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+Galaxy wrapper for OpenMS
+=========================
+
+OpenMS is an open-source software C++ library for LC/MS data management and analyses.
+It offers an infrastructure for the rapid development of mass spectrometry related software.
+OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux.
+
+More informations are available at:
+
+ * https://github.com/OpenMS/OpenMS
+ * http://open-ms.sourceforge.net
+
+
+Installation
+============
+
+Galaxy should be able to automatically install the dependencies, i.e.
+'package_openms_2_0' or 'package_qt_4_8' repository.
+
+The wrappers are included in https://testtoolshed.g2.bx.psu.edu/view/bgruening/openms.
+
+
+Generating OpenMS wrappers
+==========================
+
+ * install OpenMS (you can do this automatically through the Tool Shed)
+ * create a folder called CTD
+ * inside of your new installed openms/bin folder, execute the following command:
+    
+    ```bash
+    for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
+    ```
+
+ * clone or install CTDopts
+
+    ```bash
+    git clone https://github.com/genericworkflownodes/CTDopts
+    ```
+
+ * add CTDopts to your `$PYTHONPATH`
+
+    ```bash
+    export PYTHONPATH=/home/user/CTDopts/
+    ```
+
+ * clone or install GalaxyConfigGenerator
+
+    ```bash
+    git clone https://github.com/TorHou/GalaxyConfigGenerator.git
+    ```
+    
+ * If you have CTDopts and GalaxyConfigGenerator installed you are ready to generate Galaxy Tools from CTD definitions
+
+    ```bash
+    python ./galaxyconfiggenerator/generator.py \ 
+    -i /PATH/TO/YOUR/CTD*.ctd \
+    -o ./wrappers -t tool.conf \
+    -d OpenMS -g proteomics \
+    -b version log debug test no_progress threads \
+     in_type exe executable myrimatch_executable \
+     omssa_executable pepnovo_executable \
+     xtandem_executable \
+    -l ListOfNeededTools.txt
+    ```
+
+The list of needed Tools is a whitelist of all Tools that you want to create. It's simply a list of all tools separated by line breaks.
+An example file is located under https://gist.github.com/bgruening/421f97d36c27443e5f35
+
+
+ * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example:
+
+    ```
+    sed -i '10 a\-exe fido' wrappers/FidoAdapter.xml
+    sed -i '10 a\-executable msgfplus.jar' wrappers/MSGFPlusAdapter.xml
+    sed -i '10 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml
+    sed -i '10 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml
+    sed -i '10 a\-pepnovo_executable pepnovo' wrappers/PepNovoAdapter.xml
+    sed -i '10 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml
+    ```
+
+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.
+