diff featurestein.xml @ 0:0eb24d808e75 draft default tip

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/featurestein.xml	Mon Jul 27 11:31:14 2020 -0400
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+<tool id="featurestein" name="'FeatureStein' fragment overlay scoring" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>feature overlay scoring</description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+<![CDATA[
+        featurestein_generate -i '$fragments' -if sdf &&
+        featurestein_score -i '$ligands' -if sdf -f featurestein.p -o output -of sdf --no-gzip
+]]>
+    </command>
+    <inputs>
+        <param name="fragments" format="sdf" type="data" label="Fragments to generate feature maps" help="In SDF format"/>
+        <param name="ligands" format="sdf" type="data" label="Ligands to score" help="In SDF format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="sdf" from_work_dir="output.sdf" label="The scored ligands"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fragments" ftype='sdf' value="hits-17.sdf" />
+            <param name="ligands" ftype='sdf' value="poses.sdf" />
+            <output name="output" ftype="sdf">
+                <assert_contents>
+                    <has_n_lines n="692" />
+                    <has_text text="FeatureStein_Qual" />
+                    <has_text text="FeatureStein_Quant" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+FeatureStein involves use of merged RDKit feature maps to score ligand poses in terms of how well the features overlap
+with features from a set of ligands, typically fragment screening hits. The features are molecular features like
+hydrogen bond donors and acceptors or hydrophobic groups.
+See this Jupyter notebook for more information: https://github.com/tdudgeon/jupyter_mpro/blob/master/featurestein/FeatureStein.ipynb
+and this blog for more general info on RDKit feature maps:
+http://rdkit.blogspot.com/2017/11/using-feature-maps.html
+
+This module generates the merged feature maps from a set of molecules (typically fragment screening hits) and then.
+scores a set of ligands using those merged feature maps.
+
+The fields that are created are:
+
+- FeatureStein_Quant: the sum of the scores for each feature in the ligand
+- FeatureStein_Qual: the FeatureStein_Quant score divided by the number of features (number between 0 and 1)
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+- fragments: SD-file of fragments to generate feature maps and merge
+- ligands: SD-file of ligands to score
+
+-----
+
+.. class:: infomark
+
+ **Output**
+
+SD-file of the ligands with the FeatureStein scores added.
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>