annotate biobb_pdb2gmx.xml @ 2:4c626e984fde draft default tip

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<tool id="biobb_pdb2gmx" name="Pdb2gmx" version="0.1.5" >
    <description>: creates a ZIP Gromacs topology from a given PDB 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 pdb2gmx --input_pdb_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_gro_path $__root_dir__/database/files/000/$outname
    --output_top_zip_path $outputzip;
    #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
    </command>
    <inputs>
       <param name="outname" type="text" value="myPdb2gmx.gro" label="Output GRO name" help="Name for the Output GRO. Format: [output].gro "/>
       <param name="outzip" type="text" value="myPdb2gmx.zip" label="Output ZIP name" help="Name for the Output TOP topology. Format: [output].zip"/> 
       <param name="inputname" type="data" format="pdb"  label="Input PDB file" help="Select your input PDB file. Format: [input].pdb"/> 
        <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="${outname}"/>
        <data name="outputzip" format="zip" label="${outzip}"/>
    </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.pdb2gmx

-----

.. 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>