Mercurial > repos > goeckslab > image_learner

annotate image_learner.xml @ 17:db9be962dc13 draft default tip

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planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
author goeckslab
date Wed, 10 Dec 2025 00:24:13 +0000
parents 8729f69e9207
children
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16
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1 <tool id="image_learner" name="Image Learner" version="0.1.4.1" 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>
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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
15
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32 #if $task_selection.task == "binary"
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33 #set $selected_validation_metric = $task_selection.validation_metric_binary
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34 #elif $task_selection.task == "classification"
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35 #set $selected_validation_metric = $task_selection.validation_metric_multiclass
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36 #elif $task_selection.task == "regression"
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37 #set $selected_validation_metric = $task_selection.validation_metric_regression
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38 #else
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39 #set $selected_validation_metric = None
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40 #end if
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41
0
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42 python '$__tool_directory__/image_learner_cli.py'
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43 --csv-file "./${sanitized_input_csv}"
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44 --image-zip "$image_zip"
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45 --model-name "$model_name"
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46 #if $scratch_fine_tune.use_pretrained == "true"
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47 --use-pretrained
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48 #if $scratch_fine_tune.fine_tune == "true"
0
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49 --fine-tune
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50 #end if
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51 #end if
15
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52 #if $advanced_settings.customize_defaults == "true"
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53 #if $advanced_settings.epochs
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54 --epochs "$advanced_settings.epochs"
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55 #end if
15
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56 #if $advanced_settings.early_stop
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57 --early-stop "$advanced_settings.early_stop"
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58 #end if
15
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59 #if $advanced_settings.learning_rate_condition.learning_rate_define == "true"
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60 --learning-rate "$advanced_settings.learning_rate_condition.learning_rate"
0
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61 #end if
15
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62 #if $advanced_settings.batch_size_condition.batch_size_define == "true"
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63 --batch-size "$advanced_settings.batch_size_condition.batch_size"
0
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64 #end if
15
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65 --split-probabilities "$advanced_settings.train_split" "$advanced_settings.val_split" "$advanced_settings.test_split"
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66 #if $advanced_settings.threshold
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67 --threshold "$advanced_settings.threshold"
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68 #end if
0
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69 #end if
2
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70 #if $augmentation
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71 --augmentation "$augmentation"
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72 #end if
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73 #if $selected_validation_metric
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74 --validation-metric "$selected_validation_metric"
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75 #end if
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76 #if $column_override.override_columns == "true"
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77 #if $column_override.target_column
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78 --target-column "$column_override.target_column"
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79 #end if
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80 #if $column_override.image_column
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81 --image-column "$column_override.image_column"
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82 #end if
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83 #end if
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84 --image-resize "$image_resize"
2
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85 --random-seed "$random_seed"
0
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86 --output-dir "." &&
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87
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88 mkdir -p '$output_model.extra_files_path' &&
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89 cp -r experiment_run/model/*.json experiment_run/model/model_weights '$output_model.extra_files_path' &&
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90
2
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91 echo "Image Learner Classification Experiment is Done!"
