Mercurial > repos > goeckslab > image_learner

annotate image_learner.xml @ 20:64872c48a21f draft

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planemo upload for repository https://github.com/goeckslab/gleam.git commit d4b122527a2402e43512f9b4bda00c7bff0ec9e9
author goeckslab
date Tue, 06 Jan 2026 15:35:11 +0000
parents c460abae83eb
children d5c582cf74bc
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c460abae83eb planemo upload for repository https://github.com/goeckslab/gleam.git commit b47f0fd63d8d5d18d602d45bb21ebbe36ba4fcfe
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1 <tool id="image_learner" name="Image Learner" version="0.1.5" profile="22.01">
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2 <description>trains and evaluates an image classification/regression model</description>
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3 <requirements>
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4 <container type="docker">quay.io/goeckslab/galaxy-ludwig-gpu:0.10.1</container>
0
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5 </requirements>
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6 <required_files>
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7 <include path="constants.py" />
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8 <include path="html_structure.py" />
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9 <include path="image_learner_cli.py" />
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10 <include path="image_workflow.py" />
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11 <include path="ludwig_backend.py" />
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12 <include path="metaformer_setup.py" />
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13 <include path="plotly_plots.py" />
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14 <include path="split_data.py" />
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15 <include path="utils.py" />
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16 <include path="MetaFormer/__init__.py" />
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17 <include path="MetaFormer/metaformer_models.py" />
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18 <include path="MetaFormer/metaformer_stacked_cnn.py" />
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19 </required_files>
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20 <stdio>
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21 <exit_code range="137" level="fatal_oom" description="Out of Memory" />
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22 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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23 </stdio>
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24 <command>
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25 <![CDATA[
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26 #import re
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27 #if $input_csv
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28 #set $sanitized_input_csv = re.sub('[^\w\-_\.]', '_', $input_csv.element_identifier.strip())
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29 ln -sf '$input_csv' "./${sanitized_input_csv}";
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30 #end if
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31
20
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32 #set $selected_validation_metric = ""
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33 #if $task_selection.task == "binary"
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34 #set $selected_validation_metric = $task_selection.validation_metric_binary
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35 #elif $task_selection.task == "classification"
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36 #set $selected_validation_metric = $task_selection.validation_metric_multiclass
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37 #elif $task_selection.task == "regression"
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38 #set $selected_validation_metric = $task_selection.validation_metric_regression
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39 #else
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40 #if $task_selection.validation_metric_auto
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41 #set $selected_validation_metric = $task_selection.validation_metric_auto
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42 #end if
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43 #end if
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44
0
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45 python '$__tool_directory__/image_learner_cli.py'
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46 --csv-file "./${sanitized_input_csv}"
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47 --image-zip "$image_zip"
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48 --model-name "$model_name"
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49 #if $scratch_fine_tune.use_pretrained == "true"
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50 --use-pretrained
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51 #if $scratch_fine_tune.fine_tune == "true"
0
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52 --fine-tune
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53 #end if
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54 #end if
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55 #if $advanced_settings.customize_defaults == "true"
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56 #if $advanced_settings.epochs
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57 --epochs "$advanced_settings.epochs"
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58 #end if
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59 #if $advanced_settings.early_stop
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60 --early-stop "$advanced_settings.early_stop"
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61 #end if
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62 #if $advanced_settings.learning_rate_condition.learning_rate_define == "true"
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63 --learning-rate "$advanced_settings.learning_rate_condition.learning_rate"
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64 #end if
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65 #if $advanced_settings.batch_size_condition.batch_size_define == "true"
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66 --batch-size "$advanced_settings.batch_size_condition.batch_size"
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67 #end if
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68 --split-probabilities "$advanced_settings.train_split" "$advanced_settings.val_split" "$advanced_settings.test_split"
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69 #if $advanced_settings.threshold
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70 --threshold "$advanced_settings.threshold"
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71 #end if
0
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72 #end if
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73 #if $augmentation
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74 --augmentation "$augmentation"
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75 #end if
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76 #if $selected_validation_metric
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77 --validation-metric "$selected_validation_metric"
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78 #end if
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79 #if $column_override.override_columns == "true"
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80 #if $column_override.target_column
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81 --target-column "$column_override.target_column"
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82 #end if
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83 #if $column_override.image_column
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84 --image-column "$column_override.image_column"
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85 #end if
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86 #end if
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87 #if $sample_id_column
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88 --sample-id-column "$sample_id_column"
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89 #end if
11
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90 --image-resize "$image_resize"
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91 --random-seed "$random_seed"
0
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92 --output-dir "." &&
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93
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94 mkdir -p '$output_model.extra_files_path' &&
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95 cp -r experiment_run/model/*.json experiment_run/model/model_weights '$output_model.extra_files_path' &&
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96
2
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97 echo "Image Learner Classification Experiment is Done!"
