diff sucos_max.xml @ 0:bb5365381c8f draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sucos_max.xml	Wed Oct 02 12:57:54 2019 -0400
@@ -0,0 +1,85 @@
+<tool id="sucos_max_score" name="Max SuCOS score" version="0.1">
+    <description>- determine maximum SuCOS score of ligands against clustered fragment hits</description>
+    <macros>
+        <import>sucos_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+        python '$__tool_directory__/sucos_max.py'
+            -i '$input'
+            -o '$output'
+            -m $mode
+        #for $cluster in $clusters
+            '$cluster'
+        #end for
+    ]]></command>
+    <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"/>
+    </outputs>
+    <tests>
+        <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>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+This tool determines the maximum SuCOS score of ligands, presumed to be potential follow on compounds, compared to a
+set of clustered reference compounds, presumed to be fragment screening hits. Each ligand to be scored is compared to
+all of the reference compounds with the highest score being recorded, along with the cluster it came from and the index
+of the molecule within that cluster.
+
+The original SuCOS code is on GitHub_ under a MIT license. The SuCOS work is described here_.
+
+.. _GitHub: https://github.com/susanhleung/SuCOS
+.. _here: https://chemrxiv.org/articles/SuCOS_is_Better_than_RMSD_for_Evaluating_Fragment_Elaboration_and_Docking_Poses/8100203
+
+.. class:: infomark
+
+**Input**
+
+The clustered reference compounds are likely to have been generated using the "Cluster ligands using SuCOS" tool and
+will comprise a SDF format file for each cluster. The ligands to be scored are supplied in a SDF file.
+
+.. class:: infomark
+
+**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.
+
+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.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
+