Mercurial > repos > recetox > matchms_fingerprint_similarity
annotate matchms_fingerprint_similarity.xml @ 5:98e63fb5f8be draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
author | recetox |
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date | Wed, 22 Nov 2023 14:44:54 +0000 |
parents | 79accd21387c |
children | 5be32c7ce669 |
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79accd21387c
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a493624c962d820d962bd81c14aceede5d5be5b4
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1 <tool id="matchms_fingerprint_similarity" name="matchms fingerprint similarity" version="@TOOL_VERSION@+galaxy0" profile="21.09"> |
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84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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2 <description>calculate similarity between molecular fingerprints calculated from structural spectrum metadata descriptors</description> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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3 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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4 <macros> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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5 <import>macros.xml</import> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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6 <import>help.xml</import> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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7 </macros> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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8 <expand macro="creator"/> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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9 <edam_operations> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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10 <edam_operation>operation_0360</edam_operation> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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11 </edam_operations> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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12 <expand macro="bio.tools"/> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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13 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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14 <requirements> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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15 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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16 </requirements> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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17 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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18 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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19 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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20 python3 ${python_wrapper} |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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21 ]]> </command> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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22 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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23 <configfiles> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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24 <configfile name="python_wrapper"> |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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25 @init_logger@ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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26 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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27 from matchms.similarity import FingerprintSimilarity |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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28 similarity = FingerprintSimilarity(similarity_measure="${fingerprint_similarity}") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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29 @init_scores@ |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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30 |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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31 from matchms.filtering import add_fingerprint |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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32 import numpy as np |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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33 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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34 name="FingerprintSimilarity_${fingerprint_similarity}" |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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35 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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36 layer = similarity.matrix( |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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37 references=np.asarray(list(map(add_fingerprint, scores.references))), |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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38 queries=np.asarray(list(map(add_fingerprint, scores.queries))), |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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39 array_type = "numpy", |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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40 is_symmetric=scores.is_symmetric) |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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41 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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42 scores._scores.add_dense_matrix(layer, name) |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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43 scores.to_json("$scores_out") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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44 </configfile> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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45 </configfiles> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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46 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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47 <inputs> |
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48 <expand macro="input_param"/> |
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49 <param label="Fingerprint similarity distance" name="fingerprint_similarity" type="select" display="radio" |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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50 help="Distance measure to use to compute between the molecular fingerprints - see [2] for details regarding the used fingerprint."> |
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51 <option value="jaccard" selected="true">jaccard</option> |
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52 <option value="dice">dice</option> |
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53 <option value="cosine">cosine</option> |
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54 </param> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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55 </inputs> |
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56 |
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57 <outputs> |
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58 <data label="$fingerprint_similarity distance between fingerprints in ${on_string}" name="scores_out" format="json"/> |
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59 </outputs> |
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60 |
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61 <tests> |
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62 <test> |
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63 <param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/> |
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64 <param name="references" value="similarity/rcx_exposome_pesticides_subset.msp" ftype="msp"/> |
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65 <param name="fingerprint_similarity" value="dice" /> |
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66 <output name="scores_out" value="fingerprints/dice.json" ftype="json" /> |
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67 </test> |
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68 <test> |
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69 <param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/> |
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70 <param name="references" value="similarity/rcx_exposome_pesticides_subset.msp" ftype="msp"/> |
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71 <param name="fingerprint_similarity" value="cosine" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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72 <output name="scores_out" value="fingerprints/cosine.json" ftype="json" /> |
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73 </test> |
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74 <test> |
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75 <param name="use_scores" value="True"/> |
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76 <param name="scores_in" value="metadata_match/inner_join_ri_20.json" ftype="json"/> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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77 <param name="fingerprint_similarity" value="jaccard" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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78 <output name="scores_out" value="fingerprints/jaccard_scores.json" ftype="json" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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79 </test> |
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80 </tests> |
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81 |
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82 <help> |
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83 Description |
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84 Molecular fingerprints are a digital representation of a molecule based on specific patterns, such as substructures or physicochemical properties. |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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85 They usually have a fixed length with each entry representing the presence or absence of a certain attribute. |
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86 Similarity between molecular fingerprints can serve as a proxy for structural similarity and can therefore be used to compare molecules. |
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87 |
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88 .. rubric:: **Footnotes** |
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89 .. [1] SQL join types explained on LearnSQL_. |
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90 .. [2] Fingerprint - the `daylight fingerprint`_ is used to compute chemical similarity. |
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91 Fingerprints are derived from SMILES or InChI structure notations present in the spectrum metadata. |
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92 |
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93 .. _LearnSQL: https://learnsql.com/blog/sql-joins-types-explained/ |
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94 .. _daylight fingerprint: https://www.daylight.com/dayhtml/doc/theory/theory.finger.html |
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95 |
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96 @HELP_matchms@ |
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97 </help> |
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98 |
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99 <expand macro="citations"/> |
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100 </tool> |