0
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98 ]]>
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99 </command>
2
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100
0
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101 <inputs>
14
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102 <param name="input_csv" type="data" format="csv" optional="false" label="the metadata csv containing image_path column, label column and optional split column" />
0
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103 <param name="image_zip" type="data" format="zip" optional="false" label="Image zip" help="Image zip file containing your image data"/>
15
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104 <conditional name="task_selection">
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105 <param name="task" type="select" label="Task type" help="Pick task to see only metrics Ludwig accepts for that task; Auto lets the tool infer task and metric.">
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106 <option value="auto" selected="true">Auto (infer and use defaults)</option>
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107 <option value="binary">Binary Classification</option>
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108 <option value="classification">Multi-class Classification</option>
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109 <option value="regression">Regression</option>
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110 </param>
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111 <when value="binary">
20
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112 <param name="validation_metric_binary" type="select" optional="true" label="Validation metric (binary)" help="Metrics accepted by Ludwig 0.10.1 for binary outputs.">
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113 <option value="" selected="true">Auto (use task default)</option>
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114 <option value="roc_auc">ROC-AUC</option>
15
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115 <option value="accuracy">Accuracy</option>
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116 <option value="precision">Precision</option>
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117 <option value="recall">Recall</option>
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118 <option value="loss">Loss</option>
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119 </param>
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120 </when>
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121 <when value="classification">
20
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122 <param name="validation_metric_multiclass" type="select" optional="true" label="Validation metric (multi-class)" help="Metrics accepted by Ludwig 0.10.1 for multi-class outputs.">
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123 <option value="" selected="true">Auto (use task default)</option>
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124 <option value="accuracy">Accuracy</option>
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125 <option value="loss">Loss</option>
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126 </param>
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127 </when>
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128 <when value="regression">
20
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129 <param name="validation_metric_regression" type="select" optional="true" label="Validation metric (regression)" help="Metrics accepted by Ludwig 0.10.1 for regression outputs.">
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130 <option value="" selected="true">Auto (use task default)</option>
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131 <option value="mean_squared_error">Mean Squared Error</option>
18
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132 <option value="mean_absolute_error">Mean Absolute Error</option>
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133 <option value="root_mean_squared_error">Root Mean Squared Error</option>
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134 <option value="root_mean_squared_percentage_error">Root Mean Squared Percentage Error</option>
15
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135 <option value="loss">Loss</option>
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136 </param>
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137 </when>
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138 <when value="auto">
20
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139 <param name="validation_metric_auto" type="select" optional="true" label="Validation metric (auto)" help="Auto defers to the inferred task and picks the best default metric; use this only to override the choice.">
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140 <option value="" selected="true"></option>
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141 </param>
15
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142 </when>
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143 </conditional>
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144 <conditional name="column_override">
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145 <param name="override_columns" type="select" label="Overwrite label and/or image column names?" help="Select yes to specify custom column names instead of the defaults 'label' and 'image_path'.">
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146 <option value="false" selected="true">No</option>
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147 <option value="true">Yes</option>
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148 </param>
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149 <when value="true">
20
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150 <param name="target_column" type="data_column" data_ref="input_csv" use_header_names="true" optional="true" label="Target/label column name" help="Overrides the default 'label' column name in the metadata CSV." />
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151 <param name="image_column" type="data_column" data_ref="input_csv" use_header_names="true" optional="true" label="Image column name" help="Overrides the default 'image_path' column name in the metadata CSV." />
15
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152 </when>
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153 <when value="false">
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154 <!-- No additional parameters -->
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155 </when>
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156 </conditional>
20
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157 <param name="sample_id_column" type="data_column" data_ref="input_csv" use_header_names="true" optional="true" label="Sample ID column (optional)" help="Optional column used to group samples during splitting to prevent data leakage (e.g., patient_id or slide_id). Only used when no split column is provided." />
0
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158 <param name="model_name" type="select" optional="false" label="Select a model for your experiment" >
2
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159
0
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160 <option value="resnet18">Resnet18</option>
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161 <option value="resnet34">Resnet34</option>
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162 <option value="resnet50">Resnet50</option>
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163 <option value="resnet101">Resnet101</option>
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164 <option value="resnet152">Resnet152</option>
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165 <option value="resnext50_32x4d">Resnext50_32x4d</option>
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166 <option value="resnext101_32x8d">Resnext101_32x8d</option>