0
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92 ]]>
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93 </command>
2
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94
0
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95 <inputs>
14
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96 <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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97 <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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98 <conditional name="task_selection">
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99 <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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100 <option value="auto" selected="true">Auto (infer and use defaults)</option>
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101 <option value="binary">Binary Classification</option>
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102 <option value="classification">Multi-class Classification</option>
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103 <option value="regression">Regression</option>
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104 </param>
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105 <when value="binary">
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106 <param name="validation_metric_binary" type="select" optional="true" label="Validation metric (binary)" help="Metrics accepted by Ludwig for binary outputs.">
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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107 <option value="roc_auc" selected="true">ROC-AUC</option>
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108 <option value="accuracy">Accuracy</option>
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109 <option value="balanced_accuracy">Balanced Accuracy</option>
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110 <option value="precision">Precision</option>
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111 <option value="recall">Recall</option>
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112 <option value="f1">F1</option>
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113 <option value="specificity">Specificity</option>
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114 <option value="log_loss">Log Loss</option>
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115 <option value="loss">Loss</option>
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116 </param>
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117 </when>
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118 <when value="classification">
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119 <param name="validation_metric_multiclass" type="select" optional="true" label="Validation metric (multi-class)" help="Metrics accepted by Ludwig for multi-class outputs.">
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120 <option value="accuracy" selected="true">Accuracy</option>
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121 <option value="roc_auc">ROC-AUC</option>
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122 <option value="loss">Loss</option>
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123 <option value="balanced_accuracy">Balanced Accuracy</option>
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124 <option value="precision">Precision</option>
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125 <option value="recall">Recall</option>
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126 <option value="f1">F1</option>
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127 <option value="specificity">Specificity</option>
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128 <option value="log_loss">Log Loss</option>
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129 </param>
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130 </when>
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131 <when value="regression">
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132 <param name="validation_metric_regression" type="select" optional="true" label="Validation metric (regression)" help="Metrics accepted by Ludwig for regression outputs.">
17
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133 <option value="mae" selected="true">MAE</option>
15
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134 <option value="mse">MSE</option>
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135 <option value="rmse">RMSE</option>
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136 <option value="loss">Loss</option>
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137 </param>
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138 </when>
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139 <when value="auto">
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140 <!-- No validation metric selection; tool will infer task and metric. -->
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141 </when>
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142 </conditional>
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143 <conditional name="column_override">
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144 <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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145 <option value="false" selected="true">No</option>
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146 <option value="true">Yes</option>
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147 </param>
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148 <when value="true">
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149 <param name="target_column" type="text" optional="true" label="Target/label column name" help="Overrides the default 'label' column name in the metadata CSV." />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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150 <param name="image_column" type="text" optional="true" label="Image column name" help="Overrides the default 'image_path' column name in the metadata CSV." />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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151 </when>
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152 <when value="false">
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153 <!-- No additional parameters -->
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154 </when>
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155 </conditional>
0
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156 <param name="model_name" type="select" optional="false" label="Select a model for your experiment" >
2
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157
0
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158 <option value="resnet18">Resnet18</option>
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159 <option value="resnet34">Resnet34</option>
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160 <option value="resnet50">Resnet50</option>
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161 <option value="resnet101">Resnet101</option>
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162 <option value="resnet152">Resnet152</option>
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163 <option value="resnext50_32x4d">Resnext50_32x4d</option>
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164 <option value="resnext101_32x8d">Resnext101_32x8d</option>
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165 <option value="resnext101_64x4d">Resnext101_64x4d</option>
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166 <option value="resnext152_32x8d">Resnext152_32x8d</option>
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167 <option value="wide_resnet50_2">Wide_resnet50_2</option>
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168 <option value="wide_resnet101_2">Wide_resnet101_2</option>
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169 <option value="wide_resnet103_2">Wide_resnet103_2</option>
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170 <option value="efficientnet_b0">Efficientnet_b0</option>
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171 <option value="efficientnet_b1">Efficientnet_b1</option>
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172 <option value="efficientnet_b2">Efficientnet_b2</option>
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173 <option value="efficientnet_b3">Efficientnet_b3</option>
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174 <option value="efficientnet_b4">Efficientnet_b4</option>
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175 <option value="efficientnet_b5">Efficientnet_b5</option>
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176 <option value="efficientnet_b6">Efficientnet_b6</option>
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177 <option value="efficientnet_b7">Efficientnet_b7</option>
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178 <option value="efficientnet_v2_s">Efficientnet_v2_s</option>
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179 <option value="efficientnet_v2_m">Efficientnet_v2_m</option>
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180 <option value="efficientnet_v2_l">Efficientnet_v2_l</option>
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181 <option value="regnet_y_400mf">Regnet_y_400mf</option>
