Mercurial > repos > goeckslab > ludwig_predict

annotate ludwig_predict.xml @ 3:11b1f328f312 draft default tip

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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit ac3a43f323353716470ccafaadf79d9c38314cff
author goeckslab
date Tue, 18 Mar 2025 22:10:22 +0000
parents afc8ed4a1838
children
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1 <tool id="ludwig_predict" name="Ludwig Predict" version="@VERSION@" profile="@PROFILE@">
0a7b83ddda17 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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2 <description>loads a pretrained model to do prediction</description>
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3 <macros>
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4 <import>ludwig_macros.xml</import>
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5 </macros>
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6 <expand macro="python_requirements_gpu" />
3
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7 <required_files>
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8 <include path="utils.py" />
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9 <include path="ludwig_experiment.py" />
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10 <include path="ludwig_predict.py" />
11b1f328f312 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit ac3a43f323353716470ccafaadf79d9c38314cff
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11 </required_files>
0
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12 <expand macro="macro_stdio" />
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13 <version_command>echo "@VERSION@"</version_command>
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14 <command>
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15 <![CDATA[
0a7b83ddda17 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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16 #import re
0a7b83ddda17 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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17 mkdir -p outputs &&
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18 #if $dataset
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19 #set $sanitized_dataset = re.sub('[^\w\-_\.]', '_', $dataset.element_identifier.strip())
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20 ln -sf '$dataset' "./${sanitized_dataset}";
0a7b83ddda17 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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21 #end if
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22
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23 #if $raw_data
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24 unzip -o -q '$raw_data' -d ./;
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25 #end if
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26
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27 python '$__tool_directory__/ludwig_predict.py'
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28 #if $model_path
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29 --model_path '$model_path.extra_files_path'
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30 #end if
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31 #if $dataset
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32 --dataset "./${sanitized_dataset}"
0a7b83ddda17 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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33 #end if
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34 #if $disable_parallel_threads
0a7b83ddda17 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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35 --disable_parallel_threads
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36 #end if
0a7b83ddda17 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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37 --output_directory "./outputs"
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38 --data_format '$data_format'
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39 --split '$split'
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40 --backend local
0a7b83ddda17 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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41 --skip_save_unprocessed_output &&
0a7b83ddda17 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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42 echo "Prediction is done!"
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43
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44 ]]>
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45 </command>
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46 <configfiles>
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47 <inputs name="inputs" />
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48 </configfiles>
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49 <inputs>
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50 <param name="model_path" type="data" format="ludwig_model" label="Load the pretrained model" />
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51 <param name="dataset" type="data" format="tabular,csv,h5,json,txt" label="Input dataset" />
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52 <param name="data_format" type="select" label="Data format">
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53 <option value="auto" selected="true">auto</option>
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54 <option value="tsv">tsv</option>
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55 <option value="csv">csv</option>
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56 <option value="h5">h5</option>
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57 <option value="json">json</option>
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58 </param>
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59 <param name="split" type="select" label="Select the split portion to test the model on">
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60 <option value="training">training</option>
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61 <option value="validation">validation</option>
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62 <option value="test">test</option>
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63 <option value="full" selected="true">full</option>
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64 </param>
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65 <param name="batch_size" type="integer" value="128" optional="true" label="Batch size" min="1" max="4096" />
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66 <param name="disable_parallel_threads" type="boolean" checked="false" label="Whether to disable parallel threads for reproducibility?" />
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67 <param name="raw_data" type="data" format="zip" optional="true" label="Raw data" help="Optional. Needed for images."/>
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68 </inputs>
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69 <outputs>
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70 <collection type="list" name="output_csv" label="${tool.name} CSV on ${on_string}" >
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71 <discover_datasets pattern="(?P&lt;designation&gt;predictions_parquet\.csv)" format="csv" directory="outputs" />
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72 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.json" format="json" directory="outputs" />
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73 </collection>
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74 <!-- <data format="html" name="output_report" from_work_dir="outputs/smart_report.html" label="${tool.name} report on ${on_string}" /> -->
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75 <!-- <data format="csv" name="output_top_k" label="${tool.name} top K predictions on ${on_string}" /> -->
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76 </outputs>
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77 <tests>
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78 <test>
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79 <param name="model_path" value="" ftype="ludwig_model">
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80 <composite_data value="temp_model01/model_hyperparameters.json" />
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81 <composite_data value="temp_model01/model_weights" />
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82 <composite_data value="temp_model01/training_set_metadata.json" />
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83 <composite_data value="temp_model01/training_progress.json" />
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84 </param>
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85 <param name="dataset" value="temperature_la.csv" ftype="csv" />
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86 <param name="split" value="test" />
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87 <output_collection name="output_csv">
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88 <element name="predictions_parquet.csv">
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89 <assert_contents>
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90 <has_n_columns n="1" />
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91 </assert_contents>
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92 </element>
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93 </output_collection>
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94 </test>
0a7b83ddda17 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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95 </tests>
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96 <help>
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97 <![CDATA[
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98 **What it does**
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99 This tool conducts `ludwig predict`.
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100
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101
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102 **Input**
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103 - a trained ludwig model.
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104 - dataset to be evaluate.
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105
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106
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107 **Output**
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108 - report in html.
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109 - a collection of prediction results.
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110
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111
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112
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113 ]]>
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114 </help>
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115 <expand macro="macro_citations" />
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116 </tool>