comparison macros.xml @ 15:ea0e6d2f1be7 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0"

14:525ca7c8065f

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement>
        </requirements>
    </xml>

    <token name="@MAXWARN_CMD@">-maxwarn '$mxw'</token>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1016/j.softx.2015.06.001</citation>

                <param argument="coulombtype" type="select" label="Electrostatics">
                    <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
                    <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
                    <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
                </param>
                
                <param argument="temperature" type="integer" label="Temperature /K" value="0" min="0" max="1000000" help="Temperature" />
                <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." />
                <param argument="write_freq" type="integer" label="Number of steps that elapse between saving data points (velocities, forces, energies)" value="0" min="0" max="1000000" help="Step length in ps." />
                <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
                <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/>
                <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
                <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" />
                
            </when>

        </conditional>

    </xml>

    <xml name="maxwarn">
        <param name="mxw" value="0" min="0" argument="-maxwarn" type="integer" label="Maximum warnings to allow." help="Do not use this unless you know what you are doing. This option allows you to override non-fatal warnings, that would otherwise cause the simulation to fail."/>
    </xml>

    <xml name="log_outputs">
        <data name="report" format="txt" from_work_dir="verbose.txt" label="GROMACS log file on ${on_string}">
            <filter>capture_log</filter>
        </data>

15:ea0e6d2f1be7

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement>
        </requirements>
    </xml>
    <token name="@MAXWARN_CMD@">-maxwarn '$mxw'</token>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1016/j.softx.2015.06.001</citation>

                <param argument="coulombtype" type="select" label="Electrostatics">
                    <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
                    <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
                    <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
                </param>
                <param name="temperature" type="integer" label="Temperature (K)" value="0" min="0" max="1000000" help="Temperature" />
                <param name="systemTcouple" type="select" label="Number of groups to set for thermocoupling">
                    <option value="true">Single coupling group (System)</option>
                    <option value="false" selected="true">Two coupling groups (Protein and Non-Protein)</option>
                </param>
                <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." />
                <param argument="write_freq" type="integer" label="Number of steps that elapse between saving data points (velocities, forces, energies)" value="0" min="0" max="1000000" help="Step length in ps." />
                <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
                <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/>
                <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
                <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" help="MD steps" />
                
            </when>

        </conditional>

    </xml>

    <xml name="maxwarn">
        <param name="mxw" value="0" min="0" argument="-maxwarn" type="integer" label="Maximum warnings to allow." help="Do not use this unless you know what you are doing. This option allows you to override non-fatal warnings, that would otherwise cause the simulation to fail."/>
    </xml>


    <xml name="log_outputs">
        <data name="report" format="txt" from_work_dir="verbose.txt" label="GROMACS log file on ${on_string}">
            <filter>capture_log</filter>
        </data>