<tool id="ctb_stripit" name="Strip-it" version="1.0.1">
    <description> extracts predefined scaffolds from molecules</description>
    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism>
    <requirements>
        <requirement type="package" version="2.3.2">openbabel</requirement>
        <requirement type="package" version="1.0.1">silicos_it</requirement>
    </requirements>
    <command>
        strip-it --inputFormat ${infile.ext} --input $infile --output $outfile --noLog --noHeader 2>&#38;1
    </command>
    <inputs>
        <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" />
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="infile" type='sdf' value="CID_3037.sdf"/>
            <data name="output" type="tabular" file="Strip-it_on_CID3037.tabular" />
        </test>
    </tests>
    <help>


.. class:: infomark

**What this tool does**

Strip-it is a program that extracts predefined scaffolds from organic small
molecules.

The program comes with a number of predefined molecular scaffolds for
extraction. These scaffolds include, amongst others

    - `molecular frameworks`_ as originally described by Bemis and
      Murcko
    - `molecular frameworks and the reduced molecular frameworks`_ as
      described by Ansgar Schuffenhauer and coworkers
    - `scaffold topologies`_ as described by Sara Pollock and coworkers

.. _molecular frameworks: http://www.ncbi.nlm.nih.gov/pubmed/8709122
.. _molecular frameworks and the reduced molecular frameworks: http://peter-ertl.com/reprints/Schuffenhauer-JCIM-47-47-2007.pdf
.. _scaffold topologies: http://www.ncbi.nlm.nih.gov/pubmed/18605680

-----

.. class:: infomark


**Input**

| - `SD-Format`_
| - `SMILES Format`_
| - `MOL2 Format`_

.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
.. _MOL2 Format: http://www.tripos.com/data/support/mol2.pdf


-----

.. class:: infomark

**Output**

+-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
|     NAME    |            MOLECULE            | RINGS_WITH_LINKERS_1 |  RINGS_WITH_LINKERS_2  |       MURCKO_1       | ... |
+=============+================================+======================+========================+======================+=====+ 
|  Diclofenac | OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl | c1ccc(cc1)Nc1ccccc1  |   c1ccc(cc1)Nc1ccccc1  |  C1CCC(CC1)CC1CCCCC1 | ... |
+-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
| Bupivacaine | CCCCN1CCCCC1C(=O)Nc1c(C)cccc1C | C1CCC(NC1)CNc1ccccc1 | O=C(C1CCCCN1)Nc1ccccc1 | C1CCC(CC1)CCC1CCCCC1 | ... |
+-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
|     ...     |              ...               |         ...          |           ...          |          ...         | ... |
+-------------+--------------------------------+----------------------+------------------------+----------------------+-----+

-----

.. class:: infomark

**Cite**

`Silicos-it`_ - strip-it

.. _Silicos-it: http://silicos-it.com/software/strip-it/1.0.2/strip-it.html


    </help>
</tool>