comparison editconf.xml @ 3:0876b56a3b3d draft

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2:2f9bc346f824

            -o ./output.${output_format}
            #if $box.config == "true":
                -d $box.dim 
                -bt $box.type
            #end if
            &>> verbose.txt &&

        cp ./output.${output_format} '$output'

    ]]></command>

            <option value="gro">GRO file</option>
            <option value="pdb">PDB file</option>
        </param>
        
        <conditional name="box">
            <param argument="config" type="select" label="Configure box?">
                <option value="true">Yes</option>
                <option value="false" selected="true">No</option>
            </param>
            <when value="true">
                <param argument="dim" type="float" label="Box dimensions in nanometers" value="0.0" min="0.0" max="1000.0" help="Dimensions of the box in which simulation will take place" />

3:0876b56a3b3d

            -o ./output.${output_format}
            #if $box.config == "true":
                -d $box.dim 
                -bt $box.type
            #end if
            #if $sbox.config == "true":
                -box $sbox.dim 
                -bt $box.type
            #end if
            &>> verbose.txt &&

        cp ./output.${output_format} '$output'

    ]]></command>

            <option value="gro">GRO file</option>
            <option value="pdb">PDB file</option>
        </param>
        
        <conditional name="box">
            <param argument="config" type="select" label="Configure distance-based box?">
                <option value="true">Yes</option>
                <option value="false" selected="true">No</option>
            </param>
            <when value="true">
                <param argument="dim" type="float" label="Size to be added to the dimensions of the system" value="0.0" min="0.0" max="1000.0" help="Size to be added to the dimension of the system" />
                <param argument="type" type="select" label="Box type"
                    help="triclinic is a triclinic box, cubic is a rectangular box with all sides equal dodecahedron represents a rhombic dodecahedron and octahedron is a truncated octahedron. The last two are special cases of a triclinic box. The length of the three box vectors of the truncated octahedron is the shortest distance between two opposite hexagons. Relative to a cubic box with some periodic image distance, the volume of a dodecahedron with this same periodic distance is 0.71 times that of the cube, and that of a truncated octahedron is 0.77 times.">
                    <option value="cubic">Rectangular box with all sides equal</option>
                    <option value="triclinic">Triclinic</option>
                    <option value="dodecahedron">represents a rhombic dodecahedron</option>
                    <option value="octahedron">truncated octahedron</option>
                </param>
            </when>
            <when value="false"/>
        </conditional>

        <conditional name="sbox">
            <param argument="config" type="select" label="Configure size-based box?">
                <option value="true">Yes</option>
                <option value="false" selected="true">No</option>
            </param>
            <when value="true">
                <param argument="dim" type="float" label="Box dimensions in nanometers" value="0.0" min="0.0" max="1000.0" help="Dimensions of the box in which simulation will take place" />