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+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 also need to make a copy of the ``weeder2.loc`` file (a sample version is
+provided here) which lists the species for which frequency files are available.
+This file should be placed in the ``tool-data`` directory of your Galaxy
+installation.
+
+Additionally you will 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``.
+
+Functional tests
+================
+
+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 weeder2
+
+You will need to have set the environment variables above.
+
+Reference Data
+==============
+
+Weeder2 requires reference data in the form of frequency files for each
+species of interest. A set of reference files is provided as part of the
+Weeder2 installation.
+
+Additional frequency files can be generated for novel species using the
+``w2frequency_maker`` utility available via:
+
+- http://159.149.160.51/weederaddons/weeder2freq.html
+
+This page also explains what input data should be used.
+
+The location of the additional frequency files can then be specified by
+adding them to the ``weeder2.loc`` file (see above).
+
+History
+=======
+
+========== ======================================================================
+Version    Changes
+---------- ----------------------------------------------------------------------
+2.0.2      - Drop ``tool_dependencies.xml`` & use conda to resolve dependencies
+2.0.1      - Explicitly specify frequency files in ``weeder2.loc``.
+2.0.0      - 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.