<tool id="ctb_im_xcos" name="XCos" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>scoring</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
<![CDATA[

xcos
    -if sdf
    --fragments-format sdf
    -of sdf
    --no-gzip
    -f '$fragments'
    -i '$poses'
    -o output
]]>
    </command>
    <inputs>
        <param name="poses" format="sdf" type="data" label="Poses to score" help="In SDF format"/>
        <param name="fragments" format="sdf" type="data" label="Fragments to compare" help="In SDF format"/>
    </inputs>
    <outputs>
        <data format="sdf" name="output" from_work_dir="output.sdf" />
    </outputs>
    <tests>
        <test>
            <param name="poses" ftype='sdf' value="poses.sdf" />
            <param name="fragments" ftype='sdf' value="hits-17.sdf" />
            <output name="output" ftype='sdf'>
                <assert_contents>
                    <has_text text="XCos_RefMols" />
                    <has_text text="XCos_NumHits" />
                    <has_text text="XCos_Score1" />
                    <has_n_lines n="734" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

XCos is a reverse shape and feature overlap score for a pose compared to a set of ligands that identifies which ligands
best overlap.
The molecule is fragmented using the BRICS algorithm and each fragment (bit) is compared to the ligands using the SuCOS
methodology. The resulting scores are the combined scores of the bits.

XCos_RefMols - The fragments that the ligand overlays
XCos_NumHits - the number of fragments the ligand overlays
XCos_Score1 - The sum of each bit's feature and shape overlay score scaled by the number of heavy bit atoms.

XCos was conceived and implemented by Warren Thompson <warren.thompson@diamond.ac.uk>.
The original code can be found here: https://github.com/Waztom/xchem-XCOS

-----

.. class:: infomark

**Input**

- poses: SD-file of ligand poses to score
- fragments: SD-file of fragments to compare the poses

-----

.. class:: infomark

 **Output**

SD-file with the XCos scores added.


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