view sucos.xml @ 5:fe318c648502 draft

"planemo upload for repository commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:48:35 -0400
parents 2e67eea82ff7
children 4f1896782f7c
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<tool id="sucos_docking_scoring" name="Score docked poses using SuCOS" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>- compare shape and feature overlap of docked ligand poses to a reference molecule</description>
        <token name="@GALAXY_VERSION@">0</token>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/'
            -i '$input'
            -r '$refmol'
            -o '$output'
            --refmol-format mol
        <param type="data" name="input" format="sdf" label="Ligands to be scored" help="Input in SDF format." />
        <param type="data" name="refmol" format="sdf,mol" label="Reference molecule to overlay" help="Input in SDF or MOL format." />
        <param type="boolean" name="tanimoto" truevalue="--tanimoto" falsevalue="" label="Include Tanimoto calculations" help="Whether to handle the distance as Tanimoto." />
        <data format="sdf" name="output" label="The scored ligands"/>
            <param name="input" ftype="sdf" value="sucos_inputs.sdf"/>
            <param name="refmol" ftype="mol" value="sucos_refmol.mol"/>
            <output name="output" ftype="sdf">
                    <has_text text="SuCOS_Score" />
.. class:: infomark

**What it does**

This tool determines the shape and feature overlap of docked ligand poses compared to a reference molecule, usually a known ligand.
The RDKit FeatureMap functionality is used to do the scoring.

The original SuCOS code is on GitHub_ under a MIT license. The SuCOS work is described here_.

.. _GitHub:
.. _here:

.. class:: infomark


Molecules such as an SD file dataset from the history.

.. class:: infomark


The same SD file with a "SuCOS_Score" property added. A score of 1.0 infers a perfect overlap, a score of 0.0 no overlap.
A rule of thumb is that poses with a score greater than 0.5 can be be considered "useful".

    <expand macro="citations"/>