view filter/ob_remSmall.xml @ 11:77b82f259298

ChemicalToolBoX update.

<tool id="ctb_remSmall" name="Remove small molecules" version="1.0">
    <description></description>
    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
    <requirements>
        <requirement type="package" version="2.3.2">openbabel</requirement>
    </requirements>
    <command>
    obabel
      -i"${infile.ext}"
      "${infile}"
      -ocopy
      -O "${outfile}"
      --filter "atoms > $cutoff"
      -e
      2>&#38;1
    </command>
    <inputs>
        <param name="infile" format="sdf,mol,mol2,cml,inchi,smi" type="data" label="Molecular input file" />
        <param name="cutoff" size="3" type="integer" value="5" label="Specify the cut-off value (only molecules with more than this number of atoms will pass the filter)" />
    </inputs>
    <outputs>
        <data format_source="infile" name="outfile" />
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype="smi" value="3_mol.smi" />
            <param name="cutoff" value="5" />
            <output name="outfile" ftype="smi" file="obremsmall_on_3_mol.smi" />
        </test>
    </tests>
    <help>

.. class:: infomark

**What does this tool do?**

  This tool filters a library of compounds and removes small molecules.

-----

.. class:: warningmark

**Tip:** some libraries may contain molecules without 1D/3D descriptor. These molecules may provoke the crashing of any other tool. As a general rule, the user is strongly adviced to run this tool before proceeding to any further step.

-----

.. class:: infomark

**Output format:** is the same as the input file format.

-----

**This tool uses OpenBabel:** The Open Babel Package, version 2.3.0 http://openbabel.sourceforge.net/

    </help>
</tool>