Mercurial > repos > bgruening > sucos_max_score

annotate sucos_max.xml @ 5:d4c67ced6abc draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"
author bgruening
date Wed, 15 Apr 2020 09:26:07 -0400
parents 85fad59f8168
children 55ac04db36aa
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1 <tool id="sucos_max_score" name="Max SuCOS score" version="0.2.3">
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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 #if $filter_field and $filter_value
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12 --filter-field '$filter_field' --filter-value $filter_value
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13 #end if
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14 #for $cluster in $clusters
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15 '$cluster'
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16 #end for
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17 ]]></command>
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18 <inputs>
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19 <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input in SDF format." />
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20 <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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21 <param name="filter_field" type="text" label="Filter field" optional="true"
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22 help="Filter output using this field's values. (e.g. Max_SuCOS_Score or Cum_SuCOS_Score)">
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23 <sanitizer>
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24 <valid initial="string.printable">
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25 <remove value="&apos;"/>
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26 </valid>
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27 <mapping initial="none"/>
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28 </sanitizer>
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29 </param>
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30 <param name="filter_value" type="float" label="Filter value" optional="true"
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31 help="Filter out scores less than this value."/>
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32 </inputs>
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33 <outputs>
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34 <data format="sdf" name="output" label="The scored ligands"/>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
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39 <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
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40 <output name="output" ftype="sdf">
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41 <assert_contents>
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42 <has_text text="Max_SuCOS_Score" />
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43 <has_text text="Cum_SuCOS_Score" />
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44 <has_n_lines n="2224" />
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45 </assert_contents>
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46 </output>
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47 </test>
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48 <test>
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49 <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
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50 <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
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51 <param name="filter_field" value="Cum_SuCOS_Score"/>
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52 <param name="filter_value" value="15"/>
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53 <output name="output" ftype="sdf">
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54 <assert_contents>
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55 <has_text text="Max_SuCOS_Score" />
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56 <has_text text="Cum_SuCOS_Score" />
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57 <has_n_lines n="686" />
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58 </assert_contents>
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59 </output>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63
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64 .. class:: infomark
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65
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66 **What it does**
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67
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68 This tool determines the maximum SuCOS score of ligands, presumed to be potential follow on compounds, compared to a
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69 set of clustered reference compounds, presumed to be fragment screening hits. Each ligand to be scored is compared to
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70 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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71 of the molecule within that cluster.
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72
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73 The original SuCOS code is on GitHub_ under a MIT license. The SuCOS work is described here_.
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75 .. _GitHub: https://github.com/susanhleung/SuCOS
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76 .. _here: https://chemrxiv.org/articles/SuCOS_is_Better_than_RMSD_for_Evaluating_Fragment_Elaboration_and_Docking_Poses/8100203
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78 .. class:: infomark
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79
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80 **Input**
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81
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82 The clustered reference compounds are likely to have been generated using the "Cluster ligands using SuCOS" tool and
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83 will comprise a SDF format file for each cluster. The ligands to be scored are supplied in a SDF file.
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84
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85 Optional filtering of the output is possible, for instance to retain only records with SuCOS scores greater that a
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86 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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87 be one of the properties listed below.
d4c67ced6abc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"
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88
0
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89 .. class:: infomark
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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90
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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91 **Output**
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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92
2
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
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93 The same SD file as the input ligands with the following properties added:
0
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94
2
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
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95 * Max_SuCOS_Score - the best (maximum) SuCOS score
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
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96 * Max_SuCOS_FeatureMap_Score - the corresponding FeatureMap score
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
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97 * Max_SuCOS_Protrude_Score - the corresponding Protrude score
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
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98 * Max_SuCOS_Cluster - the file name of the cluster that contained the max score
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
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99 * Max_SuCOS_Index - the index of the cluster that contained the max score (first record is index 1)
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
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100 * Cum_SuCOS_Score - the cumulative SuCOS score for all overlays (the sum of the individual scores)
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
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101 * Cum_SuCOS_FeatureMap_Score - the corresponding FeatureMap score
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
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102 * Cum_SuCOS_Protrude_Score - the corresponding Protrude score
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103
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104 ]]></help>
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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105 <expand macro="citations"/>
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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106 </tool>
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107