diff ob_spectrophore_search.xml @ 0:7133973beaf0 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502

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+++ b/ob_spectrophore_search.xml	Sat May 20 08:40:10 2017 -0400
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+<tool id="openbabel_spectrophore_search" name="Spectrophores(TM) search:" version="@VERSION@.0">
+    <description>similarity search based on 1D chemical features</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.7.1">numpy</requirement>
+    </expand>
+    <command detect_errors="aggressive">
+<![CDATA[
+    python '$__tool_directory__/ob_spectrophore_search.py'
+      --target '$target'
+      --library '$library'
+      --output '$outfile'
+      --column $column
+]]>
+    </command>
+    <inputs>
+        <param name="target" type="data" format="sdf"
+            label="Target molecule in SDF format (it must contain its Spectrophores(TM) stored as meta-data)"/>
+        <param name="library" type="data" format="tabular"
+            label="Tabular file with pre-computed Spectrophores(TM) in one column"/>
+        <param name="column" label="Specify the column number containing the Spectrophores(TM) descriptors"
+            type="data_column" data_ref="library" accept_default="true" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="target" ftype="sdf" value="CID2244_with_spectrophore.sdf"/>
+            <param name="library" value="lib.tabular" />
+            <param name="column" value="8" />
+            <output name="outfile" ftype="tabular" file="ob_spectrophore_search.tabular" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What does this tool do?**
+
+This tool computes the Euclidean distance between the Spectrophores(TM) descriptors of the target to each molecule stored in the library.
+
+|Spectrophores (TM)| search
+		|Spectrophores (TM)| is a screening technology by Silicos_ which converts three-dimensional molecular property data into one-dimensional spectra. Typical characteristics that can be converted include electrostatic potentials, molecular shape, lipophilicity, hardness and softness potentials. The computation is independent of the position and orientation of a molecule and allows an easy comparison of |Spectrophores (TM)| of different molecules.
+
+		Molecules with similar three-dimensional properties and shape, and therefore also similar biological activities, always have similar |Spectrophores (TM)|. As a result this technique is a very powerful tool to investigate the similarity of molecules and can be applied as a screening tool for molecular databases, virtual screening, and database characterisations.
+
+*Advantages:*
+
+- |Spectrophores (TM)| can realistically compute ligand-protein interactions based on aforementioned molecular descriptors
+- |Spectrophores (TM)| can be applied in both a ligand- or target-based setting
+- |Spectrophores (TM)| can distinguish, if needed, between the different enantiomers of stereo-selective compounds
+- |Spectrophores (TM)| can be computed fast
+
+.. |Spectrophores (TM)| unicode:: Spectrophores U+2122
+
+-----
+
+.. class:: warningmark
+
+**Hint** this tool is useful to select compounds with similar chemical features to a target, but accounting for the discovery of diverse scaffolds. This is in contrast to the results expected in a similarity search based on atom connectivity.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+The target molecule must be a SD formatted file with the |Spectrophores (TM)| descriptors stored as metadata. Such files can be generated using the *Compute physico-chemical properties* tool.
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+The library of compounds is a tabular file with one line per compound. One column contains the |Spectrophores (TM)| descriptors.
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_
+
+Silicos_ - |Spectrophores (TM)| is a registered tool implemented in the open-source OpenBabel.
+
+.. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
+.. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html
+
+]]>
+    </help>
+    <expand macro="citations">
+        <citation type="doi">10.1186/1752-153X-2-5</citation>
+    </expand>
+</tool>