# HG changeset patch
# User bgruening
# Date 1595863849 14400
# Node ID 9b6210854c8c2ee06bb56ad409ee29b2e165c6c6
# Parent  73164cea9b603ea0cb9337e1d8694a91ab361808
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"

diff -r 73164cea9b60 -r 9b6210854c8c macros.xml
--- a/macros.xml	Tue Jul 21 05:22:23 2020 -0400
+++ b/macros.xml	Mon Jul 27 11:30:49 2020 -0400
@@ -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 73164cea9b60 -r 9b6210854c8c test-data/poses.sdf
--- a/test-data/poses.sdf	Tue Jul 21 05:22:23 2020 -0400
+++ b/test-data/poses.sdf	Mon Jul 27 11:30:49 2020 -0400
@@ -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 73164cea9b60 -r 9b6210854c8c xcos.xml
--- a/xcos.xml	Tue Jul 21 05:22:23 2020 -0400
+++ b/xcos.xml	Mon Jul 27 11:30:49 2020 -0400
@@ -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
 
 -----