view filter/ob_remDuplicates.xml @ 0:6493d130f018

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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>
    obabel
      -i"${infile.ext}"
       "${infile}
      -ocopy
      --unique "${descriptor}"
      -O "${outfile}"
      -e
      2>&#38;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>

.. class:: infomark

**What does this tool do?**

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

-----

.. class:: warningmark

**Tip:** 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

**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>