annotate sucos_max.xml @ 1:8eab6d2b7bdf draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6fa2a0294d615c9f267b766337dca0b2d3637219"

<tool id="sucos_max_score" name="Max SuCOS score" version="0.1.1">
    <description>- determine maximum SuCOS score of ligands against clustered fragment hits</description>
    <macros>
        <import>sucos_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/sucos_max.py'
            -i '$input'
            -o '$output'
            -m $mode
        #for $cluster in $clusters
            '$cluster'
        #end for
    ]]></command>
    <inputs>
        <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input in SDF format." />
        <param name="clusters" type="data" format="sdf" multiple="true" label="Set of clusters to score against" help="Clusters in SDF format." />
        <param name="mode" type="select" value="max" label="Mode">
            <option value="max">Max score</option>
            <option value="cum">Cumulative score</option>
        </param>
    </inputs>
    <outputs>
        <data format="sdf" name="output" label="The scored ligands"/>
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
            <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
            <param name="mode" value="max"/>
            <output name="output" ftype="sdf">
                <assert_contents>
                    <has_text text="Max_SuCOS_Score" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
            <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
            <param name="mode" value="cum"/>
            <output name="output" ftype="sdf">
                <assert_contents>
                    <has_text text="Cum_SuCOS_Score" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

This tool determines the maximum SuCOS score of ligands, presumed to be potential follow on compounds, compared to a
set of clustered reference compounds, presumed to be fragment screening hits. Each ligand to be scored is compared to
all of the reference compounds with the highest score being recorded, along with the cluster it came from and the index
of the molecule within that cluster.

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

.. _GitHub: https://github.com/susanhleung/SuCOS
.. _here: https://chemrxiv.org/articles/SuCOS_is_Better_than_RMSD_for_Evaluating_Fragment_Elaboration_and_Docking_Poses/8100203

.. class:: infomark

**Input**

The clustered reference compounds are likely to have been generated using the "Cluster ligands using SuCOS" tool and
will comprise a SDF format file for each cluster. The ligands to be scored are supplied in a SDF file.

.. class:: infomark

**Output**

The same SD file as the input ligands with a "Max_SuCOS_Score" property added containing the best (maximum) SuCOS score
along with the "Max_SuCOS_FeatureMap_Score" and "Max_SuCOS_Tanimoto_Score" of that comparison.

In addition, the "Max_SuCOS_Cluster" field shows the name of the cluster file that contained the molecule with this best 
score and the "Max_SuCOS_Index" shows the index (first record is index 1) of that molecule in the file.

    ]]></help>
    <expand macro="citations"/>
</tool>