Mercurial > repos > bgruening > sucos_clustering

annotate sucos_cluster.xml @ 1:dbfcc048cbbc draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
author bgruening
date Thu, 19 Mar 2020 13:09:24 +0000
parents c0e3a335dbfc
children aaa3f95add3e
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dbfcc048cbbc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
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1 <tool id="sucos_clustering" name="Cluster ligands using SuCOS" version="0.1.1">
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c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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2 <description>based on the overlap of 3D features</description>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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3 <macros>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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4 <import>sucos_macros.xml</import>
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5 </macros>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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6 <expand macro="requirements">
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7 <requirement type="package" version="1.3.0">scipy</requirement>
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8 </expand>
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dbfcc048cbbc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
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9 <command detect_errors="exit_code"><![CDATA[
0
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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10 python '$__tool_directory__/sucos_cluster.py'
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11 -i '$input'
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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12 -t $threshold
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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13 ]]></command>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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14 <inputs>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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15 <param type="data" name="input" format="sdf" label="Ligands to be clustered" help="Input in SDF format." />
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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16 <param name="threshold" type="float" value="0.8" min="0" max="1" label="Clustering threshold"/>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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17 </inputs>
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18 <outputs>
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19 <collection name="clusters" type="list" label="Clustered ligands">
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20 <discover_datasets pattern="(?P&lt;designation&gt;^cluster\d+)\.sdf$" ext="sdf"/>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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21 </collection>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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22 </outputs>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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23 <tests>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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24 <test>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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25 <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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26 <output_collection name="clusters" type="list" count="6">
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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27 <element name="cluster1" ftype="sdf" file="cluster1.sdf" compare="sim_size" />
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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28 <element name="cluster2" ftype="sdf" file="cluster2.sdf" compare="sim_size" />
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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29 <element name="cluster3" ftype="sdf" file="cluster3.sdf" compare="sim_size" />
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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30 <element name="cluster4" ftype="sdf" file="cluster4.sdf" compare="sim_size" />
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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31 <element name="cluster5" ftype="sdf" file="cluster5.sdf" compare="sim_size" />
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32 <element name="cluster6" ftype="sdf" file="cluster6.sdf" compare="sim_size" />
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33 </output_collection>
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34 </test>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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35 </tests>
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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36 <help><![CDATA[
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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37 .. class:: infomark
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c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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39 **What it does?**
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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41 This tool clusters molecules based on the overlap of 3D features as determined by SuCOS.
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c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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43 Clustering uses a clustering threshold that can be set by the user. The default threshold is 0.8.
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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44
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45 The original SuCOS code is on GitHub_ under a MIT license. The SuCOS work is described here_.
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c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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47 .. _GitHub: https://github.com/susanhleung/SuCOS
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48 .. _here: https://chemrxiv.org/articles/SuCOS_is_Better_than_RMSD_for_Evaluating_Fragment_Elaboration_and_Docking_Poses/8100203
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c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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50 .. class:: infomark
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c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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52 **Input**
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c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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54 Molecules such as an SD file dataset in the history.
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c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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56 .. class:: infomark
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c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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58 **Output**
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c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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60 A series of SD files, one for each cluster containing the molecules in that cluster.
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61
c0e3a335dbfc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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62 ]]></help>
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63 <expand macro="citations"/>
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64 </tool>
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65