<tool id="biobb_mdrun" name="Mdrun" version="0.1.5" >
    <description>: performs molecular dynamics simulations from an input Gromacs TPR file. </description>
    <requirements>
        <requirement type="binary">docker</requirement>
    </requirements>
   <command detect_errors="aggressive">
   ln -f -s ${inputname} ${inputname}.${inputname.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 mdrun --input_tpr_path $inputname.${inputname.ext} 
    #if $config.sele == "option1":
	--config ${config.properties}.${config.properties.ext}
    #else if $config.sele == "option2":
	--config ${config.jsonstr}
    #end if
    --output_log_path $__root_dir__/database/files/000/$outname_log
    --output_gro_path $__root_dir__/database/files/000/$outname
    --output_trr_path $__root_dir__/database/files/000/$outname_trr
    --output_edr_path $__root_dir__/database/files/000//$outname_edr
    --output_xtc_path $__root_dir__/database/files/000/$outname_xtc
    --output_cpt_path $__root_dir__/database/files/000/$outname_cpt;
    #if $config.sele == "option1":
	rm -f ${config.properties}.${config.properties.ext};
    #end if
rm -f ${inputname}.${inputname.ext};
mv  $__root_dir__/database/files/000/$outname $output;
mv  $__root_dir__/database/files/000/$outname_trr $output_trr;
mv  $__root_dir__/database/files/000//$outname_edr $output_edr;
mv  $__root_dir__/database/files/000/$outname_xtc $output_xtc;
mv  $__root_dir__/database/files/000/$outname_cpt $output_cpt;
mv  $__root_dir__/database/files/000/$outname_log $output_log
    </command>
    <inputs>
       <param name="inputname" type="data" format="tpr"  label="TPR file" help="Select your portable binary run input file. Format: [input].tpr"/> 
       <param name="outname" type="text" value="mdrun.gro" label="Output GRO name" help="Name for the Output GROMACS structure. Format: [output].gro "/>
       <param name="outname_trr" type="text" value="mdrun.trr" label="Output TRR name" help="Name for the Output GROMACS uncompressed raw. Format: [output].trr"/> 
       <param name="outname_edr" type="text" value="mdrun.edr" label="Output EDR name" help="Name for the Output GROMACS portable energy file. Format: [output].edr"/>
       <param name="outname_xtc" type="text" value="mdrun.xtc" optional="True" label="Output XTC name" help="Name for the Output GROMACS compressed trajectory file. Format: [output].xtc"/>
       <param name="outname_cpt" type="text" value="mdrun.cpt" optional="True" label="Output CPT name" help="Name for the Output GROMACS checkpoint file. Format: [output].cpt"/>
       <param name="outname_log" type="text" value="mdrun.log" label="Output LOG name" help="Name for the Output GROMACS trajectory file. Format: [output].log"/>
        <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" format="gro" label="${outname}"/>
        <data name="output_trr" format="trr" label="${outname_trr}"/>
        <data name="output_edr" format="edr" label="${outname_edr}"/>
        <data name="output_xtc" format="xtc" label="${outname_xtc}"/>
        <data name="output_cpt" format="cpt" label="${outname_cpt}"/>
        <data name="output_log" format="log" label="${outname_log}"/>
    </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.mdrun

-----

.. 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>