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182 <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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183 <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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184 <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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185 <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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186 <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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187 <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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188 <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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189 <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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190 <option value="regnet_x_800mf">Regnet_x_800mf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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191 <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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192 <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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193 <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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194 <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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195 <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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196 <option value="vgg11">Vgg11</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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197 <option value="vgg11_bn">Vgg11_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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198 <option value="vgg13">Vgg13</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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199 <option value="vgg13_bn">Vgg13_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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200 <option value="vgg16">Vgg16</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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diff changeset
201 <option value="vgg16_bn">Vgg16_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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202 <option value="vgg19">Vgg19</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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203 <option value="vgg19_bn">Vgg19_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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204 <option value="shufflenet_v2_x0_5">Shufflenet_v2_x0_5</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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205 <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
parents:
diff changeset
206 <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
207 <option value="shufflenet_v2_x2_0">Shufflenet_v2_x2_0</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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208 <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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209 <option value="squeezenet1_1">Squeezenet1_1</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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210 <option value="swin_t">Swin_t</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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211 <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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212 <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
213 <option value="swin_v2_t">Swin_v2_t</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_v2_s">Swin_v2_s</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
215 <option value="swin_v2_b">Swin_v2_b</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
216 <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
217 <option value="vit_b_32">Vit_b_32</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
218 <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
219 <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
220 <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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diff changeset
221 <option value="convnext_tiny">Convnext_tiny</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
222 <option value="convnext_small">Convnext_small</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
223 <option value="convnext_base">Convnext_base</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
224 <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
225 <option value="maxvit_t">Maxvit_t</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
226 <option value="alexnet">Alexnet</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
227 <option value="googlenet">Googlenet</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
228 <option value="inception_v3">Inception_v3</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
229 <option value="mobilenet_v2">Mobilenet_v2</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
230 <option value="mobilenet_v3_large">Mobilenet_v3_large</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
231 <option value="mobilenet_v3_small">Mobilenet_v3_small</option>
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
232 <!-- MetaFormer Models -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
233 <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
234 <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
235 <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
236 <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
237 <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
238 <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
239 <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
240 <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
241 <option value="randformer_m36">RandFormer M36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
242 <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
243 <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
244 <option value="poolformerv2_s24">PoolFormerV2 S24</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
245 <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
246 <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
247 <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
248 <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
249 <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
250 <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
251 <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
252 <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
253 <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
254 <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
255 <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
256 <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
257 <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
258 <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
259 <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
260 <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
261 <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
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diff changeset
262 <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
263 <option value="convformer_b36">ConvFormer B36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
264 <option value="convformer_b36_384">ConvFormer B36 384</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
265 <option value="convformer_b36_in21ft1k">ConvFormer B36 ImageNet21k</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_in21ft1k">ConvFormer B36 384 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
267 <option value="convformer_b36_in21k">ConvFormer B36 ImageNet21k Pretrained</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
268 <option value="caformer_s18">CAFormer S18</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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269 <option value="caformer_s18_384">CAFormer S18 384</option>
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270 <option value="caformer_s18_in21ft1k">CAFormer S18 ImageNet21k</option>
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271 <option value="caformer_s18_384_in21ft1k">CAFormer S18 384 ImageNet21k</option>
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272 <option value="caformer_s18_in21k">CAFormer S18 ImageNet21k Pretrained</option>
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273 <option value="caformer_s36">CAFormer S36</option>
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274 <option value="caformer_s36_384">CAFormer S36 384</option>
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275 <option value="caformer_s36_in21ft1k">CAFormer S36 ImageNet21k</option>
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276 <option value="caformer_s36_384_in21ft1k">CAFormer S36 384 ImageNet21k</option>
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277 <option value="caformer_s36_in21k">CAFormer S36 ImageNet21k Pretrained</option>
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278 <option value="caformer_m36">CAFormer M36</option>
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279 <option value="caformer_m36_384">CAFormer M36 384</option>
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280 <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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281 <option value="caformer_m36_384_in21ft1k">CAFormer M36 384 ImageNet21k</option>
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282 <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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283 <option value="caformer_b36">CAFormer B36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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284 <option value="caformer_b36_384">CAFormer B36 384</option>
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285 <option value="caformer_b36_in21ft1k">CAFormer B36 ImageNet21k</option>
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286 <option value="caformer_b36_384_in21ft1k">CAFormer B36 384 ImageNet21k</option>
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287 <option value="caformer_b36_in21k">CAFormer B36 ImageNet21k Pretrained</option>
0
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288 </param>
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289
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290 <conditional name="scratch_fine_tune">
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291 <param name="use_pretrained" type="select"
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292 label="Use pretrained weights?"