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167 <option value="resnext101_64x4d">Resnext101_64x4d</option>
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168 <option value="resnext152_32x8d">Resnext152_32x8d</option>
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169 <option value="wide_resnet50_2">Wide_resnet50_2</option>
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170 <option value="wide_resnet101_2">Wide_resnet101_2</option>
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171 <option value="wide_resnet103_2">Wide_resnet103_2</option>
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172 <option value="efficientnet_b0">Efficientnet_b0</option>
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173 <option value="efficientnet_b1">Efficientnet_b1</option>
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174 <option value="efficientnet_b2">Efficientnet_b2</option>
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175 <option value="efficientnet_b3">Efficientnet_b3</option>
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176 <option value="efficientnet_b4">Efficientnet_b4</option>
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177 <option value="efficientnet_b5">Efficientnet_b5</option>
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178 <option value="efficientnet_b6">Efficientnet_b6</option>
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179 <option value="efficientnet_b7">Efficientnet_b7</option>
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180 <option value="efficientnet_v2_s">Efficientnet_v2_s</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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181 <option value="efficientnet_v2_m">Efficientnet_v2_m</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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182 <option value="efficientnet_v2_l">Efficientnet_v2_l</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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183 <option value="regnet_y_400mf">Regnet_y_400mf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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184 <option value="regnet_y_800mf">Regnet_y_800mf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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185 <option value="regnet_y_1_6gf">Regnet_y_1_6gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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186 <option value="regnet_y_3_2gf">Regnet_y_3_2gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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187 <option value="regnet_y_8gf">Regnet_y_8gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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188 <option value="regnet_y_16gf">Regnet_y_16gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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189 <option value="regnet_y_32gf">Regnet_y_32gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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190 <option value="regnet_y_128gf">Regnet_y_128gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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191 <option value="regnet_x_400mf">Regnet_x_400mf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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192 <option value="regnet_x_800mf">Regnet_x_800mf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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193 <option value="regnet_x_1_6gf">Regnet_x_1_6gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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194 <option value="regnet_x_3_2gf">Regnet_x_3_2gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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195 <option value="regnet_x_8gf">Regnet_x_8gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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196 <option value="regnet_x_16gf">Regnet_x_16gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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197 <option value="regnet_x_32gf">Regnet_x_32gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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198 <option value="vgg11">Vgg11</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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199 <option value="vgg11_bn">Vgg11_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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200 <option value="vgg13">Vgg13</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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201 <option value="vgg13_bn">Vgg13_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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202 <option value="vgg16">Vgg16</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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203 <option value="vgg16_bn">Vgg16_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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204 <option value="vgg19">Vgg19</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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205 <option value="vgg19_bn">Vgg19_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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206 <option value="shufflenet_v2_x0_5">Shufflenet_v2_x0_5</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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207 <option value="shufflenet_v2_x1_0">Shufflenet_v2_x1_0</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
208 <option value="shufflenet_v2_x1_5">Shufflenet_v2_x1_5</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
209 <option value="shufflenet_v2_x2_0">Shufflenet_v2_x2_0</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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210 <option value="squeezenet1_0">Squeezenet1_0</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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211 <option value="squeezenet1_1">Squeezenet1_1</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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212 <option value="swin_t">Swin_t</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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213 <option value="swin_s">Swin_s</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
214 <option value="swin_b">Swin_b</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
215 <option value="swin_v2_t">Swin_v2_t</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
216 <option value="swin_v2_s">Swin_v2_s</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
217 <option value="swin_v2_b">Swin_v2_b</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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218 <option value="vit_b_16">Vit_b_16</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
219 <option value="vit_b_32">Vit_b_32</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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220 <option value="vit_l_16">Vit_l_16</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
221 <option value="vit_l_32">Vit_l_32</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
222 <option value="vit_h_14">Vit_h_14</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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223 <option value="convnext_tiny">Convnext_tiny</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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diff changeset
224 <option value="convnext_small">Convnext_small</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
225 <option value="convnext_base">Convnext_base</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff changeset
226 <option value="convnext_large">Convnext_large</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
