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+pal_finder: find microsatellite repeats and design PCR primers
+==============================================================
+
+Galaxy tool wrapper for the pal_finder microsatellite and PCR primer design script.
+
+Automated installation
+======================
+
+Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
+the pal_finder and primer3_core programs, and setting the appropriate environment
+variables.
+
+Manual Installation
+===================
+
+There are two files to install:
+
+- ``pal_finder_wrapper.xml`` (the Galaxy tool definition)
+- ``pal_finder_wrapper.sh`` (the shell script wrapper)
+
+The suggested location is in a ``tools/pal_finder_wrapper/`` 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="pal_finder/pal_finder_wrapper.xml" />
+
+You will also need to install the pal_finder and primer3 packages:
+
+- ``pal_finder`` can be obtained from http://sourceforge.net/projects/palfinder/
+- ``Primer3`` version 2.0.0-alpha (see the pal_finder installation notes) can be
+  obtained from http://primer3.sourceforge.net/releases.php
+
+The tool wrapper must be able to locate the pal_finder Perl script, the example
+pal_finder config.txt and simple.ref data files, and the primer3_core program - the
+locations of these are taken from the following enviroment variables which you will
+need to set manually:
+
+- ``PALFINDER_SCRIPT_DIR``: location of the pal_finder Perl script (defaults to /usr/bin)
+- ``PALFINDER_DATA_DIR``: location of the pal_finder data files (specifically config.txt
+  and simple.ref; defaults to /usr/share/pal_finder_v0.02.04)
+- ``PRIMER3_CORE_EXE``: name of the primer3_core program, which should include the
+  full path if it's not on the Galaxy user's PATH (defaults to primer3_core)
+
+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 microsat_pal_finder
+
+You will need to have set the environment variables above.
+
+History
+=======
+
+========== ======================================================================
+Version    Changes
+---------- ----------------------------------------------------------------------
+0.02.04.1  - Add option to run Graeme Fox's ``pal_finder_filter.pl`` script to
+             filter and sort the pal_finder output (Illumina input data only).
+             Update version number to reflect the pal_finder version.
+0.0.6      - Allow input data to be either Illumina paired-end data in fastq
+             format or single-end 454 data in fasta format.
+0.0.5      - Allow custom mispriming library to be specified; added
+             ``tool_dependencies.xml`` file to install pal_finder and primer3
+             programs  and configure environment for Galaxy automatically.
+0.0.4      - Added more custom options for primer3_core for selecting primers on
+             size, GC and melting temperature criteria.
+0.0.3      - Check that pal_finder script & config file, and primer3_core
+             executable are all available; move PRIMER_MIN_TM parameter to new
+             "custom" section for primer3 settings
+0.0.2      - Updated pal_finder_wrapper.sh to allow locations of pal_finder Perl
+             script, data files and primer_core3 program to be set via environment
+             variables
+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/pal_finder
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
+the ``package_pal_finder.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.