diff sucos.xml @ 0:f8f53668d5a2 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.xml	Wed Oct 02 12:58:43 2019 -0400
@@ -0,0 +1,63 @@
+<tool id="sucos_docking_scoring" name="Score docked poses using SuCOS" version="0.1">
+    <description>- compare shape and feature overlap of docked ligand poses to a reference molecule</description>
+    <macros>
+        <import>sucos_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+        python '$__tool_directory__/sucos.py'
+            -i '$input'
+            -r '$refmol'
+            -o '$output'
+            --refmol-format mol
+            $tanimoto
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" format="sdf" label="Ligands to be scored" help="Input in SDF format." />
+        <param type="data" name="refmol" format="sdf,mol" label="Reference molecule to overlay" help="Input in SDF or MOL format." />
+        <param type="boolean" name="tanimoto" truevalue="--tanimoto" falsevalue="" label="Include Tanimoto calculations" help="Whether to handle the distance as Tanimoto." />
+    </inputs>
+    <outputs>
+        <data format="sdf" name="output" label="The scored ligands"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="sdf" value="sucos_inputs.sdf"/>
+            <param name="refmol" ftype="mol" value="sucos_refmol.mol"/>
+            <output name="output" ftype="sdf">
+                <assert_contents>
+                    <has_text text="SuCOS_Score" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+This tool determines the shape and feature overlap of docked ligand poses compared to a reference molecule, usually a known ligand.
+The RDKit FeatureMap functionality is used to do the scoring.
+
+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**
+
+Molecules such as an SD file dataset from the history.
+
+.. class:: infomark
+
+**Output**
+
+The same SD file with a "SuCOS_Score" property added. A score of 1.0 infers a perfect overlap, a score of 0.0 no overlap.
+A rule of thumb is that poses with a score greater than 0.5 can be be considered "useful".
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
+