comparison confab.xml @ 27:7198475e0755 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit ed9b6859de648aa5f7cde483732f5df20aaff90e

26:b0a28a5fd431

        '${infile}'
        -O '${outfile}'
        -i ${infile.ext}
        -o sdf
        --confab
        --rcutoff $RMSD
        --ecutoff $energy
        --conf $conformers
        $first_conformer

]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/>
        <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
        <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
        <param name='conformers' type='integer' value='100' label='Max number of conformers to test' />
        <param name='first_conformer' type='boolean' truevalue='--original' falsevalue=''
            label='Include the input conformation as the first conformer' />
    </inputs>
    <outputs>
        <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>

.. class:: infomark

**What this tool does**

Confab_ is a conformation generator. The algorithm starts with an input 3D structure which, after some initialisation steps, is used to generate multiple conformers which are filtered on-the-fly to identify diverse low energy conformers.

.. _Confab: https://code.google.com/p/confab/

-----

.. class:: infomark

27:7198475e0755

        '${infile}'
        -O '${outfile}'
        -i ${infile.ext}
        -o sdf
        --confab
        --verbose
        --rcutoff $RMSD
        --ecutoff $energy
        --conf $conformers
        $first_conformer

]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates in SDF or MOL2 format" help="Dataset missing? See TIP below"/>
        <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (Å)' help='Minimum RMSD deviation from the original conformation in order to be classified as a separate conformer.'/>
        <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' help='Minimum energy difference to the original conformation in order to be classified as a separate conformer.'/>
        <param name='conformers' type='integer' value='1000000' label='Max number of conformers to test' />
        <param name='first_conformer' type='boolean' truevalue='--original' falsevalue=''
            label='Include the input conformation as the first conformer' help='If yes, the original conformation is included in the output file'/>
    </inputs>
    <outputs>
        <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>

.. class:: infomark

**What this tool does**

Confab_ is a conformation generator. The algorithm starts with an input 3D structure which, after some initialization steps, is used to generate multiple conformers, which are filtered on-the-fly to identify diverse low-energy conformers.

.. _Confab: https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html#confab

-----

.. class:: infomark