9
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293 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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294 <option value="false">No</option>
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295 <option value="true" selected="true">Yes</option>
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296 </param>
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297 <when value="true">
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298 <param name="fine_tune" type="select" label="Fine tune the encoder?"
8
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299 help="Whether to fine tune the encoder(combiner and decoder will be fine-tuned anyway)" >
0
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300 <option value="false" >No</option>
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301 <option value="true" selected="true">Yes</option>
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302 </param>
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303 </when>
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304 <when value="false">
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305 <!-- No additional parameters to show if the user selects 'No' -->
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306 </when>
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307 </conditional>
14
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308 <param name="image_resize"
11
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309 type="select"
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310 label="Image Resize"
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311 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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312 <option value="original" selected="true">Original Size (No Resize)</option>
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313 <option value="96x96">96x96</option>
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314 <option value="128x128">128x128</option>
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315 <option value="160x160">160x160</option>
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316 <option value="192x192">192x192</option>
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317 <option value="220x220">220x220</option>
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318 <option value="224x224">224x224</option>
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319 <option value="256x256">256x256</option>
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320 <option value="299x299">299x299</option>
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321 <option value="320x320">320x320</option>
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322 <option value="384x384">384x384</option>
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323 <option value="448x448">448x448</option>
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324 <option value="512x512">512x512</option>
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325 </param>
14
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326 <param name="augmentation"
2
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327 type="select"
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328 multiple="true"
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329 display="checkboxes"
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330 label="Image Augmentation"
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331 help="Pick any combination of augmentations to apply">
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332 <option value="random_horizontal_flip">Random Horizontal Flip</option>
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333 <option value="random_vertical_flip">Random Vertical Flip</option>
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334 <option value="random_rotate">Random Rotate</option>
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335 <option value="random_blur">Random Blur</option>
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336 <option value="random_brightness">Random Brightness</option>
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337 <option value="random_contrast">Random Contrast</option>
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338 </param>
0
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339 <param argument="random_seed" type="integer" value="42" optional="true" label="Random seed (set for reproducibility)" min="0" max="999999"/>
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340 <conditional name="advanced_settings">
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341 <param name="customize_defaults" type="select" label="Customize Default Settings?" help="Select yes if you want to customize the default settings of the experiment.">
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342 <option value="false" selected="true">No</option>
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343 <option value="true">Yes</option>
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344 </param>
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345 <when value="true">
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346 <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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347 <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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348 <conditional name="learning_rate_condition">
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349 <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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350 <option value="false" selected="true" >No</option>
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351 <option value="true">Yes</option>
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352 </param>
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353 <when value="true">
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354 <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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355 </when>
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356 <when value="false">
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357 <!-- No additional parameters to show if the user selects 'No' -->
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358 </when>
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359 </conditional>
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360 <conditional name="batch_size_condition">
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361 <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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362 <option value="false" selected="true" >No</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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363 <option value="true">Yes</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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364 </param>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
365 <when value="true">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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366 <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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diff changeset
367 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
368 <when value="false">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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369 <!-- 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
370 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
371 </conditional>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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372 <param name="train_split" type="float"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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373 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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diff changeset
374 value="0.7"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
375 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
parents:
diff changeset
376 <param name="val_split" type="float"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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diff changeset
377 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
378 value="0.1"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
379 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
380 <param name="test_split" type="float"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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diff changeset
381 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
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diff changeset
382 value="0.2"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff changeset
383 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
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384 <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
385 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
386 <when value="false">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff changeset
387 <!-- 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
388 </when>
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
389 </conditional>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
390 </inputs>
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
391 <outputs>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
392 <data format="ludwig_model" name="output_model" label="${tool.name} trained model on ${on_string}" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
393 <data format="html" name="output_report" from_work_dir="image_classification_results_report.html" label="${tool.name} report on ${on_string}" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
394 <collection type="list" name="output_pred_csv" label="${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
395 <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
396 <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
397 <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
398 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" format="png" directory="experiment_run/visualizations/test" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
399 </collection>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
400 </outputs>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