227 <option value="maxvit_t">Maxvit_t</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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228 <option value="alexnet">Alexnet</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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229 <option value="googlenet">Googlenet</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
230 <option value="inception_v3">Inception_v3</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
231 <option value="mobilenet_v2">Mobilenet_v2</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
232 <option value="mobilenet_v3_large">Mobilenet_v3_large</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
233 <option value="mobilenet_v3_small">Mobilenet_v3_small</option>
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
234 <!-- MetaFormer Models -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
235 <option value="identityformer_s12">IdentityFormer S12</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
236 <option value="identityformer_s24">IdentityFormer S24</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
237 <option value="identityformer_s36">IdentityFormer S36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
238 <option value="identityformer_m36">IdentityFormer M36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
239 <option value="identityformer_m48">IdentityFormer M48</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
240 <option value="randformer_s12">RandFormer S12</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
241 <option value="randformer_s24">RandFormer S24</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
242 <option value="randformer_s36">RandFormer S36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
243 <option value="randformer_m36">RandFormer M36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
244 <option value="randformer_m48">RandFormer M48</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
245 <option value="poolformerv2_s12">PoolFormerV2 S12</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
246 <option value="poolformerv2_s24">PoolFormerV2 S24</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
247 <option value="poolformerv2_s36">PoolFormerV2 S36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
248 <option value="poolformerv2_m36">PoolFormerV2 M36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
249 <option value="poolformerv2_m48">PoolFormerV2 M48</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
250 <option value="convformer_s18">ConvFormer S18</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
251 <option value="convformer_s18_384">ConvFormer S18 384</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
252 <option value="convformer_s18_in21ft1k">ConvFormer S18 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
253 <option value="convformer_s18_384_in21ft1k">ConvFormer S18 384 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
254 <option value="convformer_s18_in21k">ConvFormer S18 ImageNet21k Pretrained</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
255 <option value="convformer_s36">ConvFormer S36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
256 <option value="convformer_s36_384">ConvFormer S36 384</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
257 <option value="convformer_s36_in21ft1k">ConvFormer S36 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
258 <option value="convformer_s36_384_in21ft1k">ConvFormer S36 384 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
259 <option value="convformer_s36_in21k">ConvFormer S36 ImageNet21k Pretrained</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
260 <option value="convformer_m36">ConvFormer M36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
261 <option value="convformer_m36_384">ConvFormer M36 384</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
262 <option value="convformer_m36_in21ft1k">ConvFormer M36 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
263 <option value="convformer_m36_384_in21ft1k">ConvFormer M36 384 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
264 <option value="convformer_m36_in21k">ConvFormer M36 ImageNet21k Pretrained</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
265 <option value="convformer_b36">ConvFormer B36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
266 <option value="convformer_b36_384">ConvFormer B36 384</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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267 <option value="convformer_b36_in21ft1k">ConvFormer B36 ImageNet21k</option>
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268 <option value="convformer_b36_384_in21ft1k">ConvFormer B36 384 ImageNet21k</option>
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269 <option value="convformer_b36_in21k">ConvFormer B36 ImageNet21k Pretrained</option>
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270 <option value="caformer_s18">CAFormer S18</option>
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271 <option value="caformer_s18_384">CAFormer S18 384</option>
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272 <option value="caformer_s18_in21ft1k">CAFormer S18 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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273 <option value="caformer_s18_384_in21ft1k">CAFormer S18 384 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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274 <option value="caformer_s18_in21k">CAFormer S18 ImageNet21k Pretrained</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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275 <option value="caformer_s36">CAFormer S36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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276 <option value="caformer_s36_384">CAFormer S36 384</option>
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277 <option value="caformer_s36_in21ft1k">CAFormer S36 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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278 <option value="caformer_s36_384_in21ft1k">CAFormer S36 384 ImageNet21k</option>
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279 <option value="caformer_s36_in21k">CAFormer S36 ImageNet21k Pretrained</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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280 <option value="caformer_m36">CAFormer M36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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281 <option value="caformer_m36_384">CAFormer M36 384</option>
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282 <option value="caformer_m36_in21ft1k">CAFormer M36 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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283 <option value="caformer_m36_384_in21ft1k">CAFormer M36 384 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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284 <option value="caformer_m36_in21k">CAFormer M36 ImageNet21k Pretrained</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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285 <option value="caformer_b36">CAFormer B36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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286 <option value="caformer_b36_384">CAFormer B36 384</option>
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287 <option value="caformer_b36_in21ft1k">CAFormer B36 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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288 <option value="caformer_b36_384_in21ft1k">CAFormer B36 384 ImageNet21k</option>
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289 <option value="caformer_b36_in21k">CAFormer B36 ImageNet21k Pretrained</option>
0
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290 </param>
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291
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292 <conditional name="scratch_fine_tune">
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293 <param name="use_pretrained" type="select"
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294 label="Use pretrained weights?"
