<tool id="biobb_grompp" name="Grompp" version="0.1.5" >
    <description>:Gromacs preprocessor. Reads topology file to create TPR atomic description</description>
    <requirements>
        <requirement type="binary">docker</requirement>
    </requirements> 
   <command detect_errors="aggressive">
   ln -f -s ${inputname} ${inputname}.${inputname.ext};
   ln -f -s ${inputzip} ${inputzip}.${inputzip.ext};
   ln -f -s ${inputgro} ${inputgro}.${inputgro.ext};
    #if $config.sele == "option1":
	ln -s -f ${config.properties} ${config.properties}.${config.properties.ext};
    #end if
    docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 grompp --input_cpt_path $inputname.${inputname.ext} --input_top_zip_path  ${inputzip}.${inputzip.ext} --input_gro_path ${inputgro}.${inputgro.ext}
    #if $config.sele == "option1":
	--config ${config.properties}.${config.properties.ext}
    #else if $config.sele == "option2":
	--config ${config.jsonstr}
    #end if
    --output_tpr_path $__root_dir__/database/files/000/$outname;
    #if $config.sele == "option1":
	rm -f ${config.properties}.${config.properties.ext};
    #end if
  rm -f ${inputname}.${inputname.ext} ${inputzip}.${inputzip.ext} ${inputgro}.${inputgro.ext};
  mv $__root_dir__/database/files/000/$outname $output_tpr
    </command>
    <inputs>
       <param name="inputgro" type="data" format="gro"  label="Structure file" help="Select your input GROMACS structure file. Format: [input].gro"/>
       <param name="inputzip" type="data" format="zip"  label="Topology file" help="Select your input GROMACS topology TOP and ITP file. Format: [input].zip"/>
       <param name="inputname" type="data" format="cpt"  label="Check point file" optional="True" help="Select your input GROMACS checkpoint file. Format: [input].cpt"/>
       <param name="outname" type="text" value="myGrompp.tpr" label="Output TPR name" help="Name for the Output binary run file. Format: [output].tpr "/>
        <conditional name="config">
	    <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
	        <option value="option1">from configuration file</option>
	        <option value="option2">from JSON string</option>
                <option value="option3" selected="true">by default</option>
	    </param>
	    <when value="option1">
	        <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
	    </when>
	    <when value="option2">
	        <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
	    </when>
	    <when value="option3">
	    </when>
	</conditional>
    </inputs>
    <outputs>
        <data name="output_tpr" format="tpr" label="${outname}"/>
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>
.. class:: warningmark


Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp

-----

.. image:: ${static_path}/images/biobb.png
    :height: 57
    :width: 150


**https://bioexcel.eu**
   </help>
   <citations>
        <citation type="bibtex">
@misc{githubbiobb,
  author = {Andrio P, Hospital A, Gelpi JL},
  year = {2019},
  title = {biobb: BioExcel building blocks },
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/bioexcel/biobb_io},
}</citation>
 </citations>
</tool>