401 <tests>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
402 <test expect_num_outputs="3">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
403 <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
404 <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
405 <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
406 <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
407 <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
408 <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
409 <output name="output_report">
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
410 <assert_contents>
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 14
diff changeset
411 <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
412 <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
413 <has_text text="Test Results" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
414 </assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
415 </output>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
416
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
417 <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
418 <element name="predictions.csv" >
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
419 <assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
420 <has_n_columns n="1" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
421 </assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
422 </element>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
423 </output_collection>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
424 </test>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
425 <test expect_num_outputs="3">
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
426 <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
427 <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
428 <param name="model_name" value="resnet18" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
429 <output name="output_report">
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
430 <assert_contents>
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 14
diff changeset
431 <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
432 <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
433 <has_text text="Test Results" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
434 </assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
435 </output>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
436 <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
437 <element name="predictions.csv" >
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 <has_n_columns n="1" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
440 </assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
441 </element>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
442 </output_collection>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
443 </test>
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
444 <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
445 <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
446 <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
447 <param name="model_name" value="caformer_s18" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
448 <output name="output_report">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
449 <assert_contents>
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 14
diff changeset
450 <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
451 <has_text text="Training and Validation Results" />
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
452 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
453 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
454 </output>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
455
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456 <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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457 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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458 <assert_contents>
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459 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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460 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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461 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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462 </output_collection>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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463 </test>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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464 <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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465 <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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466 <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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467 <param name="model_name" value="randformer_s12" />
14
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468 <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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469 <param name="advanced_settings|epochs" value="5" />
11
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470 <output name="output_report">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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471 <assert_contents>
15
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472 <has_text text="Test Performance Summary" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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473 <has_text text="Training and Validation Results" />
11
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474 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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475 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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476 </output>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
477
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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478 <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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479 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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480 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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481 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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482 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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483 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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484 </output_collection>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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485 </test>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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486 <!-- Test 7: MetaFormer with 384x384 input - verifies model correctly handles non-224x224 dimensions -->
16
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487 <!-- <test expect_num_outputs="3">
11
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488 <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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489 <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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490 <param name="model_name" value="caformer_s18_384" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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491 <param name="image_resize" value="384x384" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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492 <output name="output_report">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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493 <assert_contents>
15
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494 <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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495 <has_text text="Training and Validation Results" />
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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496 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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497 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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498 </output>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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499 <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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500 <element name="predictions.csv" >
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 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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503 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
504 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
505 <element name="description" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
506 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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507 <has_text text="384" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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508 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
509 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
510 </output_collection>
16
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diff changeset
511 </test> -->
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
512 <!-- 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
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diff changeset
513 <!-- <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
514 <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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515 <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
516 <param name="model_name" value="resnet18" />
15
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diff changeset
517 <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
518 <param name="advanced_settings|threshold" value="0.6" />
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
519 <output name="output_report">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
