Mercurial > repos > bgruening > sucos_max_score

annotate sucos_max.xml @ 6:55ac04db36aa 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 08:47:57 -0400
parents d4c67ced6abc
children
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1 <tool id="sucos_max_score" name="Max SuCOS score" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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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 <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 '$__tool_directory__/sucos_max.py'
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10 -i '$input'
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11 -o '$output'
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12 #if $filter_field and $filter_value
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13 --filter-field '$filter_field' --filter-value $filter_value
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14 #end if
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15 #for $cluster in $clusters
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16 '$cluster'
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17 #end for
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18 ]]></command>
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19 <inputs>
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20 <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input in SDF format." />
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21 <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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22 <param name="filter_field" type="text" label="Filter field" optional="true"
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23 help="Filter output using this field's values. (e.g. Max_SuCOS_Score or Cum_SuCOS_Score)">
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24 <sanitizer>
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25 <valid initial="string.printable">
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26 <remove value="&apos;"/>
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27 </valid>
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28 <mapping initial="none"/>
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29 </sanitizer>
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30 </param>
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31 <param name="filter_value" type="float" label="Filter value" optional="true"
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32 help="Filter out scores less than this value."/>
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33 </inputs>
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34 <outputs>
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35 <data format="sdf" name="output" label="The scored ligands"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
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40 <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
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41 <output name="output" ftype="sdf">
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42 <assert_contents>
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43 <has_text text="Max_SuCOS_Score" />
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44 <has_text text="Cum_SuCOS_Score" />
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45 <has_n_lines n="2224" />
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46 </assert_contents>
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47 </output>
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48 </test>
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49 <test>
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50 <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
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51 <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
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52 <param name="filter_field" value="Cum_SuCOS_Score"/>
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53 <param name="filter_value" value="15"/>
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54 <output name="output" ftype="sdf">
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55 <assert_contents>
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56 <has_text text="Max_SuCOS_Score" />
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57 <has_text text="Cum_SuCOS_Score" />
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58 <has_n_lines n="463" />
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59 </assert_contents>
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60 </output>
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64
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65 .. class:: infomark
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66
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67 **What it does**
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68
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69 This tool determines the maximum SuCOS score of ligands, presumed to be potential follow on compounds, compared to a
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70 set of clustered reference compounds, presumed to be fragment screening hits. Each ligand to be scored is compared to
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71 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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72 of the molecule within that cluster.
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73
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74 The original SuCOS code is on GitHub_ under a MIT license. The SuCOS work is described here_.
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75
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76 .. _GitHub: https://github.com/susanhleung/SuCOS
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77 .. _here: https://chemrxiv.org/articles/SuCOS_is_Better_than_RMSD_for_Evaluating_Fragment_Elaboration_and_Docking_Poses/8100203
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78
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79 .. class:: infomark
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80
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81 **Input**
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82
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83 The clustered reference compounds are likely to have been generated using the "Cluster ligands using SuCOS" tool and
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84 will comprise a SDF format file for each cluster. The ligands to be scored are supplied in a SDF file.
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85
5
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86 Optional filtering of the output is possible, for instance to retain only records with SuCOS scores greater that a
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87 certain value. Use the optional 'Filter field' and 'Filter value' parameters. The 'Filter field' would typically
d4c67ced6abc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"
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88 be one of the properties listed below.
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89
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90 .. class:: infomark
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91
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92 **Output**
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93
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94 The same SD file as the input ligands with the following properties added:
0
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95
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96 * Max_SuCOS_Score - the best (maximum) SuCOS score
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97 * Max_SuCOS_FeatureMap_Score - the corresponding FeatureMap score
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98 * Max_SuCOS_Protrude_Score - the corresponding Protrude score
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99 * Max_SuCOS_Cluster - the file name of the cluster that contained the max score
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100 * Max_SuCOS_Index - the index of the cluster that contained the max score (first record is index 1)
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101 * Cum_SuCOS_Score - the cumulative SuCOS score for all overlays (the sum of the individual scores)
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102 * Cum_SuCOS_FeatureMap_Score - the corresponding FeatureMap score
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103 * Cum_SuCOS_Protrude_Score - the corresponding Protrude score
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104
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105 ]]></help>
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106 <expand macro="citations"/>
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107 </tool>
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108