Mercurial > repos > goeckslab > ludwig_experiment

annotate ludwig_experiment.xml @ 2:e1c7d044b759 draft default tip

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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 008bc5a8ee2c80f70fc224a23b5d2cd0c8ef1810
author goeckslab
date Fri, 14 Mar 2025 16:49:20 +0000
parents 78e6686a218e
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78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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1 <tool id="ludwig_experiment" name="Ludwig Experiment" version="@VERSION@" profile="@PROFILE@">
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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2 <description>trains and evaluates a model</description>
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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3 <macros>
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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4 <import>ludwig_macros.xml</import>
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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5 </macros>
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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6 <expand macro="python_requirements_gpu" />
2
e1c7d044b759 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 008bc5a8ee2c80f70fc224a23b5d2cd0c8ef1810
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7 <required_files>
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8 <include path="utils.py" />
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9 </required_files>
0
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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10 <expand macro="macro_stdio" />
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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11 <version_command>echo "@VERSION@"</version_command>
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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12 <command>
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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13 <![CDATA[
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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14 #import re
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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15 #if $config
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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16 ln -sf '$config' "./config.yml";
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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17 #end if
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19 #if $dataset
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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21 #set $sanitized_dataset = re.sub('[^\w\-_\.]', '_', $dataset.element_identifier.strip())
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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22 ln -sf '$dataset' "./${sanitized_dataset}";
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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23 #end if
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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25 #if $training_set
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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26 #set $sanitized_training_set = re.sub('[^\w\-_\.]', '_', $training_set.element_identifier.strip())
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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27 ln -sf '$training_set' "./${sanitized_training_set}";
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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28 #end if
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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30 #if $validation_set
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31
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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32 #set $sanitized_validation_set = re.sub('[^\w\-_\.]', '_', $validation_set.element_identifier.strip())
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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33 ln -sf '$validation_set' "./${sanitized_validation_set}";
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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34 #end if
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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36 #if $test_set
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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37
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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38 #set $sanitized_test_set = re.sub('[^\w\-_\.]', '_', $test_set.element_identifier.strip())
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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39 ln -sf '$test_set' "./${sanitized_test_set}";
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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40 #end if
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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41
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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42 #if $raw_data
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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43 unzip -o -q '$raw_data' -d ./;
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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44 #end if
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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45
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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46 python '$__tool_directory__/ludwig_experiment.py'
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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47 #if $config
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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48 --config "./config.yml"
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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49 #end if
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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50 #if $model_load_path
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51 --model_load_path '$model_load_path.extra_files_path'
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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52 #end if
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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53 #if $model_resume_path
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54 --model_resume_path '$model_resume_path.model_resume_path'
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55 #end if
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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56 #if $dataset
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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57 --dataset "./${sanitized_dataset}"
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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58 #end if
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59 #if $training_set
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60 --training_set "./${sanitized_training_set}"
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61 #end if
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62 #if $validation_set
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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63 --validation_set "./${sanitized_validation_set}"
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64 #end if
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65 #if $test_set
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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66 --test_set "./${sanitized_test_set}"
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67 #end if
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68 #if $training_set_metadata
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69 --training_set_metadata '$training_set_metadata'
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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70 #end if
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71 #if $disable_parallel_threads
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72 --disable_parallel_threads
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73 #end if
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74 #if $k_fold
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75 --k_fold '$k_fold'
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76 #end if
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77 --output_directory "."
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78 --data_format '$data_format'
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79 --backend local
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80 --eval_split '$eval_split'
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81 --random_seed $random_seed
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82 --skip_save_unprocessed_output
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83 --skip_save_k_fold_split_indices &&
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84
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85 mkdir -p '$output_model.extra_files_path' &&
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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86 cp -r experiment_run/model/*.json experiment_run/model/model_weights '$output_model.extra_files_path' &&
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87
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88 echo "Experiment is Done!"
