Mercurial > repos > bgruening > openbabel_spectrophore_search

annotate ob_spectrophore_search.xml @ 12:afd14e10a318 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:35:45 -0400
parents f93f3e01abe8
children f5d7ffbb2d33
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1 <tool id="openbabel_spectrophore_search" name="Spectrophores search" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>- similarity search based on 1D chemical features</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="1.19.1">numpy</requirement>
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9 </expand>
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10 <command detect_errors="aggressive">
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11 <![CDATA[
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12 python '$__tool_directory__/ob_spectrophore_search.py'
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13 --target '$target'
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14 --library '$library'
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15 --output '$outfile'
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16 --column $column
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="target" type="data" format="sdf"
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21 label="Target molecule in SDF format (it must contain Spectrophores stored as meta-data)"/>
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22 <param name="library" type="data" format="tabular"
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23 label="Tabular file with pre-computed Spectrophores in one column"/>
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24 <param name="column" label="Specify the column number containing the Spectrophores descriptors"
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25 type="data_column" data_ref="library" accept_default="true" />
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26 </inputs>
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27 <outputs>
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28 <data format="tabular" name="outfile"/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="target" ftype="sdf" value="CID2244_with_spectrophore.sdf"/>
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33 <param name="library" value="lib.tabular" />
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34 <param name="column" value="8" />
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35 <output name="outfile" ftype="tabular" file="ob_spectrophore_search.tabular" />
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36 </test>
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37 </tests>
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38 <help>
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39 <![CDATA[
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41 .. class:: infomark
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43 **What does this tool do?**
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44
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45 This tool computes the Euclidean distance between the |Spectrophores (TM)| descriptors of the target to each molecule stored in the library.
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47 |Spectrophores (TM)| search
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48 |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 easy comparison of |Spectrophores (TM)| of different molecules.
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50 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.
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52 *Advantages:*
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54 - |Spectrophores (TM)| can realistically compute ligand-protein interactions based on aforementioned molecular descriptors
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55 - |Spectrophores (TM)| can be applied in both a ligand- or target-based setting
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56 - |Spectrophores (TM)| can distinguish, if needed, between the different enantiomers of stereo-selective compounds
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57 - |Spectrophores (TM)| can be computed rapidly
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60 -----
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62 .. class:: warningmark
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63
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64 **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.
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66 -----
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68 .. class:: infomark
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70 **Input**
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72 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.
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74 -----
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76 .. class:: infomark
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78 **Output**
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80 The library of compounds is a tabular file with one line per compound. One column contains the |Spectrophores (TM)| descriptors.
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82 -----
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84 .. class:: infomark
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85
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86 **Cite**
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87
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88 N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_
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89
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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90 Silicos_ - |Spectrophores (TM)| is a registered tool implemented in the open-source OpenBabel.
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91
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92 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
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93 .. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html
7
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94 .. |Spectrophores (TM)| unicode:: Spectrophores U+2122
0
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95
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96 ]]>
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97 </help>
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98 <expand macro="citations">
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99 <citation type="doi">10.1186/1752-153X-2-5</citation>
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100 </expand>
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101 </tool>