--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcos.xml	Tue Jul 21 05:22:23 2020 -0400
@@ -0,0 +1,80 @@
+<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_Score3" />
+                    <has_n_lines n="818" />
+                </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.
+
+XCoseScore1 -
+XCoseScore2 -
+XCoseScore3 -
+
+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-notebooks/blob/master/XCOS.ipynb
+
+-----
+
+.. 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>