Mercurial > repos > bgruening > sucos_clustering

annotate sucos_cluster.xml @ 5:12725d4b90f3 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 08:48:16 -0400
parents 334ad24525db
children
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1 <tool id="sucos_clustering" name="Cluster ligands using SuCOS" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>based on the overlap of 3D features</description>
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3 <macros>
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4 <import>sucos_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="1.3.0">scipy</requirement>
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9 </expand>
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10 <command detect_errors="exit_code"><![CDATA[
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11 python '$__tool_directory__/sucos_cluster.py'
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12 -i '$input'
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13 -t $threshold
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14 ]]></command>
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15 <inputs>
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16 <param type="data" name="input" format="sdf" label="Ligands to be clustered" help="Input in SDF format." />
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17 <param name="threshold" type="float" value="0.8" min="0" max="1" label="Clustering threshold"/>
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18 </inputs>
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19 <outputs>
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20 <collection name="clusters" type="list" label="Clustered ligands">
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21 <discover_datasets pattern="(?P&lt;designation&gt;^cluster\d+)\.sdf$" ext="sdf"/>
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22 </collection>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
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27 <output_collection name="clusters" type="list" count="8">
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28 <element name="cluster1" ftype="sdf" file="cluster1.sdf" compare="sim_size" />
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29 <element name="cluster2" ftype="sdf" file="cluster2.sdf" compare="sim_size" />
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30 <element name="cluster3" ftype="sdf" file="cluster3.sdf" compare="sim_size" />
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31 <element name="cluster4" ftype="sdf" file="cluster4.sdf" compare="sim_size" />
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32 <element name="cluster5" ftype="sdf" file="cluster5.sdf" compare="sim_size" />
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33 <element name="cluster6" ftype="sdf" file="cluster6.sdf" compare="sim_size" />
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34 </output_collection>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 .. class:: infomark
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40 **What it does?**
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42 This tool clusters molecules based on the overlap of 3D features as determined by SuCOS.
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44 Clustering uses a clustering threshold that can be set by the user. The default threshold is 0.8.
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46 The original SuCOS code is on GitHub_ under a MIT license. The SuCOS work is described here_.
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48 .. _GitHub: https://github.com/susanhleung/SuCOS
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49 .. _here: https://chemrxiv.org/articles/SuCOS_is_Better_than_RMSD_for_Evaluating_Fragment_Elaboration_and_Docking_Poses/8100203
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51 .. class:: infomark
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53 **Input**
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55 Molecules such as an SD file dataset in the history.
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57 .. class:: infomark
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59 **Output**
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61 A series of SD files, one for each cluster containing the molecules in that cluster.
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63 ]]></help>
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64 <expand macro="citations"/>
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65 </tool>
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