Mercurial > repos > goeckslab > ludwig_render_config

annotate ludwig_macros.xml @ 0:ed8a9ea5bc73 draft default tip

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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
author goeckslab
date Tue, 07 Jan 2025 22:45:58 +0000
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0
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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1 <macros>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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2 <token name="@LUDWIG_VERSION@">0.10.1</token>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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3
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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4 <token name="@SUFFIX@">0</token>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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6 <token name="@VERSION@">@LUDWIG_VERSION@+@SUFFIX@</token>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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8 <token name="@PROFILE@">21.05</token>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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9
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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10 <xml name="python_requirements_gpu">
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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11 <requirements>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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12 <container type="docker">quay.io/goeckslab/galaxy-ludwig-gpu:latest</container>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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13 </requirements>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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14 </xml>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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15
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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16 <xml name="python_requirements">
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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17 <requirements>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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18 <container type="docker">quay.io/goeckslab/galaxy-ludwig:0.10.3</container>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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19 </requirements>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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20 </xml>
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21
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22 <xml name="macro_stdio">
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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23 <stdio>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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24 <exit_code range="137" level="fatal_oom" description="Out of Memory" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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25 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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26 </stdio>
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27 </xml>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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28
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29 <xml name="macro_citations">
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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30 <citations>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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31 <citation type="bibtex">
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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32 @misc{https://doi.org/10.48550/arxiv.1909.07930,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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33 doi = {10.48550/ARXIV.1909.07930},
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34 url = {https://arxiv.org/abs/1909.07930},
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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35 author = {Molino, Piero and Dudin, Yaroslav and Miryala, Sai Sumanth},
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36 title = {Ludwig: a type-based declarative deep learning toolbox},
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37 publisher = {arXiv},
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38 year = {2019},
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39 copyright = {arXiv.org perpetual, non-exclusive license}
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40 }
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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41 </citation>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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42 </citations>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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43 </xml>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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44
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45 <xml name="encoder_parameters">
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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46 <param argument="name" type="text" value="" label="Name of the column containing the input feature" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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47 <param argument="norm" type="select" label="Select the norm mode">
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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48 <option value="none" selected="true">Null</option>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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49 <option value="batch">batch</option>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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50 <option value="layer">layer</option>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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51 </param>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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52 <param argument="tied_weights" type="text" value="" optional="true" label="Name of the input feature to tie the weights of the encoder with" help="It needs to be the name of a feature of the same type and with the same encoder parameters. Optional" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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53 <yield />
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54 </xml>
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55
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56 <xml name="visualize_file_format">
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57 <param type="select" name="file_format" label="Choose the output format">
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58 <option value="pdf" selected="true">pdf</option>
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59 <option value="png">png</option>
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60 </param>
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61 </xml>
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62
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63 <xml name="visualize_output_feature_name">
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64 <param argument="output_feature_name" type="text" value="" optional="true" label="Name of the output feature" help="If `None`, use all output features." />
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65 </xml>
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66
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67 <xml name="visualize_training_statistics">
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68 <param argument="training_statistics" type="data" format="html,json" multiple="true" label="Training statistics" />
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69 </xml>
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70
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71 <xml name="visualize_test_statistics">
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72 <param argument="test_statistics" type="data" format="html,json" multiple="true" label="Choose experiment test statistics file(s)" />
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73 </xml>
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74
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75 <xml name="visualize_hyperopt_stats_path">
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76 <param argument="hyperopt_stats_path" type="data" format="json" label="Select the hyperopt result (JSON)" />
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77 </xml>
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78
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79 <xml name="visualize_model_names">
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80 <param argument="model_names" type="text" value="" optional="true" label="Model name(s) to use as labels" help="Comma delimited for multiple." />
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81 </xml>
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82
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83 <xml name="visualize_probabilities">
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84 <param argument="probabilities" type="data" format="html" multiple="true" label="Choose the prediction results to extract probabilities from" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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85 </xml>
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86
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87 <xml name="visualize_ground_truth_metadata">
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88 <param argument="ground_truth_metadata" type="data" format="ludwig_model,json" label="Choose the file containing feature metadata json file created during training" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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89 </xml>
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91 <xml name="visualize_split_file">
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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92 <param argument="split_file" type="data" format="csv" optional="true" label="Choose the file containing split values" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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93 </xml>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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94
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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95 <xml name="visualize_ground_truth_split">
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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96 <param argument="ground_truth_split" type="select" label="Select the ground truth split" >
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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97 <option value="0">0 -- training</option>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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98 <option value="1">1 -- validation</option>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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99 <option value="2">2 -- test</option>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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100 </param>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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101 </xml>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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102
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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103 <xml name="visualize_ground_truth">
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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104 <param argument="ground_truth" type="text" value="" label="Choose the ground truth file" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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105 </xml>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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106
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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107 <xml name="visualize_predictions">
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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108 <param argument="predictions" type="data" format="html" multiple="true" label="Choose the prediction result files" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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109 </xml>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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110
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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111 <xml name="visualize_top_n_classes">
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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112 <param argument="top_n_classes" type="text" value="" label="Type in the list containing numbers of classes to plot" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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113 </xml>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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114
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115 <xml name="visualize_threshold_output_feature_names">
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116 <param argument="threshold_output_feature_names" type="text" value="" label="Type in the list containing two output feature names for visualization" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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117 </xml>
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118
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119 <xml name="visualize_labels_limit">
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120 <param argument="labels_limit" type="integer" value="" optional="true" label="Set the upper limit on the numeric encoded label value" help="Encoded numeric label values in dataset that are higher than `label_limit` are considered to be 'rare' labels." min="1" max="1000"/>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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121 </xml>
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122
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123 <xml name="visualize_metrics">
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124 <param argument="metrics" type="select" multiple="true" label="Select the metrics to display" >
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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125 <option value="f1" selected="true">f1</option>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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126 <option value="precision">precision</option>
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127 <option value="recall">recall</option>
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128 <option value="accuracy">accuracy</option>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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129 </param>
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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130 </xml>
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131
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132 <xml name="visualize_positive_label">
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133 <param argument="positive_label" type="integer" value="1" label="Numeric encoded value for the positive class" min="1" max="1000" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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134 </xml>
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135
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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136 <xml name="visualize_ground_truth_apply_idx">
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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137 <param argument="ground_truth_apply_idx" type="boolean" checked="true" label="Whether to use metadata['str2idx'] in np.vectorize?" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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138 </xml>
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139
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140 <xml name="visualize_normalize">
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141 <param argument="normalize" type="boolean" checked="false" label="Whether to normalize rows in confusion matrix?" />
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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142 </xml>
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143 </macros>