Mercurial > repos > bgruening > sucos_docking_scoring

annotate sucos.xml @ 5:fe318c648502 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:48:35 -0400
parents 2e67eea82ff7
children 4f1896782f7c
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fe318c648502 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="sucos_docking_scoring" name="Score docked poses using SuCOS" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>- compare shape and feature overlap of docked ligand poses to a reference molecule</description>
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3 <macros>
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4 <import>sucos_macros.xml</import>
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fe318c648502 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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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 <command detect_errors="exit_code"><![CDATA[
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9 python '$__tool_directory__/sucos.py'
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10 -i '$input'
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11 -r '$refmol'
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12 -o '$output'
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13 --refmol-format mol
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14 $tanimoto
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15 ]]></command>
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16 <inputs>
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17 <param type="data" name="input" format="sdf" label="Ligands to be scored" help="Input in SDF format." />
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18 <param type="data" name="refmol" format="sdf,mol" label="Reference molecule to overlay" help="Input in SDF or MOL format." />
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19 <param type="boolean" name="tanimoto" truevalue="--tanimoto" falsevalue="" label="Include Tanimoto calculations" help="Whether to handle the distance as Tanimoto." />
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20 </inputs>
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21 <outputs>
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22 <data format="sdf" name="output" label="The scored ligands"/>
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23 </outputs>
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24 <tests>
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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25 <test>
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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26 <param name="input" ftype="sdf" value="sucos_inputs.sdf"/>
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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27 <param name="refmol" ftype="mol" value="sucos_refmol.mol"/>
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28 <output name="output" ftype="sdf">
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29 <assert_contents>
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30 <has_text text="SuCOS_Score" />
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31 </assert_contents>
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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32 </output>
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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33 </test>
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34 </tests>
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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35 <help><![CDATA[
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36 .. class:: infomark
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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38 **What it does**
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f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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40 This tool determines the shape and feature overlap of docked ligand poses compared to a reference molecule, usually a known ligand.
f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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41 The RDKit FeatureMap functionality is used to do the scoring.
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43 The original SuCOS code is on GitHub_ under a MIT license. The SuCOS work is described here_.
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45 .. _GitHub: https://github.com/susanhleung/SuCOS
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46 .. _here: https://chemrxiv.org/articles/SuCOS_is_Better_than_RMSD_for_Evaluating_Fragment_Elaboration_and_Docking_Poses/8100203
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48 .. class:: infomark
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50 **Input**
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f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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52 Molecules such as an SD file dataset from the history.
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54 .. class:: infomark
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f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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56 **Output**
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f8f53668d5a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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58 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.
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59 A rule of thumb is that poses with a score greater than 0.5 can be be considered "useful".
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61 ]]></help>
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62 <expand macro="citations"/>
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63 </tool>
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