annotate sucos_max.xml @ 4:85fad59f8168 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 2a74332a201fa9bb53f8e7dc3cc497f653d12929"

<tool id="sucos_max_score" name="Max SuCOS score" version="0.2.2">
    <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'
        #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." />
    </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"/>
            <output name="output" ftype="sdf">
                <assert_contents>
                    <has_text text="Max_SuCOS_Score" />
                    <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  the following properties added:

* Max_SuCOS_Score - the best (maximum) SuCOS score
* Max_SuCOS_FeatureMap_Score - the corresponding FeatureMap score
* Max_SuCOS_Protrude_Score - the corresponding Protrude score
* Max_SuCOS_Cluster - the file name of the cluster that contained the max score
* Max_SuCOS_Index - the index of the cluster that contained the max score (first record is index 1)
* Cum_SuCOS_Score - the cumulative SuCOS score for all overlays (the sum of the individual scores)
* Cum_SuCOS_FeatureMap_Score - the corresponding FeatureMap score
* Cum_SuCOS_Protrude_Score - the corresponding Protrude score

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