520 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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521 <has_text text="Results Summary" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
522 <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
523 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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524 <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
525 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
526 </output>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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527 <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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diff changeset
528 <element name="predictions.csv" >
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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530 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
531 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
532 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
533 <element name="test_statistics.json" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
534 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
535 <has_text text="roc_auc" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
536 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
537 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
538 </output_collection>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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539 </test> -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
540 <!-- 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
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diff changeset
541 <!-- 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
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diff changeset
542 <!-- <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
543 <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
544 <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
545 <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
546 <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
547 <param name="advanced_settings|epochs" value="3" />
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
548 <output name="output_report">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
549 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
550 <has_text text="Results Summary" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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parents: 9
diff changeset
551 <has_text text="Train/Validation Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
552 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
553 <has_text text="ROC-AUC Curves" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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554 <has_text text="Micro-average ROC" />
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555 </assert_contents>
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556 </output>
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557 <output_collection name="output_pred_csv" type="list" >
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558 <element name="predictions.csv" >
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559 <assert_contents>
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560 <has_n_columns n="1" />
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561 </assert_contents>
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562 </element>
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563 </output_collection>
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564 </test> -->
12
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565 <test expect_num_outputs="3">
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566 <param name="input_csv" value="mnist_subset_binary.csv" ftype="csv" />
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567 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
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568 <param name="model_name" value="resnet18" />
14
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569 <param name="advanced_settings|customize_defaults" value="true" />
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570 <param name="advanced_settings|threshold" value="0.6" />
15
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571 <param name="task_selection|task" value="classification" />
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572 <param name="task_selection|validation_metric_multiclass" value="balanced_accuracy" />
12
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573 <output name="output_report">
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574 <assert_contents>
15
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575 <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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576 <has_text text="Training and Validation Results" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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577 <has_text text="Test Results" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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578 <has_text text="Threshold" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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579 <has_text text="0.60" />
12
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580 </assert_contents>
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581 </output>
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582 <output_collection name="output_pred_csv" type="list" >
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583 <element name="predictions.csv" >
bcfa2e234a80 planemo upload for repository https://github.com/goeckslab/gleam.git commit 96bab8325992d16fcaad8e0a4dc4c62b00e2abc2
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584 <assert_contents>
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585 <has_n_columns n="1" />
bcfa2e234a80 planemo upload for repository https://github.com/goeckslab/gleam.git commit 96bab8325992d16fcaad8e0a4dc4c62b00e2abc2
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586 </assert_contents>
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587 </element>
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588 </output_collection>
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589 </test>
9
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590 </tests>
0
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591 <help>
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592 <![CDATA[
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593 **What it does**
9
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594 Image Learner for Classification/regression: trains and evaluates a image classification/regression model.
0
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595 It uses the metadata csv to find the image paths and labels.
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596 The metadata csv should contain a column with the name 'image_path' and a column with the name 'label'.
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597 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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598 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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599
11
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600 **Models Available**
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601 This tool supports a wide range of state-of-the-art image classification models including:
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602 - Traditional CNNs (ResNet, EfficientNet, VGG, etc.)
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603 - Vision Transformers (ViT, Swin Transformer)
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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604 - Modern architectures (ConvNeXt, MaxViT)
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605 - MetaFormer family models (IdentityFormer, RandFormer, PoolFormerV2, ConvFormer, CAFormer)
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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606
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607 **MetaFormer Models**
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608 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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609
9
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610 **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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611
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612 **Outputs**
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613 The tool will output a trained model in the form of a ludwig_model file,
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614 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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615 The html report will contain metrics&experiment setup parameters, train&val plots and test plots.
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616
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617 ]]>
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618 </help>
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619 <citations>
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620 <citation type="bibtex">
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621 @misc{https://doi.org/10.48550/arxiv.1909.07930,
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622 doi = {10.48550/ARXIV.1909.07930},
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623 url = {https://arxiv.org/abs/1909.07930},
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624 author = {Molino, Piero and Dudin, Yaroslav and Miryala, Sai Sumanth},
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625 title = {Ludwig: a type-based declarative deep learning toolbox},
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626 publisher = {arXiv},
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627 year = {2019},
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628 copyright = {arXiv.org perpetual, non-exclusive license}
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629 }
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630 </citation>
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631 </citations>
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632 </tool>