view filter/ob_remSmall.xml @ 2:125da3a296ca draft default tip

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<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>
<![CDATA[
    obabel
      -i"${infile.ext}"
      "${infile}"
      -ocopy
      -O "${outfile}"
      --filter "atoms > $cutoff"
      -e
      2>&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>
<![CDATA[

.. class:: infomark

**What this tool does**

Filters a library of compounds and removes small molecules below a predefined input number of atoms.

-----

.. class:: warningmark

**Hint**

Some libraries may contain molecules without a 1D/3D descriptor. These molecules may provoke crashes of any other tool. It is strongly adviced to run this tool before proceeding to any further steps.

-----

.. class:: infomark

**Output**

Same as input format.

-----

.. class:: infomark

**Cite**

N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_

.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33

`Open Babel`_

.. _`Open Babel`: http://openbabel.org/wiki/Main_Page

]]>
    </help>
</tool>