comparison readme.md @ 1:85a6d0d7872b draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

0:a5e996f13660

    ```

 * clone or install CTD2Galaxy

    ```bash
    git clone https://github.com/blankclemens/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. 

    ```bash
    python generator.py \ 
    -i /PATH/TO/YOUR/CTD/*.ctd \
    -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \

    #end if
    
    [...]
    ]]>
    ```
 * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line
 
        -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit
     
   and change it to
   
        -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit"

 * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
 
        <data name="param_out" metadata_source="param_in" auto_format="true"/>
        

1:85a6d0d7872b

    ```

 * 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.

    ```bash
    python generator.py \ 
    -i /PATH/TO/YOUR/CTD/*.ctd \
    -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \

    #end if
    
    [...]
    ]]>
    ```

 * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
 
        <data name="param_out" metadata_source="param_in" auto_format="true"/>