annotate md_converter.xml @ 1:f40eb1f8536f draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"

<tool id="md_converter" name="MDTraj file converter" version="1.9.3">

    <description>- interconvert between MD trajectory or structure file formats.</description>

    <requirements>
        <requirement type="package" version="1.9.3">mdtraj</requirement>
        <requirement type="package" version="2019.1">gromacs</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[

        #if $input.conversion == 'str':
            ln -s '$input_file' ./input.$input_file.ext &&
            gmx editconf -f ./input.$input_file.ext -o ./output.${input.output_format} &&
            cp ./output.${input.output_format} $output
        #end if

        #if $input.conversion == 'traj':
            ln -s '$input_file' ./input.$input_file.ext &&
            mdconvert ./input.$input_file.ext -o ./output.${input.output_format} &&
            cp ./output.${input.output_format} $output
    
        #end if

    ]]></command>
    <inputs>
        <conditional name="input">
            <param argument="conversion" type="select" label="Type of conversion">
                <option value="traj">Trajectory file</option>
                <option value="str">Structure file</option>
            </param>
            <when value="traj">
                <param argument="input_file" type="data" format='xtc, trr, dcd' label="Input file for conversion"/>
                <param argument="output_format" type="select" label="Output format">
                    <option value="trr">TRR file</option>
                    <option value="xtc">XTC file</option>
                    <option value="dcd">DCD file</option>
                </param>
            </when>
            <when value="str">
                <param argument="input_file" type="data" format='gro, pdb' label="Input file for conversion"/>
                <param argument="output_format" type="select" label="Output format">
                    <option value="gro">GRO file</option>
                    <option value="pdb">PDB file</option>
                </param>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="output">
            <change_format>
                <when input="output_format" value="gro" format="gro"/>
                <when input="output_format" value="pdb" format="pdb"/>
                <when input="output_format" value="trr" format="trr"/>
                <when input="output_format" value="xtc" format="xtc"/>
                <when input="output_format" value="dcd" format="dcd"/>
            </change_format>
        </data>
    </outputs> 

    <tests>
        <test>
            <param name="conversion" value="traj" />
            <param name="output_format" value="dcd" />
            <param name="input_file" value="traj.xtc" ftype="xtc"/>
            <output name="output" file="traj.dcd" compare="sim_size"/>
        </test>
        <test>
            <param name="conversion" value="traj" />
            <param name="output_format" value="trr" />
            <param name="input_file" value="traj.dcd" ftype="dcd"/>
            <output name="output" file="traj.trr"/>
        </test>
        <test>
            <param name="conversion" value="str" />
            <param name="output_format" value="gro" />
            <param name="input_file" value="str.pdb" ftype="pdb"/>
            <output name="output" file="str.gro" compare="sim_size"/>
        </test>
        <test>
            <param name="conversion" value="str" />
            <param name="output_format" value="pdb" />
            <param name="input_file" value="str.gro" ftype="gro"/>
            <output name="output" file="str2.pdb" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**
        
This tool interconverts between MD file formats: xtc, trr and dcd (trajectory formats) and pdb and gro (structure formats).

_____


.. class:: infomark

**Input**

       - Trajectory file (trr, xtc, dcd) or structure file (pdb, gro)
     
_____

        
.. class:: infomark

**Output**

       - Trajectory file (trr, xtc, dcd) or structure file (pdb, gro)
    ]]></help>
    <citations>
        <citation type="doi">10.1016/j.bpj.2015.08.015</citation>
        <citation type="doi">10.1016/j.softx.2015.06.001</citation>
    </citations>
</tool>