# HG changeset patch
# User bgruening
# Date 1595863456 0
# Node ID 81b52a4e531801bb7cff2fa7a1d25aa35b734b70
# Parent  20e8a83eaadaaf6f7ccfeab2e38cabe42fd31ae2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"

diff -r 20e8a83eaada -r 81b52a4e5318 macros.xml
--- a/macros.xml	Tue Jul 21 09:16:37 2020 +0000
+++ b/macros.xml	Mon Jul 27 15:24:16 2020 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.1.3</token>
+    <token name="@TOOL_VERSION@">1.1.4</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">im-pipelines</requirement>
@@ -7,7 +7,7 @@
     </xml>
 
     <xml name="input">
-        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF or JSON format"/>
+        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
     </xml>
 
     <xml name="outputs" token_output_format="sdf" token_filetype="sdf">
@@ -21,16 +21,16 @@
         <citations>
             <citation type="bibtex">
                 @article{rdkit,
-                    author = {Greg Landrum and others},
-                    title = {RDKit: Open-source cheminformatics},
-                    url = {http://www.rdkit.org}
-            }</citation>
+                author = {Greg Landrum and others},
+                title = {RDKit: Open-source cheminformatics},
+                url = {http://www.rdkit.org}
+                }</citation>
             <citation type="bibtex">
                 @article{im-pipelines,
-                    author = {Tim Dudgeon and others},
-                    title = {InformaticsMatters pipeline components for cheminformatics and computational chemistry.},
-                    url = {https://github.com/InformaticsMatters/pipelines}
-            }</citation>
+                author = {Tim Dudgeon and others},
+                title = {InformaticsMatters pipeline components for cheminformatics and computational chemistry.},
+                url = {https://github.com/InformaticsMatters/pipelines}
+                }</citation>
             <yield />
         </citations>
     </xml>
diff -r 20e8a83eaada -r 81b52a4e5318 test-data/poses.sdf
--- a/test-data/poses.sdf	Tue Jul 21 09:16:37 2020 +0000
+++ b/test-data/poses.sdf	Mon Jul 27 15:24:16 2020 +0000
@@ -961,4 +961,4 @@
 >  <TETHERED ATOMS>  (14)
 1,2,3,4,5,6,7,8,9,10,11,15,16
 
-$$$$
+$$$$
\ No newline at end of file
diff -r 20e8a83eaada -r 81b52a4e5318 xcos.xml
--- a/xcos.xml	Tue Jul 21 09:16:37 2020 +0000
+++ b/xcos.xml	Mon Jul 27 15:24:16 2020 +0000
@@ -31,8 +31,10 @@
             <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" />
+                    <has_text text="XCos_RefMols" />
+                    <has_text text="XCos_NumHits" />
+                    <has_text text="XCos_Score1" />
+                    <has_n_lines n="734" />
                 </assert_contents>
             </output>
         </test>
@@ -49,12 +51,12 @@
 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_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-notebooks/blob/master/XCOS.ipynb
+The original code can be found here: https://github.com/Waztom/xchem-XCOS
 
 -----