9
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295 help="If select no, the encoder, combiner, and decoder will all be initialized and trained from scratch. (e.g. when your images are very different from ImageNet or no suitable pretrained model exists.)">
0
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296 <option value="false">No</option>
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297 <option value="true" selected="true">Yes</option>
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298 </param>
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299 <when value="true">
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300 <param name="fine_tune" type="select" label="Fine tune the encoder?"
8
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301 help="Whether to fine tune the encoder(combiner and decoder will be fine-tuned anyway)" >
0
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302 <option value="false" >No</option>
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303 <option value="true" selected="true">Yes</option>
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304 </param>
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305 </when>
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306 <when value="false">
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307 <!-- No additional parameters to show if the user selects 'No' -->
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308 </when>
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309 </conditional>
14
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310 <param name="image_resize"
11
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311 type="select"
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312 label="Image Resize"
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313 help="Select the size to resize images to. Original size keeps images as-is, while other options resize all images to the specified dimensions.">
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314 <option value="original" selected="true">Original Size (No Resize)</option>
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315 <option value="96x96">96x96</option>
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316 <option value="128x128">128x128</option>
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317 <option value="160x160">160x160</option>
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318 <option value="192x192">192x192</option>
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319 <option value="220x220">220x220</option>
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320 <option value="224x224">224x224</option>
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321 <option value="256x256">256x256</option>
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322 <option value="299x299">299x299</option>
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323 <option value="320x320">320x320</option>
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324 <option value="384x384">384x384</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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325 <option value="448x448">448x448</option>
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326 <option value="512x512">512x512</option>
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327 </param>
14
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328 <param name="augmentation"
2
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329 type="select"
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330 multiple="true"
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331 display="checkboxes"
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332 label="Image Augmentation"
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333 help="Pick any combination of augmentations to apply">
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334 <option value="random_horizontal_flip">Random Horizontal Flip</option>
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335 <option value="random_vertical_flip">Random Vertical Flip</option>
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336 <option value="random_rotate">Random Rotate</option>
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337 <option value="random_blur">Random Blur</option>
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338 <option value="random_brightness">Random Brightness</option>
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339 <option value="random_contrast">Random Contrast</option>
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340 </param>
0
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341 <param argument="random_seed" type="integer" value="42" optional="true" label="Random seed (set for reproducibility)" min="0" max="999999"/>
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342 <conditional name="advanced_settings">
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343 <param name="customize_defaults" type="select" label="Customize Default Settings?" help="Select yes if you want to customize the default settings of the experiment.">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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344 <option value="false" selected="true">No</option>
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345 <option value="true">Yes</option>
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346 </param>
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347 <when value="true">
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348 <param name="epochs" type="integer" value="10" min="1" max="99999" label="Epochs" help="Total number of full passes through the training dataset. Higher values may improve accuracy but increase training time. Default: 10." />
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349 <param name="early_stop" type="integer" value="5" min="1" max="99999" label="Early Stop" help="Number of epochs with no improvement after which training will be stopped. Default: 5." />
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350 <conditional name="learning_rate_condition">
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351 <param name="learning_rate_define" type="select" label="Define an initial learning rate?" help="Want to change the initial learning rate from default to a number? See ludwig.ai for more info. Default: No" >
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352 <option value="false" selected="true" >No</option>
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353 <option value="true">Yes</option>
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354 </param>
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355 <when value="true">
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356 <param name="learning_rate" type="float" value="0.001" min="0.0001" max="1.0" label="Learning Rate" help="Initial learning rate for the optimizer. Default: 0.001." />
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357 </when>
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358 <when value="false">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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359 <!-- No additional parameters to show if the user selects 'No' -->
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
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360 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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361 </conditional>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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362 <conditional name="batch_size_condition">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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363 <param name="batch_size_define" type="select" label="Define your batch size?" help="Want to change the batch size from auto to a number? See ludwig.ai for more info. Default: No" >
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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364 <option value="false" selected="true" >No</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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365 <option value="true">Yes</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
366 </param>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
367 <when value="true">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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368 <param name="batch_size" type="integer" value="32" min="1" max="99999" label="Batch Size" help="Number of samples per gradient update. Default: 32." />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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369 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
370 <when value="false">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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diff changeset
371 <!-- No additional parameters to show if the user selects 'No' -->
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
372 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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373 </conditional>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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374 <param name="train_split" type="float"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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375 label="Training split proportion (only works if no split column in the metadata csv)"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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376 value="0.7"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
