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

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<tool id="ctb_remDuplicates" name="Remove duplicated 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
      --unique "${descriptor}"
      -O "${outfile}"
      -e
      2>&1
]]>
  </command>
  <inputs>
    <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Molecular input file"/>
    <param name="descriptor" type="select" label="Select descriptor for molecule comparison">
      <option value="inchi" checked="True">InChI (default)</option>
      <option value="cansmi">Canonical SMILES</option>
      <option value="cansmiNS">Canonical SMILES (without stereo)</option>
    </param>
  </inputs>
  <outputs>
    <data format_source="infile" name="outfile"/>
  </outputs>
  <tests>
    <test>
        <param name="infile" ftype="smi" value="2_mol.smi"/>
            <param name="descriptor" value="inchi" />
        <output name="outfile" ftype="smi" file="ob_remDuplicates_on_2_mol.smi" />
    </test>
  </tests>
  <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Filters a library of compounds and removes duplicated molecules.

-----

.. class:: warningmark

**Hint**

Comparison based on Canonical SMILES without stereochemistry may be useful in cases where this information is not crucial for library preparation. Several VS tools will automatically generate stereoisomeric forms.

-----

.. class:: infomark

**Input**

| - `InChI`_
| - `SMILES Format`_

.. _InChI: http://www.iupac.org/home/publications/e-resources/inchi.html
.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification

-----

.. 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>