view select_points_SDF.xml @ 0:355c1759835c draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"

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−<tool id="ctb_frankenstein_ligand" name="Create Frankenstein ligand" version="0.1.0">
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−    <description>for docking active site definition</description>
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−    <requirements>
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−        <requirement type="package" version="3.7">python</requirement>
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−    </requirements>
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−    <command detect_errors="exit_code"><![CDATA[
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−        python '$__tool_directory__/select_points_SDF.py'
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−            -i '$infile'
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−            -o '$outfile'
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−    ]]></command>
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−    <inputs>
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−        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
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−    </inputs>    
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−    <outputs>
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−        <data name="outfile" format="sdf"/>
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−    </outputs>
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−    <tests>
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−        <test>
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−            <param name="infile" value="input.sdf" ftype="sdf"/>
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−            <output name="outfile" ftype='sdf' file="select_points_output.sdf"/>
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−        </test>
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−        <test>
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−            <param name="infile" value="input_v3000.sdf" ftype="sdf"/>
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−            <output name="outfile" ftype='sdf' file="select_points_output_v3000.sdf"/>
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−        </test>
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−    </tests>
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−    <help><![CDATA[
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−
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−.. class:: infomark
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−
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−**What it does**
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−
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−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.
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−
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−This tool is based on a Perl script originally written by Peter Schmidtke.
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−
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−_____
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−
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−.. class:: infomark
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−
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−**Input**
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−
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−       - SD file containing multiple molecules.
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−
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−_____
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−        
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−.. class:: infomark
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−
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−**Output**
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−
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−       - SD file containing the 'Frankenstein ligand'.
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−    ]]></help>
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−       <citations>
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−            <citation type="doi">10.1371/journal.pcbi.1003571</citation>
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−            <citation type="bibtex">
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−            @article{rdock,
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−                author = {Peter Schmidtke},
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−                title = {'Select points' script for generation of a Frankenstein ligand},
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−                url = {https://github.com/InformaticsMatters/docking-validation/blob/master/scripts/select_points_SDF.pl}
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−        }</citation>
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−       </citations>
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−</tool>