--- a/README.markdown	Mon Dec 01 10:40:07 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-Trimmomatic
-===========
-
-XML tool file and shell script wrapper for the Trimmomatic program, which provides
-various functions for manipluating Illumina FASTQ files.
-
-Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university:
-
- * <http://www.usadellab.org/cms/index.php?page=trimmomatic>
-
-The reference for Trimmomatic is:
-
- * Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. RobiNA: a
-   user-friendly, integrated software solution for RNA-Seq-based transcriptomics.
-   Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7)
-
-Trimmomatic 0.32 can be obtained from:
-
- * <http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip>
-
-The tool assumes that two environment variables have been set, in order to find the
-appropriate files:
-
- * `TRIMMOMATIC_DIR` should point to the directory holding the
-   `trimmomatic-0.32.jar` file, and
-
- * `TRIMMOMATIC_ADAPTERS_DIR` should point to the directory holding the adapter
-    sequence files (used by the `ILLUMINACLIP` option).
-
-Both variables will be set automatically if installing the tool dependencies e.g. via
-a toolshed; otherwise they will need to be set manually in the Galaxy environment.
-
-To add to Galaxy add the following to tool_conf.xml:
-
-    <tool file="trimmomatic/trimmomatic.xml" />
-
-(The tool no longer uses a `.loc` file to point to the location of the adapter
-sequence files)
-
-### Changes ###
-
-0.32.1: Remove `trimmomatic_adapters.loc.sample` and hard-code adapter files into
-        the XML wrapper.
-
-0.32.0: Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and
-        (set the environment). Update tool versioning to use Trimmomatic version
-	number (i.e. `0.32`) with tool iteration appended (i.e. `.1`).
-
-0.0.4: Specify '-threads 6' in <command> section.
-
-0.0.3 : Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic.
-
-0.0.2: Updated ILLUMINACLIP option to use standard adapter sequences (requires the
-       trimmomatic_adapters.loc file; sample version is supplied) plus cosmetic
-       updates to wording and help text for some options.
-
-0.0.1: Initial version

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Tue Dec 09 09:41:33 2014 -0500
@@ -0,0 +1,104 @@
+Trimmomatic: flexible read trimming tool for Illumina NGS data
+==============================================================
+
+Galaxy tool wrapper for the Trimmomatic program, which provides various functions for
+manipluating Illumina FASTQ files (both single and paired-end).
+
+Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university
+http://www.usadellab.org/cms/index.php?page=trimmomatic
+
+The reference for Trimmomatic is:
+
+- Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer
+  for Illumina Sequence Data. Bioinformatics, btu170.
+
+Automated installation
+======================
+
+Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
+the trimmomatic program and data, and setting the appropriate environment variables.
+
+Manual Installation
+===================
+
+There are two files to install:
+
+- ``trimmomatic.xml`` (the Galaxy tool definition)
+- ``trimmomatic.sh`` (the shell script wrapper)
+
+The suggested location is in a ``tools/trimmomatic/`` 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="trimmomatic/trimmomatic.xml" />
+
+You will also need to install trimmomatic 0.32:
+
+- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
+
+The tool wrapper uses the following environment variables in order to find the
+appropriate files:
+
+- ``TRIMMOMATIC_DIR`` should point to the directory holding the
+  ``trimmomatic-0.32.jar`` file
+- ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter
+  sequence files (used by the ``ILLUMINACLIP`` option).
+
+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
+---------- ----------------------------------------------------------------------
+0.32.1     - Remove ``trimmomatic_adapters.loc.sample`` and hard-code adapter files
+             into the XML wrapper.
+0.32.0     - Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and
+             set the environment.
+           - Update tool versioning to use Trimmomatic version number (i.e. ``0.32``)
+             with tool iteration appended (i.e. ``.1``).
+0.0.4      - Specify '-threads 6' in <command> section.
+0.0.3      - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic.
+0.0.2      - Updated ILLUMINACLIP option to use standard adapter sequences (requires
+             the trimmomatic_adapters.loc file; sample version is supplied) plus
+             cosmetic updates to wording and help text for some options.
+0.0.1      - Initial version
+========== ======================================================================
+
+
+Developers
+==========
+
+This tool is developed on the following GitHub repository:
+https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
+the ``package_trimmomatic.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/trimmomatic.xml	Mon Dec 01 10:40:07 2014 -0500
+++ b/trimmomatic.xml	Tue Dec 09 09:41:33 2014 -0500
@@ -223,11 +223,18 @@
 
 The reference for Trimmomatic is:
 
- * Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. RobiNA: a
-   user-friendly, integrated software solution for RNA-Seq-based transcriptomics.
-   Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7)
+ * Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer
+   for Illumina Sequence Data. Bioinformatics, btu170.
 
 Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you
 use it.
   </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">10.1093/bioinformatics/btu170</citation>
+  </citations>
 </tool>