annotate select_points_SDF.xml @ 2:7255688c77f3 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"

<tool id="ctb_frankenstein_ligand" name="Create Frankenstein ligand" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>for docking active site definition</description>
    <macros>
        <import>rdock_macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/select_points_SDF.py'
            -i '$infile'
            -o '$outfile'
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
    </inputs>    
    <outputs>
        <data name="outfile" format="sdf"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="input.sdf" ftype="sdf"/>
            <output name="outfile" ftype='sdf' file="select_points_output.sdf"/>
        </test>
        <test>
            <param name="infile" value="input_v3000.sdf" ftype="sdf"/>
            <output name="outfile" ftype='sdf' file="select_points_output_v3000.sdf"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

Converts an SD file containing multiple molecules into a 'Frankenstein ligand' with a 3D shape combining all ligands, which can be used for definition of an active site with rDock.

This tool is based on a Perl script originally written by Peter Schmidtke.

_____

.. class:: infomark

**Input**

       - SD file containing multiple molecules.

_____
        
.. class:: infomark

**Output**

       - SD file containing the 'Frankenstein ligand'.
    ]]></help>
       <citations>
            <citation type="doi">10.1371/journal.pcbi.1003571</citation>
            <citation type="bibtex">
            @article{rdock,
                author = {Peter Schmidtke},
                title = {'Select points' script for generation of a Frankenstein ligand},
                url = {https://github.com/InformaticsMatters/docking-validation/blob/master/scripts/select_points_SDF.pl}
        }</citation>
       </citations>
</tool>