annotate energy.xml @ 9:97872d87ba80 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit bf18581ac3de6b65bdc0a988e6f844cea6e77975"

<tool id="gmx_energy" name="Extract energy components with GROMACS" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>

    <expand macro="requirements" />

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

        ln -s '$edr_input' ./edr_input.edr &&
        echo #echo str($terms).replace(',', ' ')# | gmx energy -f ./edr_input.edr -o ./energy.xvg
        ## echo #echo ' '.join(str($terms).split(','))# | gmx energy -f ./edr_input.edr -o ./energy.xvg
        #if $fmt == 'tabular':
            &&
            grep '@\|#' energy.xvg &&
            grep -v '@\|#' energy.xvg | sed 's/[[:space:]]*//' | sed  's/  /\t/g' > energy.tabular
        #end if

    ]]></command>

    <inputs>
        <param argument="edr_input" type="data" format="edr" label="EDR file" help="GROMACS energy binary file"/>
        <param argument="terms" type='select' label="Terms to calculate" multiple="true" help="Select terms for which values should be calculated.">
            <option value="1">Angle</option>
            <option value="2">Proper dihedrals</option>
            <option value="3">Ryckaert-Bellemans dihedrals</option>
            <option value="4">Lennard-Jones (1-4 interactions)</option>
            <option value="5">Coulomb (1-4 interactions)</option>
            <option value="6">Lennard-Jones energies (short range)</option>
            <option value="7">Dispersion correction</option>
            <option value="8">Coulomb (short range)</option>
            <option value="9">Reciprocal Coulomb energy</option>
            <option value="10" selected="True">Potential</option>
            <option value="11">Kinetic energy</option>
            <option value="12">Total energy</option>
            <option value="13">Temperature</option>
            <option value="14">Pressure DC</option>
            <option value="15">Pressure</option>
            <option value="16">Constr. RMSD</option>
            <option value="17">Box-X</option>
            <option value="18">Box-Y</option>
            <option value="19">Box-Z</option>
            <option value="20">Volume</option>
            <option value="21">Density</option>
            <option value="22">pV</option>
            <option value="23">Enthalpy</option>
            <option value="24">Virial(XX)</option>
            <option value="25">Virial(XY)</option>
            <option value="26">Virial(XZ)</option>
            <option value="27">Virial(YX)</option>
            <option value="28">Virial(YY)</option>
            <option value="29">Virial(YZ)</option>
            <option value="30">Virial(ZX)</option>
            <option value="31">Virial(ZY)</option>
            <option value="32">Virial(ZZ)</option>
            <option value="33">Pressure(XX)</option>
            <option value="34">Pressure(XY)</option>
            <option value="35">Pressure(XZ)</option>
            <option value="36">Pressure(YX)</option>
            <option value="37">Pressure(YY)</option>
            <option value="38">Pressure(YZ)</option>
            <option value="39">Pressure(ZX)</option>
            <option value="40">Pressure(ZY)</option>
            <option value="41">Pressure(ZZ)</option>
            <option value="42">Surface tension</option>
            <option value="43">Box-Vel-XX</option>
            <option value="44">Box-Vel-YY</option>
            <option value="45">Box-Vel-ZZ</option>
            <option value="46">Protein temperature</option>
            <option value="47">Non-protein temperature</option>
            <option value="48">Protein lambda values</option>
            <option value="49">Non-protein lambda values</option>
        </param>
        <param argument="fmt" type='select' label="Output format" help="Format for output; either standard GROMACS XVG, or Galaxy tabular file.">
            <option value="xvg">GROMACS XVG format</option>
            <option value="tabular" selected="true">Galaxy tabular</option>
        </param>

    <expand macro="log" />

    </inputs>
    <outputs>
        <data name="output1" format="xvg" from_work_dir="energy.xvg">
            <filter>fmt == 'xvg'</filter>
        </data>
        <data name="output2" format="tabular" from_work_dir="energy.tabular">
            <filter>fmt == 'tabular'</filter>
        </data>
        <expand macro="log_outputs" />
    </outputs>
    <tests>
        <test>
            <param name="edr_input" value="outp.edr" />
            <param name="terms" value="10,12,13" />
            <param name="fmt" value="xvg" />
            <output name="output1" file="outp.xvg" ftype="xvg" lines_diff="12"/>
        </test>
        <test>
            <param name="edr_input" value="outp.edr" />
            <param name="terms" value="10,12,13" />
            <param name="fmt" value="tabular" />
            <output name="output1" file="outp.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

This tool extracts energy components from an energy (EDR) binary file. A list of terms to select is provided.

_____

.. class:: infomark

**Input**

       - EDR binary file.
       - Selection of terms to extract.
     
_____

        
.. class:: infomark

**Output**

       - Tabular or XVG file containing selected terms and some header lines

    ]]></help>

    <expand macro="citations" />
</tool>