Mercurial > repos > bgruening > sucos_max_score

annotate sucos_max.xml @ 3:bf99565cec1f draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 8542cbcae3ebed4cb9a6c20b1fabd418a6efb7e8"
author bgruening
date Sat, 28 Mar 2020 05:16:25 -0400
parents 2f110aef9b53
children 85fad59f8168
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bf99565cec1f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 8542cbcae3ebed4cb9a6c20b1fabd418a6efb7e8"
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1 <tool id="sucos_max_score" name="Max SuCOS score" version="0.2.1">
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2 <description>- determine maximum SuCOS score of ligands against clustered fragment hits</description>
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3 <macros>
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4 <import>sucos_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 python '$__tool_directory__/sucos_max.py'
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9 -i '$input'
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10 -o '$output'
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11 #for $cluster in $clusters
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12 '$cluster'
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13 #end for
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14 ]]></command>
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15 <inputs>
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16 <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input in SDF format." />
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17 <param name="clusters" type="data" format="sdf" multiple="true" label="Set of clusters to score against" help="Clusters in SDF format." />
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18 </inputs>
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19 <outputs>
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20 <data format="sdf" name="output" label="The scored ligands"/>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
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25 <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
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26 <output name="output" ftype="sdf">
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27 <assert_contents>
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28 <has_text text="Max_SuCOS_Score" />
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29 <has_text text="Cum_SuCOS_Score" />
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30 </assert_contents>
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31 </output>
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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36 .. class:: infomark
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38 **What it does**
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40 This tool determines the maximum SuCOS score of ligands, presumed to be potential follow on compounds, compared to a
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41 set of clustered reference compounds, presumed to be fragment screening hits. Each ligand to be scored is compared to
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42 all of the reference compounds with the highest score being recorded, along with the cluster it came from and the index
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43 of the molecule within that cluster.
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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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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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50 .. class:: infomark
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52 **Input**
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54 The clustered reference compounds are likely to have been generated using the "Cluster ligands using SuCOS" tool and
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55 will comprise a SDF format file for each cluster. The ligands to be scored are supplied in a SDF file.
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57 .. class:: infomark
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59 **Output**
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60
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61 The same SD file as the input ligands with the following properties added:
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63 * Max_SuCOS_Score - the best (maximum) SuCOS score
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64 * Max_SuCOS_FeatureMap_Score - the corresponding FeatureMap score
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65 * Max_SuCOS_Protrude_Score - the corresponding Protrude score
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66 * Max_SuCOS_Cluster - the file name of the cluster that contained the max score
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67 * Max_SuCOS_Index - the index of the cluster that contained the max score (first record is index 1)
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68 * Cum_SuCOS_Score - the cumulative SuCOS score for all overlays (the sum of the individual scores)
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69 * Cum_SuCOS_FeatureMap_Score - the corresponding FeatureMap score
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70 * Cum_SuCOS_Protrude_Score - the corresponding Protrude score
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72 ]]></help>
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73 <expand macro="citations"/>
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74 </tool>
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75