<tool id="ctb_np-likeness-calculator" name="Natural Product" version="0.2.1">
    <description>likeness calculator</description>
    <!--<parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile,outfragments"></parallelism>-->
    <requirements>
        <requirement type="package" version="2.0">np-likeness-scorer</requirement>
    </requirements>
    <command>
        ## NPLC is really picky with file extensions. We need to specify every datatype as file extension
        ## A workaround is to create a symlink with a proper file-extension.
        #import tempfile
        #set $temp_file = tempfile.NamedTemporaryFile()
        #set $temp_link = "%s.%s" % ($temp_file.name, $infile.ext)
        $temp_file.close()
        ln -s $infile $temp_link;

        java -jar \$NPLS_JAR_PATH/NP-Likeness-2.0.jar
            -in "${temp_link}"
            -out "${outfile}"
            #if $reconstruct_fragments:
                -reconstructFragments true
                -outFragments $outfragments
            #end if
        ;
        rm $temp_link
    </command>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <inputs>
        <param format="smi,sdf" name="infile" type="data" label="Molecule file" help="Dataset missing? See TIP below"/>
        <param name='reconstruct_fragments' type='boolean' label='Fragments-scores are written out in SMILES format' truevalue='' falsevalue='' />
    </inputs>
    <outputs>
        <data format_source="infile" name="outfile" />
        <data format="tabular" name="outfragments">
            <filter>reconstruct_fragments is True</filter>
        </data>
    </outputs>
    <tests>
    </tests>
    <help>


.. class:: infomark

**What this tool does**

The `Natural-Product-Likeness Scorer`_ calculates the Natural Product(NP)-likeness of a molecule, i.e. the similarity of the molecule to the structure space covered by known natural products. The more positive the score, the higher is the NP-likeness and vice versa.

.. _Natural-Product-Likeness Scorer: http://sourceforge.net/projects/np-likeness/

.. image:: $PATH_TO_IMAGES/score_distribution.png


-----

.. class:: infomark

**Cite**

| KV Jayaseelan, C Steinbeck, P Moreno, A Truszkowski, P Ertl - `Natural product-likeness score revisited: an open-source, open-data implementation`_
| 
| P Ertl, S Roggo, and A Schuffenhauer - `Natural product-likeness score and its application for prioritization of compound libraries`_

.. _`Natural product-likeness score revisited: an open-source, open-data implementation`: http://www.biomedcentral.com/1471-2105/13/106/abstract
.. _`Natural product-likeness score and its application for prioritization of compound libraries`: http://www.ncbi.nlm.nih.gov/pubmed/18034468

    </help>
</tool>