Mercurial > repos > recetox > matchms_subsetting

annotate macros.xml @ 7:f40e2572fbdc draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
author recetox
date Thu, 14 Dec 2023 13:42:12 +0000
parents 2b61ec493df6
children c4835715c7ac
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2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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1 <macros>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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2 <token name="@TOOL_VERSION@">0.24.0</token>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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3
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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4 <xml name="creator">
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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5 <creator>
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6 <yield/>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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7 <person
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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8 givenName="Helge"
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9 familyName="Hecht"
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10 url="https://github.com/hechth"
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11 identifier="0000-0001-6744-996X" />
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12 <person
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13 givenName="Maksym"
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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14 familyName="Skoryk"
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15 url="https://github.com/maximskorik"
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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16 identifier="0000-0003-2056-8018" />
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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17 <person
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18 givenName="Zargham"
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19 familyName="Ahmad"
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20 url="https://github.com/zargham-ahmad"
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21 identifier="0000-0002-6096-224X" />
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22 <person
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23 givenName="Wudmir"
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24 familyName="Rojas"
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25 url="https://github.com/wverastegui"
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26 identifier="0000-0001-7036-9987" />
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27 <organization
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28 url="https://www.recetox.muni.cz/"
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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29 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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30 name="RECETOX MUNI" />
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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31 </creator>
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32 </xml>
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33
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34 <xml name="bio.tools">
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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35 <xrefs>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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36 <xref type="bio.tools">matchms</xref>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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37 </xrefs>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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38 </xml>
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39
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40 <xml name="similarity_metrics">
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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41 <option value="CosineGreedy" selected="true">CosineGreedy</option>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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42 <option value="CosineHungarian">CosineHungarian</option>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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43 <option value="ModifiedCosine">ModifiedCosine</option>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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44 <option value="NeutralLossesCosine">NeutralLossesCosine</option>
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45 </xml>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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46
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47 <xml name="similarity_algorithm_params">
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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48 <section name="algorithm" title="Algorithm Parameters" expanded="true">
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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49 <param label="tolerance [Da]" name="tolerance" type="float" value="0.1"
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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50 help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm."/>
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51 <param label="mz_power" name="mz_power" type="float" value="0.0"
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52 help="The power to raise mz to in the cosine function."/>
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53 <param label="intensity_power" name="intensity_power" type="float" value="1.0"
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54 help="The power to raise intensity to in the cosine function."/>
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55 </section>
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56 </xml>
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57
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58 <xml name="input_param">
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59 <conditional name="scores">
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60 <param name="use_scores" label="Use Scores Object" type="select">
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61 <option value="False" selected="true">FALSE</option>
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62 <option value="True">TRUE</option>
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63 </param>
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64 <when value="True">
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65 <param label="Scores object" name="scores_in" type="data" format="json"
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66 help="Scores objects calculated previously using one of the matchms similarity tools." />
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67 <param label="join type" name="join_type" type="select" display="radio"
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68 help="The join type to use for appending scores - see [1] for details.">
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69 <option value="left" selected="true">left</option>
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70 <option value="inner">inner</option>
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71 <option value="right">right</option>
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72 <option value="outer">outer</option>
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73 </param>
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74 </when>
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75 <when value="False">
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76 <param label="Queries spectra" name="queries" type="data" format="msp"
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77 help="Query mass spectra to match against references."/>
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78 <param label="Reference spectra" name="references" type="data" format="msp"
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79 help="Reference mass spectra to match against as library."/>
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80 </when>
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81 </conditional>
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82 </xml>
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83
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84 <xml name="citations">
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85 <citations>
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86 <citation type="doi">10.5281/zenodo.7178586</citation>
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87 <citation type="doi">10.21105/joss.02411</citation>
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88 </citations>
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89 </xml>
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90
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91 <token name="@init_scores@">
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92 from matchms.importing import load_from_msp, scores_from_json
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93 from matchms import Scores
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94 #if $scores.use_scores == "True"
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95 scores = scores_from_json("$scores_in")
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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96 join_type = "$scores.join_type"
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97 #else
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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98 scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False)
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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99 join_type = "left"
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100 #end if
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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101 </token>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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102
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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103 <token name="@init_logger@">
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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104 from matchms import set_matchms_logger_level
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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105 set_matchms_logger_level("WARNING")
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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106 </token>
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107 </macros>