaired.xml
+    test-data/sanger-pairs-forward.fastq
+    test-data/sanger-pairs-interleaved.fastq
+    test-data/sanger-pairs-mixed.fastq
+    test-data/sanger-pairs-reverse.fastq
+    test-data/sanger-pairs-singles.fastq
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

--- a/tools/fastq/fastq_paired_unpaired.txt	Tue Apr 30 14:08:37 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-Galaxy tool to divide FASTQ files into paired and unpaired reads
-================================================================
-
-This tool is copyright 2010 by Peter Cock, SCRI, UK. All rights reserved.
-See the licence text below.
-
-This tool is a short Python script (using the Biopython library functions) which
-divides a FASTQ file into paired reads, and single or orphan reads. You can have
-separate files for the forward/reverse reads, or have them interleaved in a
-single file.
-
-Note that the FASTQ variant is unimportant (Sanger, Solexa, Illumina, or even
-Color Space should all work equally well).
-
-There are just two files to install:
-
-* fastq_paired_unpaired.py (the Python script)
-* fastq_paired_unpaired.xml (the Galaxy tool definition)
-
-The suggested location is in the Galaxy folder tools/fastq next to other FASTQ
-tools provided with Galaxy.
-
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer
-the tool. One suggested location is next to the fastq_filter.xml entry. Simply
-add the line:
-
-<tool file="fastq/fastq_paired_unpaired.xml" />
-
-That's it.
-
-
-History
-=======
-
-v0.0.1 - Initial version, using Biopython
-v0.0.2 - Help text; cope with multiple pairs per template
-v0.0.3 - Galaxy XML wrappers added
-v0.0.4 - Use Galaxy library to handle FASTQ files (avoid Biopython dependency)
-v0.0.5 - Handle Illumina 1.8 style pair names
-v0.0.6 - Record script version when run from Galaxy
-       - Added unit test (FASTQ file using Sanger naming)
-
-
-Developers
-==========
-
-This script and other tools for filtering FASTA, FASTQ and SFF files are
-currently being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
-
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder:
-
-$ tar -czf fastq_paired_unpaired.tar.gz tools/fastq/fastq_paired_unpaired.* test-data/sanger-pairs-*.fastq
-
-Check this worked:
-
-$ tar -tzf fastq_paired_unpaired.tar.gz
-fastq/fastq_paired_unpaired.py
-fastq/fastq_paired_unpaired.txt
-fastq/fastq_paired_unpaired.xml
-test-data/sanger-pairs-forward.fastq
-test-data/sanger-pairs-interleaved.fastq
-test-data/sanger-pairs-mixed.fastq
-test-data/sanger-pairs-reverse.fastq
-test-data/sanger-pairs-singles.fastq
-
-
-Licence (MIT/BSD style)
-=======================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.

--- a/tools/fastq/fastq_paired_unpaired.xml	Tue Apr 30 14:08:37 2013 -0400
+++ b/tools/fastq/fastq_paired_unpaired.xml	Wed Sep 18 06:13:27 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.6">
+<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.7">
 	<description>using the read name suffices</description>
 	<version_command interpreter="python">fastq_paired_unpaired.py --version</version_command>
 	<command interpreter="python">
@@ -97,5 +97,17 @@
  * WTSI_1055_4p17.p1kapIBF paired with WTSI_1055_4p17.q1kapIBR
  * WTSI_1055_4p17.p1kpIBF paired with WTSI_1055_4p17.q1kpIBR
 
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following paper:
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+This tool is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired
 	</help>
 </tool>