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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89 ]]>
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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90 </command>
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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91 <configfiles>
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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92 <inputs name="inputs" />
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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93 </configfiles>
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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94 <inputs>
78e6686a218e planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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95 <param argument="config" type="data" format="yaml" label="Select the dataset containing model configuration" />
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96 <param argument="model_load_path" type="data" format="ludwig_model" optional="true" label="Load a pretrained model as initialization" help="Optional." />
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97 <param argument="model_resume_path" type="data" format="ludwig_model" optional="true" label="Load a pretained model to resume training" help="Optional." />
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98 <param argument="dataset" type="data" format="tabular,csv,h5,json,txt" optional="true" label="Input dataset" />
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99 <param argument="training_set" type="data" format="tabular,csv,h5,json" optional="true" label="Input traning dataset" />
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100 <param argument="validation_set" type="data" format="tabular,csv,h5,json" optional="true" label="Input validation dataset" />
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101 <param argument="test_set" type="data" format="tabular,csv,h5,json" optional="true" label="Input test dataset" />
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102 <param argument="training_set_metadata" type="data" format="json" optional="true" label="Training set metadata" />
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103 <param argument="data_format" type="select" label="Data format">
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104 <option value="auto" selected="true">auto</option>
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105 <option value="tsv">tsv</option>
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106 <option value="csv">csv</option>
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107 <option value="h5">h5</option>
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108 <option value="json">json</option>
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109 </param>
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110 <param argument="eval_split" type="select" label="Select the split portion for evaluation">
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111 <option value="training">training</option>
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112 <option value="validation">validation</option>
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113 <option value="test" selected="true">test</option>
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114 <option value="full">full</option>
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115 </param>
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116 <param argument="k_fold" type="integer" value="" optional="true" label="number of folds for a k-fold cross validation run" min="2" max="10"/>
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117 <param argument="random_seed" type="integer" value="42" label="Randomness seed" min="0" max="999999"/>
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118 <param argument="disable_parallel_threads" type="boolean" checked="false" label="Whether to disable parallel threads for reproducibility?" />
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119 <!-- <param argument="skip_save_predictions" type="boolean" checked="false" label="Whether to skip saving predictions?" /> -->
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120 <param name="raw_data" type="data" format="zip" optional="true" label="Raw data" help="Optional. Needed for images."/>
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121 </inputs>
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122 <outputs>
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123 <data format="ludwig_model" name="output_model" label="${tool.name} trained model on ${on_string}" />
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124 <data format="html" name="output_report" from_work_dir="ludwig_experiment_report.html" label="${tool.name} report on ${on_string}" />
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125 <collection type="list" name="output_pred_csv" label="${tool.name} predictions CSVs/experiment stats on ${on_string}" >
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126 <discover_datasets pattern="(?P&lt;designation&gt;predictions_parquet\.csv)" format="csv" directory="experiment_run" />
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127 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.json" format="json" directory="experiment_run" />
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128 </collection>
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129 </outputs>
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130 <tests>
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131 <test expect_num_outputs="3">
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132 <param name="dataset" value="temperature_la.csv" ftype="csv" />
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133 <param name="config" value="temperature_config.yml" ftype="yaml" />
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134 <param name="data_format" value="csv" />
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135 <output name="output_report" file="ludwig_experiment_report_test.html" compare="sim_size" delta="20000" >
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136 <assert_contents>
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137 <has_text text="Experiment" />
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138 </assert_contents>
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139 </output>
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140
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141 <output_collection name="output_pred_csv" type="list" >
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142 <element name="predictions_parquet.csv" >
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143 <assert_contents>
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144 <has_n_columns n="1" />
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145 </assert_contents>
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146 </element>
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147 </output_collection>
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148 </test>
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149 </tests>
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150 <help>
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151 <![CDATA[
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152 **What it does**
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153 Ludwig Experiment: train on one (portion of) dataset and evalue the model performance on another (portion of) dataset.
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154
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155
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156 **Output**
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157 An HTML containing the evaluation report of the trained model.
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158 A trained Ludwig model composite dataset.
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159 Predictions results (csv and jsons) from the model evaluations.
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160
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161
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162 ]]>
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163 </help>
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164 <expand macro="macro_citations" />
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165 </tool>