view natural_product_likeness_calculator.xml @ 9:92fd361bb36b

upgrade to version 2.0

<tool id="ctb_np-likeness-calculator" name="Natural Product" version="0.1">
    <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>
        java -jar \$JAVA_JAR_PATH/NPLikenessCalculator-2.0.jar 
            -in "${infile}"
            -out "${outfile}"
            #if $reconstruct_fragments:
                -reconstructFragments true
                -outFragments $outfragments
            #end if
    </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="sdf" name="outfile" />
        <data format="tabular" name="outfragments">
            <filter>reconstruct_fragments is True</filter>
        </data>
    </outputs>
    <tests>
    </tests>
    <help>


.. class:: infomark

**INFO:** The more positive the score, the higher is the NP-likeness and vice versa.

.. image:: $PATH_TO_IMAGES/score_distribution.png


**What it is**

The `Natural-Product-Likeness Scorer`_ is an open-source, open-data re-implementation of 
Peter Ertls previous work [2] and calculates a natural product-likeness score.

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

-----

    
**Cite**
[1] KV Jayaseelan, C Steinbeck, P Moreno, A Truszkowski, P Ertl, Natural product-likeness score revisited:
an open-source, open-data implementation, BMC Bioinformatics 2012, 13:106

http://www.biomedcentral.com/1471-2105/13/106/abstract

[2] P Ertl, S Roggo, and A Schuffenhauer, Natural product-likeness score and its application for prioritization
of compound libraries., J. Chem. Inf. Model, 2008 vol. 48 (1) pp. 68-74

http://www.ncbi.nlm.nih.gov/pubmed/18034468

    </help>
</tool>