view natural_product_likeness_calculator.xml @ 3:6052dd3fa475 draft default tip

"planemo upload for repository https://github.com/CS76/NP-Likeness commit 7fb96a3844b4771084f18de2346ed6d5e241d839"

<tool id="ctb_np-likeness-calculator" name="Natural Product likeness calculator" version="@TOOL_VERSION@">
    <description>- calculates the similarity of the molecule to the structure space covered by known natural products</description>
    <macros>
        <token name="@TOOL_VERSION@">2.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">np-likeness-scorer</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
        np-likeness
            -in '$infile'
            -intype $infile.ext
            -out '$outfile'
            -outtype $infile.ext
            #if $reconstruct_fragments:
                -reconstructFragments true
                -outFragments $outfragments
            #end if
    ]]>
    </command>
    <inputs>
        <param format="smi,sdf" name="infile" type="data"
            label="Molecule file" help="Dataset missing? See TIP below"/>
        <param name='reconstruct_fragments' type='boolean'
            truevalue='' falsevalue=''
            label='Write out fragments (in SMILES format) and scores?' />
    </inputs>
    <outputs>
        <data format_source="infile" name="outfile" />
        <data format="tabular" name="outfragments">
            <filter>reconstruct_fragments is True</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="CID_3037.sdf"/>
            <param name="reconstruct_fragments" value="true"/>
            <output name="outfile" file="Score.sdf" ftype="sdf" lines_diff="4"/>
            <output name="outfragments" file="fragments.sdf" ftype="tabular" compare="contains"/>
        </test>
    </tests>
    <help>
<![CDATA[

**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 the NP-likeness and vice versa.

.. _Natural-Product-Likeness Scorer: http://sourceforge.net/projects/np-likeness/
.. image:: $PATH_TO_IMAGES/score_distribution.png

]]>
    </help>
    <citations>
        <citation type="doi">10.1186/1471-2105-13-106</citation>
        <citation type="doi">10.1021/ci700286x</citation>
    </citations>
</tool>