377 help="Fraction of data for training (e.g., 0.7). train split + val split + test split should = 1"/>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
378 <param name="val_split" type="float"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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379 label="Validation split proportion (only works if no split column in the metadata csv)"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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diff changeset
380 value="0.1"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
381 help="Fraction of data for validation (e.g., 0.1). train split + val split + test split should = 1"/>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
382 <param name="test_split" type="float"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
383 label="Test split proportion (only works if no split column in the metadata csv)"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
384 value="0.2"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff changeset
385 help="Fraction of data for testing (e.g., 0.2) train split + val split + test split should = 1."/>
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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parents: 5
diff changeset
386 <param name="threshold" type="float" value="0.5" min="0.0" max="1.0" optional="true" label="Decision Threshold (binary only)" help="Set the decision threshold for binary classification (0.0–1.0). Only applies when task is binary; default is 0.5." />
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
387 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
388 <when value="false">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
389 <!-- No additional parameters to show if the user selects 'No' -->
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
390 </when>
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
391 </conditional>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
392 </inputs>
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
393 <outputs>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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394 <data format="ludwig_model" name="output_model" label="${tool.name} trained model on ${on_string}" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
395 <data format="html" name="output_report" from_work_dir="image_classification_results_report.html" label="${tool.name} report on ${on_string}" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
396 <collection type="list" name="output_pred_csv" label="${tool.name} predictions CSVs/experiment stats/plots on ${on_string}" >
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
397 <discover_datasets pattern="(?P&lt;designation&gt;predictions\.csv)" format="csv" directory="experiment_run" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
398 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.json" format="json" directory="experiment_run" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
399 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" format="png" directory="experiment_run/visualizations/train" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
400 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" format="png" directory="experiment_run/visualizations/test" />
19
c460abae83eb planemo upload for repository https://github.com/goeckslab/gleam.git commit b47f0fd63d8d5d18d602d45bb21ebbe36ba4fcfe
goeckslab
parents: 18
diff changeset
401 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" format="png" directory="experiment_run/feature_importance_examples" />
c460abae83eb planemo upload for repository https://github.com/goeckslab/gleam.git commit b47f0fd63d8d5d18d602d45bb21ebbe36ba4fcfe
goeckslab
parents: 18
diff changeset
402 <discover_datasets pattern="(?P&lt;designation&gt;feature_importance_examples\.zip)" format="zip" directory="experiment_run" />
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
403 </collection>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
404 </outputs>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
405 <tests>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
406 <test expect_num_outputs="3">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
407 <param name="input_csv" value="mnist_subset.csv" ftype="csv" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
408 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
409 <param name="model_name" value="resnet18" />
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
410 <param name="augmentation" value="random_horizontal_flip,random_vertical_flip,random_rotate" />
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 14
diff changeset
411 <param name="task_selection|task" value="classification" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 14
diff changeset
412 <param name="task_selection|validation_metric_multiclass" value="accuracy" />
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
413 <output name="output_report">
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
414 <assert_contents>
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 14
diff changeset
415 <has_text text="Config and Overall Performance Summary" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 14
diff changeset
416 <has_text text="Training and Validation Results" />
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
417 <has_text text="Test Results" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
418 </assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
419 </output>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
420
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
421 <output_collection name="output_pred_csv" type="list" >
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
422 <element name="predictions.csv" >
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
423 <assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
424 <has_n_columns n="1" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
425 </assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
426 </element>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
427 </output_collection>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
428 </test>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
429 <test expect_num_outputs="3">
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
430 <param name="input_csv" value="utkface_labels.csv" ftype="csv" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
431 <param name="image_zip" value="age_regression.zip" ftype="zip" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
432 <param name="model_name" value="resnet18" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
433 <output name="output_report">
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
434 <assert_contents>
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 14
diff changeset
435 <has_text text="Config and Overall Performance Summary" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 14
diff changeset
436 <has_text text="Training and Validation Results" />
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
437 <has_text text="Test Results" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
438 </assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
439 </output>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
440 <output_collection name="output_pred_csv" type="list" >
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
441 <element name="predictions.csv" >
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
442 <assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
443 <has_n_columns n="1" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
444 </assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
445 </element>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
446 </output_collection>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
447 </test>
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
448 <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
449 <param name="input_csv" value="mnist_subset.csv" ftype="csv" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
450 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
451 <param name="model_name" value="caformer_s18" />
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452 <output name="output_report">
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453 <assert_contents>
15
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454 <has_text text="Config and Overall Performance Summary" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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455 <has_text text="Training and Validation Results" />
11
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456 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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457 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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458 </output>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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459
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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460 <output_collection name="output_pred_csv" type="list" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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461 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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462 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
