--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.rst	Wed Jul 24 11:56:22 2013 -0400
@@ -0,0 +1,109 @@
+Galaxy tool to extract top BLAST hit descriptions from BLAST XML
+================================================================
+
+This tool is copyright 2012-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+This tool is a short Python script to parse a BLAST XML file, and extract the
+identifiers with description for the top matches (by default the top 3), and
+output these as a simple tabular file along with the query identifiers.
+
+It is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
+
+This requires the 'blast_datatypes' repository from the Galaxy Tool Shed
+to provide the 'blastxml' file format definition.
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically install the
+'blast_datatypes' dependency.
+
+
+Manual Installation
+===================
+
+If you haven't done so before, first install the 'blast_datatypes' repository.
+
+There are just two files to install (if doing this manually):
+
+* blastxml_to_top_descr.py (the Python script)
+* blastxml_to_top_descr.xml (the Galaxy tool definition)
+
+The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to
+the NCBI BLAST+ tool wrappers.
+
+You will also need to modify the tools_conf.xml file to tell Galaxy to offer
+the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line::
+
+    <tool file="filters/seq_select_by_id.xml" />
+
+To run the tool's tests, also add this line to tools_conf.xml.sample then::
+
+    $ sh run_functional_tests.sh -id blastxml_to_top_descr
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version.
+v0.0.2  - Since BLAST+ was moved out of the Galaxy core, now have a dependency
+          on the 'blast_datatypes' repository in the Tool Shed.
+v0.0.3  - Include the test files required to run the unit tests
+v0.0.4  - Quote filenames in case they contain spaces (internal change)
+v0.0.5  - Include number of queries with BLAST matches in stdout (peek text)
+v0.0.6  - Check for errors via the script's return code (internal change)
+v0.0.7  - Link to Tool Shed added to help text and this documentation.
+        - Tweak dependency on blast_datatypes to also work on Test Tool Shed
+        - Adopt standard MIT License.
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools are being developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/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 blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* tools/ncbi_blast_plus/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular
+
+Check this worked::
+
+    $ tar -tzf blastxml_to_top_descr.tar.gz
+    tools/ncbi_blast_plus/blastxml_to_top_descr.py
+    tools/ncbi_blast_plus/blastxml_to_top_descr.rst
+    tools/ncbi_blast_plus/blastxml_to_top_descr.xml
+    tools/ncbi_blast_plus/repository_dependencies.xml
+    test-data/blastp_four_human_vs_rhodopsin.xml
+    test-data/blastp_four_human_vs_rhodopsin_top3.tabular
+
+
+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/ncbi_blast_plus/blastxml_to_top_descr.txt	Wed Apr 17 11:46:03 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
-Galaxy tool to extract top BLAST hit descriptions from BLAST XML
-================================================================
-
-This tool is copyright 2012-2013 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-This tool is a short Python script to parse a BLAST XML file, and extract the
-identifiers with description for the top matches (by default the top 3), and
-output these as a simple tabular file along with the query identifiers.
-
-This requires the 'blast_datatypes' repository from the Galaxy Tool Shed
-to provide the 'blastxml' file format definition.
-
-
-Automated Installation
-======================
-
-This should be straightforward, Galaxy should automatically install the
-'blast_datatypes' dependency.
-
-
-Manual Installation
-===================
-
-If you haven't done so before, first install the 'blast_datatypes' repository.
-
-There are just two files to install (if doing this manually):
-
-* blastxml_to_top_descr.py (the Python script)
-* blastxml_to_top_descr.xml (the Galaxy tool definition)
-
-The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to
-the NCBI BLAST+ tool wrappers.
-
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer
-the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line:
-
-<tool file="filters/seq_select_by_id.xml" />
-
-To run the tool's tests, also add this line to tools_conf.xml.sample then:
-
-$ sh run_functional_tests.sh -id blastxml_to_top_descr
-
-
-History
-=======
-
-v0.0.1 - Initial version.
-v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency
-         on the 'blast_datatypes' repository in the Tool Shed.
-v0.0.3 - Include the test files required to run the unit tests
-v0.0.4 - Quote filenames in case they contain spaces (internal change)
-v0.0.5 - Include number of queries with BLAST matches in stdout (peek text)
-v0.0.6 - Check for errors via the script's return code (internal change)
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/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 blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* tools/ncbi_blast_plus/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular
-
-Check this worked:
-
-$ tar -tzf blastxml_to_top_descr.tar.gz
-tools/ncbi_blast_plus/blastxml_to_top_descr.py
-tools/ncbi_blast_plus/blastxml_to_top_descr.txt
-tools/ncbi_blast_plus/blastxml_to_top_descr.xml
-tools/ncbi_blast_plus/repository_dependencies.xml
-test-data/blastp_four_human_vs_rhodopsin.xml
-test-data/blastp_four_human_vs_rhodopsin_top3.tabular
-
-
-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/ncbi_blast_plus/blastxml_to_top_descr.xml	Wed Apr 17 11:46:03 2013 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.xml	Wed Jul 24 11:56:22 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.6">
+<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.7">
     <description>Make a table from BLAST XML</description>
     <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command>
     <command interpreter="python">
@@ -49,5 +49,10 @@
 to spot some problems (e.g. bacterial contaimination could be very
 obvious).
 
+**Citation**
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
+
     </help>
 </tool>

--- a/tools/ncbi_blast_plus/repository_dependencies.xml	Wed Apr 17 11:46:03 2013 -0400
+++ b/tools/ncbi_blast_plus/repository_dependencies.xml	Wed Jul 24 11:56:22 2013 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
 <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format).">
-<!-- Revision 4:f9a7783ed7b6 on the main tool shed is v0.0.14 which added BLAST databases -->
-<repository toolshed="http://toolshed.g2.bx.psu.edu" name="blast_datatypes" owner="devteam" changeset_revision="f9a7783ed7b6" />
+<!-- Revision 4:f9a7783ed7b6 on the main (and test) tool shed is v0.0.14 which added BLAST databases -->
+<repository changeset_revision="f9a7783ed7b6" name="blast_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
 </repositories>