comparison readme.md @ 12:d5f9567d0e1c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

11:f88a8c2335a6

    ```

 * clone or install CTD2Galaxy

    ```bash
    git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
    ```
    
 * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it.

    ```bash
    python generator.py \ 
    -i /PATH/TO/YOUR/CTD/*.ctd \
    -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \
    -d datatypes_conf.xml -g openms \
    -b version log debug test no_progress threads \
     in_type executable myrimatch_executable \
     fido_executable fidocp_executable \
     omssa_executable pepnovo_executable \
     xtandem_executable param_model_directory \
     java_executable java_memory java_permgen \
     r_executable rt_concat_trafo_out param_id_pool \
    -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \
    -s PATH/TO/SKIP_TOOLS_FILES.txt
    ```


 * 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 '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml
    sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml
    sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml

            <param name="param_in" value="DecoyDatabase_input.fasta"/>
            <output name="param_out" file="DecoyDatabase_output.fasta"/>
        </test>
    </tests>
    ```
    

 * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in
   by the automatic conversion step and are therefore in `SKIP_TOOLS_FILES.txt`:
    * SeedListGenerator
    * SpecLibSearcher
    * MapAlignerIdentification
    * MapAlignerPoseClustering
    * MapAlignerSpectrum
    * MapAlignerRTTransformer
    
 * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well:
    * OMSSAAdapter
    * MyrimatchAdapter
    

12:d5f9567d0e1c

    ```

 * clone or install CTD2Galaxy

    ```bash
    git clone https://github.com/WorkflowConversion/CTDConverter.git
    ```
    
 * If you have CTDopts and CTDConverter installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. Further information can be found on the CTDConverter page.

    ```bash
    python convert.py galaxy \ 
    -i /PATH/TO/YOUR/CTD/*.ctd \
    -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \
    -d datatypes_conf.xml -g openms \
    -b version log debug test no_progress threads \
     in_type executable myrimatch_executable \
     fido_executable fidocp_executable \
     omssa_executable pepnovo_e xecutable \
     xtandem_executable param_model_directory \
     java_executable java_memory java_permgen \
     r_executable rt_concat_trafo_out param_id_pool \
    -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \
    -s PATH/TO/tools_blacklist.txt
    ```


 * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. Some of these tools might already be deprecated and the files might not exist:

    ```
    sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml
    sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml
    sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml

            <param name="param_in" value="DecoyDatabase_input.fasta"/>
            <output name="param_out" file="DecoyDatabase_output.fasta"/>
        </test>
    </tests>
    ```
    
 * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well:
    * OMSSAAdapter
    * MyrimatchAdapter