463 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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464 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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465 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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466 </output_collection>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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467 </test>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
468 <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
469 <param name="input_csv" value="mnist_subset.csv" ftype="csv" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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470 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
471 <param name="model_name" value="randformer_s12" />
14
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472 <param name="advanced_settings|customize_defaults" value="true" />
94cd9ac4a9b1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 3188005878e1ad81b0ca59c9c4d4d40dd981acf7
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473 <param name="advanced_settings|epochs" value="5" />
11
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474 <output name="output_report">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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475 <assert_contents>
15
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476 <has_text text="Test Performance Summary" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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477 <has_text text="Training and Validation Results" />
11
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478 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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479 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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480 </output>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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481
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
482 <output_collection name="output_pred_csv" type="list" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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483 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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484 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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485 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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486 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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487 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
488 </output_collection>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
489 </test>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
490 <!-- Test 7: MetaFormer with 384x384 input - verifies model correctly handles non-224x224 dimensions -->
16
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diff changeset
491 <!-- <test expect_num_outputs="3">
11
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diff changeset
492 <param name="input_csv" value="mnist_subset.csv" ftype="csv" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
493 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
494 <param name="model_name" value="caformer_s18_384" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
495 <param name="image_resize" value="384x384" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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496 <output name="output_report">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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497 <assert_contents>
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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diff changeset
498 <has_text text="Config and Overall Performance Summary" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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499 <has_text text="Training and Validation Results" />
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
500 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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501 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
502 </output>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
503 <output_collection name="output_pred_csv" type="list" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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parents: 9
diff changeset
504 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
505 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
506 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
507 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
508 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
509 <element name="description" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
510 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
511 <has_text text="384" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
512 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
513 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
514 </output_collection>
16
8729f69e9207 planemo upload for repository https://github.com/goeckslab/gleam.git commit bb4bcdc888d73bbfd85d78ce8999a1080fe813ff
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diff changeset
515 </test> -->
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
516 <!-- Test 8: Binary classification with custom threshold - verifies ROC curve generation for binary tasks; need to find a test dataset -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
517 <!-- <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
518 <param name="input_csv" value="binary_classification.csv" ftype="csv" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
519 <param name="image_zip" value="binary_images.zip" ftype="zip" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
520 <param name="model_name" value="resnet18" />
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
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diff changeset
521 <param name="advanced_settings|customize_defaults" value="true" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
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diff changeset
522 <param name="advanced_settings|threshold" value="0.6" />
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
523 <output name="output_report">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
524 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
525 <has_text text="Results Summary" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
526 <has_text text="Train/Validation Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
527 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
528 <has_text text="ROC-AUC Curves" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
529 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
530 </output>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
531 <output_collection name="output_pred_csv" type="list" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
532 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
533 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
534 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
535 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
536 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
537 <element name="test_statistics.json" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
538 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
539 <has_text text="roc_auc" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
540 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
541 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
542 </output_collection>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
543 </test> -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
544 <!-- Test 9: PoolFormerV2 model configuration - verifies custom_model parameter persists in config -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
545 <!-- Test 10: Multi-class classification with ROC curves - verifies robust ROC-AUC plot generation -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
546 <!-- <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
547 <param name="input_csv" value="mnist_subset.csv" ftype="csv" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
548 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
549 <param name="model_name" value="resnet18" />
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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diff changeset
550 <param name="advanced_settings|customize_defaults" value="true" />
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551 <param name="advanced_settings|epochs" value="3" />
11
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552 <output name="output_report">
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553 <assert_contents>
