changeset 1:81b52a4e5318 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"

--- 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>

--- 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

--- 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 <[e-mail]>.
-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
 
 -----