--- a/README.markdown	Wed Nov 19 07:56:27 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-weeder2
-=======
-
-Galaxy tool for motif discovery using weeder2.
-
-weeder2_wrapper
----------------
-
-XML and wrapper script for weeder motif discovery package version 2.0.
-
-`weeder2` can be obtained from <http://159.149.160.51/modtools/downloads/weeder2.html>.
-
-To add to Galaxy add the following to tool_conf.xml:
-
-    <tool file="weeder2/weeder2_wrapper.xml" />
-
-### Changes ###
-
-2.0.0.0: initial version
-

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Tue Dec 09 11:27:19 2014 -0500
@@ -0,0 +1,90 @@
+weeder2: motif discovery in sequences from coregulated genes of a single species
+================================================================================
+
+Galaxy tool for the Weeder2 motif discovery package:
+
+- Zambelli, F., Pesole, G. and Pavesi, G. 2014. Using Weeder, Pscan, and PscanChIP
+  for the Discovery of Enriched Transcription Factor Binding Site Motifs in
+  Nucleotide Sequences. Current Protocols in Bioinformatics. 47:2.11:2.11.1–2.11.31.
+  http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0211s47/full
+
+See http://159.149.160.51/modtools/
+
+Automated installation
+======================
+
+Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
+the Weeder2 program and data, and setting the appropriate environment variables.
+
+Manual Installation
+===================
+
+There are two files to install:
+
+- ``weeder2_wrapper.xml`` (the Galaxy tool definition)
+- ``weeder2_wrapper.sh`` (the shell script wrapper)
+
+The suggested location is in a ``tools/weeder2/`` folder. You will then
+need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
+by adding the line:
+
+    <tool file="weeder2/weeder2_wrapper.xml" />
+
+You will also need to install ``weeder2`` from:
+
+- http://159.149.160.51/modtools/downloads/weeder2.html
+
+The tool wrapper uses the following environment variables in order to find the
+appropriate files:
+
+- ``WEEDER_FREQFILES_DIR`` should point to the ``FreqFiles`` directory
+
+Also the directory holding the Weeder2 executables should be on your ``PATH``.
+
+If you want to run the functional tests, copy the sample test files under
+sample test files under Galaxy's ``test-data/`` directory. Then:
+
+    ./run_tests.sh -id trimmomatic
+
+You will need to have set the environment variables above.
+
+History
+=======
+
+========== ======================================================================
+Version    Changes
+---------- ----------------------------------------------------------------------
+2.0.0.0    - Initial version
+========== ======================================================================
+
+
+Developers
+==========
+
+This tool is developed on the following GitHub repository:
+https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/weeder2
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
+the ``package_weeder2.sh`` script.
+
+
+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/weeder2_wrapper.xml	Wed Nov 19 07:56:27 2014 -0500
+++ b/weeder2_wrapper.xml	Tue Dec 09 11:27:19 2014 -0500
@@ -178,4 +178,12 @@
 Please kindly acknowledge both this Galaxy tool, the Weeder package and the utility
 scripts if you use it in your work.
   </help>
+  <citations>
+    <!--
+    See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+    Can be either DOI or Bibtex
+    Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
+    -->
+    <citation type="doi">10.1002/0471250953.bi0211s47</citation>
+  </citations>
 </tool>