diff sucos_max.xml @ 2:2f110aef9b53 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"

--- a/sucos_max.xml	Fri Oct 11 18:25:27 2019 -0400
+++ b/sucos_max.xml	Thu Mar 19 09:43:31 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="sucos_max_score" name="Max SuCOS score" version="0.1.1">
+<tool id="sucos_max_score" name="Max SuCOS score" version="0.2.0">
     <description>- determine maximum SuCOS score of ligands against clustered fragment hits</description>
     <macros>
         <import>sucos_macros.xml</import>
@@ -8,7 +8,6 @@
         python '$__tool_directory__/sucos_max.py'
             -i '$input'
             -o '$output'
-            -m $mode
         #for $cluster in $clusters
             '$cluster'
         #end for
@@ -16,10 +15,6 @@
     <inputs>
         <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input in SDF format." />
         <param name="clusters" type="data" format="sdf" multiple="true" label="Set of clusters to score against" help="Clusters in SDF format." />
-        <param name="mode" type="select" value="max" label="Mode">
-            <option value="max">Max score</option>
-            <option value="cum">Cumulative score</option>
-        </param>
     </inputs>
     <outputs>
         <data format="sdf" name="output" label="The scored ligands"/>
@@ -28,19 +23,9 @@
         <test>
             <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
             <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
-            <param name="mode" value="max"/>
             <output name="output" ftype="sdf">
                 <assert_contents>
                     <has_text text="Max_SuCOS_Score" />
-                </assert_contents>
-            </output>
-        </test>
-        <test>
-            <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
-            <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
-            <param name="mode" value="cum"/>
-            <output name="output" ftype="sdf">
-                <assert_contents>
                     <has_text text="Cum_SuCOS_Score" />
                 </assert_contents>
             </output>
@@ -73,11 +58,16 @@
 
 **Output**
 
-The same SD file as the input ligands with a "Max_SuCOS_Score" property added containing the best (maximum) SuCOS score
-along with the "Max_SuCOS_FeatureMap_Score" and "Max_SuCOS_Tanimoto_Score" of that comparison.
+The same SD file as the input ligands with  the following properties added:
 
-In addition, the "Max_SuCOS_Cluster" field shows the name of the cluster file that contained the molecule with this best 
-score and the "Max_SuCOS_Index" shows the index (first record is index 1) of that molecule in the file.
+* Max_SuCOS_Score - the best (maximum) SuCOS score
+* Max_SuCOS_FeatureMap_Score - the corresponding FeatureMap score
+* Max_SuCOS_Protrude_Score - the corresponding Protrude score
+* Max_SuCOS_Cluster - the file name of the cluster that contained the max score
+* Max_SuCOS_Index - the index of the cluster that contained the max score (first record is index 1)
+* Cum_SuCOS_Score - the cumulative SuCOS score for all overlays (the sum of the individual scores)
+* Cum_SuCOS_FeatureMap_Score - the corresponding FeatureMap score
+* Cum_SuCOS_Protrude_Score - the corresponding Protrude score
 
     ]]></help>
     <expand macro="citations"/>