comparison readme.md @ 4:472809ff333b draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64

3:20d8fceb0c05

     in_type executable myrimatch_executable \
     fido_executable fidocp_executable \
     omssa_executable pepnovo_executable \
     xtandem_executable param_model_directory \
     java_executable java_memory java_permgen \
    -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 fido_choose_parameters' wrappers/FidoAdapter.xml
    sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml
    sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml
    sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml
    ```
    

    
    [...]
    ]]>
    ```
    
 * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
 
   ```
    <command><![CDATA[
   

4:472809ff333b

     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 \
    -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
    sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml
    sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml
    ```
    

    
    [...]
    ]]>
    ```
    
 * In `MetaProSIP.xml` add `R` as a requirement:
 
   ```
   <expand macro="requirements">
       <requirement type="package" version="3.3.1">r-base</requirement>
   </expand>
   ```
   
 * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
 
   ```
    <command><![CDATA[