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554 <has_text text="Results Summary" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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555 <has_text text="Train/Validation Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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556 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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557 <has_text text="ROC-AUC Curves" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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558 <has_text text="Micro-average ROC" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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559 </assert_contents>
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560 </output>
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561 <output_collection name="output_pred_csv" type="list" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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562 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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563 <assert_contents>
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564 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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565 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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566 </element>
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567 </output_collection>
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568 </test> -->
12
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569 <test expect_num_outputs="3">
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570 <param name="input_csv" value="mnist_subset_binary.csv" ftype="csv" />
bcfa2e234a80 planemo upload for repository https://github.com/goeckslab/gleam.git commit 96bab8325992d16fcaad8e0a4dc4c62b00e2abc2
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571 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
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572 <param name="model_name" value="resnet18" />
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573 <param name="advanced_settings|customize_defaults" value="true" />
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574 <param name="advanced_settings|threshold" value="0.6" />
15
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575 <param name="task_selection|task" value="classification" />
20
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576 <param name="task_selection|validation_metric_multiclass" value="accuracy" />
12
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577 <output name="output_report">
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578 <assert_contents>
15
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579 <has_text text="Config and Overall Performance Summary" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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580 <has_text text="Training and Validation Results" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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581 <has_text text="Test Results" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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582 <has_text text="Threshold" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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583 <has_text text="0.60" />
12
bcfa2e234a80 planemo upload for repository https://github.com/goeckslab/gleam.git commit 96bab8325992d16fcaad8e0a4dc4c62b00e2abc2
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diff changeset
584 </assert_contents>
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585 </output>
bcfa2e234a80 planemo upload for repository https://github.com/goeckslab/gleam.git commit 96bab8325992d16fcaad8e0a4dc4c62b00e2abc2
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586 <output_collection name="output_pred_csv" type="list" >
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587 <element name="predictions.csv" >
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588 <assert_contents>
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589 <has_n_columns n="1" />
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590 </assert_contents>
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591 </element>
bcfa2e234a80 planemo upload for repository https://github.com/goeckslab/gleam.git commit 96bab8325992d16fcaad8e0a4dc4c62b00e2abc2
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592 </output_collection>
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593 </test>
9
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594 </tests>
0
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595 <help>
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596 <![CDATA[
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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597 **What it does**
9
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598 Image Learner for Classification/regression: trains and evaluates a image classification/regression model.
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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599 It uses the metadata csv to find the image paths and labels.
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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600 The metadata csv should contain a column with the name 'image_path' and a column with the name 'label'.
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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601 Optionally, you can also add a column with the name 'split' to specify which split each row belongs to (train, val, test).
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602 If you do not provide a split column, the tool will automatically split the data into train, val, and test sets based on the proportions you specify or [0.7, 0.1, 0.2] by default.
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603 You can optionally specify a sample ID column to keep related samples in the same split and prevent data leakage.
0
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604
11
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605 **Models Available**
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606 This tool supports a wide range of state-of-the-art image classification models including:
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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607 - Traditional CNNs (ResNet, EfficientNet, VGG, etc.)
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608 - Vision Transformers (ViT, Swin Transformer)
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609 - Modern architectures (ConvNeXt, MaxViT)
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610 - MetaFormer family models (IdentityFormer, RandFormer, PoolFormerV2, ConvFormer, CAFormer)
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611
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612 **MetaFormer Models**
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613 The MetaFormer family represents a unified perspective on transformer-like architectures. These models demonstrate that the success of transformers is largely due to their general architecture rather than specific components like attention mechanisms. All MetaFormer models use pretrained weights from Hugging Face and provide explicit confirmation of weight loading.
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614
9
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615 **If the selected label column has more than 10 unique values, the tool will automatically treat the task as a regression problem and apply appropriate metrics (e.g., MSE, RMSE, R²).**
0
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616
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617 **Outputs**
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618 The tool will output a trained model in the form of a ludwig_model file,
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619 a report in the form of an HTML file, and a collection of CSV/json/png files containing the predictions, experiment stats and visualizations.
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620 The html report will contain metrics&experiment setup parameters, train&val plots and test plots.
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621
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622 ]]>
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623 </help>
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624 <citations>
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625 <citation type="bibtex">
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626 @misc{https://doi.org/10.48550/arxiv.1909.07930,
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627 doi = {10.48550/ARXIV.1909.07930},
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628 url = {https://arxiv.org/abs/1909.07930},
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629 author = {Molino, Piero and Dudin, Yaroslav and Miryala, Sai Sumanth},
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630 title = {Ludwig: a type-based declarative deep learning toolbox},
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631 publisher = {arXiv},
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632 year = {2019},
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633 copyright = {arXiv.org perpetual, non-exclusive license}
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634 }
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635 </citation>
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636 </citations>
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637 </tool>