Mercurial > repos > goeckslab > image_learner

annotate image_learner.xml @ 21:d5c582cf74bc draft default tip

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planemo upload for repository https://github.com/goeckslab/gleam.git commit eed8c1e1d99a8a0c8f3a6bfdd8af48a5bfa19444
author goeckslab
date Tue, 20 Jan 2026 01:25:35 +0000
parents 64872c48a21f
children
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c460abae83eb planemo upload for repository https://github.com/goeckslab/gleam.git commit b47f0fd63d8d5d18d602d45bb21ebbe36ba4fcfe
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1 <tool id="image_learner" name="Image Learner" version="0.1.5" profile="22.01">
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2 <description>trains and evaluates an image classification/regression model</description>
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3 <requirements>
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4 <container type="docker">quay.io/goeckslab/galaxy-ludwig-gpu:0.10.1</container>
0
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5 </requirements>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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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" />
94cd9ac4a9b1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 3188005878e1ad81b0ca59c9c4d4d40dd981acf7
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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" />
94cd9ac4a9b1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 3188005878e1ad81b0ca59c9c4d4d40dd981acf7
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12 <include path="metaformer_setup.py" />
94cd9ac4a9b1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 3188005878e1ad81b0ca59c9c4d4d40dd981acf7
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13 <include path="plotly_plots.py" />
94cd9ac4a9b1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 3188005878e1ad81b0ca59c9c4d4d40dd981acf7
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14 <include path="split_data.py" />
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15 <include path="utils.py" />
14
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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\-_\.]', '_', $input_csv.element_identifier.strip())
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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29 ln -sf '$input_csv' "./${sanitized_input_csv}";
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30 #end if
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31 #set $TORCH_HOME = "./torch_cache";
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32 mkdir -p "$TORCH_HOME";
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33
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34 #set $selected_validation_metric = ""
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35 #if $task_selection.task == "binary"
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36 #set $selected_validation_metric = $task_selection.validation_metric_binary
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37 #elif $task_selection.task == "classification"
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38 #set $selected_validation_metric = $task_selection.validation_metric_multiclass
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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39 #elif $task_selection.task == "regression"
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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40 #set $selected_validation_metric = $task_selection.validation_metric_regression
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41 #else
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42 #if $task_selection.validation_metric_auto
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43 #set $selected_validation_metric = $task_selection.validation_metric_auto
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44 #end if
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45 #end if
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46
0
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47 python '$__tool_directory__/image_learner_cli.py'
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48 --csv-file "./${sanitized_input_csv}"
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49 --image-zip "$image_zip"
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50 --model-name "$model_name"
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51 #if $scratch_fine_tune.use_pretrained == "true"
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52 --use-pretrained
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53 #if $scratch_fine_tune.fine_tune == "true"
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54 --fine-tune
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55 #end if
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56 #end if
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57 #if $advanced_settings.customize_defaults == "true"
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58 #if $advanced_settings.epochs
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59 --epochs "$advanced_settings.epochs"
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60 #end if
15
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61 #if $advanced_settings.early_stop
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62 --early-stop "$advanced_settings.early_stop"
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63 #end if
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64 #if $advanced_settings.learning_rate_condition.learning_rate_define == "true"
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65 --learning-rate "$advanced_settings.learning_rate_condition.learning_rate"
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66 #end if
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67 #if $advanced_settings.batch_size_condition.batch_size_define == "true"
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68 --batch-size "$advanced_settings.batch_size_condition.batch_size"
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69 #end if
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70 --split-probabilities "$advanced_settings.train_split" "$advanced_settings.val_split" "$advanced_settings.test_split"
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71 #if $advanced_settings.threshold
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72 --threshold "$advanced_settings.threshold"
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73 #end if
0
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74 #end if
2
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75 #if $augmentation
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76 --augmentation "$augmentation"
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77 #end if
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78 #if $selected_validation_metric
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79 --validation-metric "$selected_validation_metric"
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80 #end if
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81 #if $column_override.override_columns == "true"
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82 #if $column_override.target_column
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83 --target-column "$column_override.target_column"
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84 #end if
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85 #if $column_override.image_column
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86 --image-column "$column_override.image_column"
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87 #end if
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88 #end if
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89 #if $sample_id_column
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90 --sample-id-column "$sample_id_column"
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91 #end if
11
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92 --image-resize "$image_resize"
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93 --random-seed "$random_seed"
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94 --torch-home "$TORCH_HOME"
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95 --output-dir "." &&
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96
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97 mkdir -p '$output_model.extra_files_path' &&
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98 cp -r experiment_run/model/*.json experiment_run/model/model_weights '$output_model.extra_files_path' &&
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99
2
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100 echo "Image Learner Classification Experiment is Done!"
0
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101 ]]>
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102 </command>
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103
0
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104 <inputs>
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105 <param name="input_csv" type="data" format="csv" optional="false" label="the metadata csv containing image_path column, label column and optional split column" />
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106 <param name="image_zip" type="data" format="zip" optional="false" label="Image zip" help="Image zip file containing your image data"/>
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107 <conditional name="task_selection">
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108 <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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109 <option value="auto" selected="true">Auto (infer and use defaults)</option>
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110 <option value="binary">Binary Classification</option>
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111 <option value="classification">Multi-class Classification</option>
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112 <option value="regression">Regression</option>
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113 </param>
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114 <when value="binary">
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115 <param name="validation_metric_binary" type="select" optional="true" label="Validation metric (binary)" help="Metrics accepted by Ludwig 0.10.1 for binary outputs.">
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116 <option value="" selected="true">Auto (use task default)</option>
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117 <option value="roc_auc">ROC-AUC</option>
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118 <option value="accuracy">Accuracy</option>
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119 <option value="precision">Precision</option>
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120 <option value="recall">Recall</option>
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121 <option value="loss">Loss</option>
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122 </param>
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123 </when>
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124 <when value="classification">
20
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125 <param name="validation_metric_multiclass" type="select" optional="true" label="Validation metric (multi-class)" help="Metrics accepted by Ludwig 0.10.1 for multi-class outputs.">
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126 <option value="" selected="true">Auto (use task default)</option>
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127 <option value="accuracy">Accuracy</option>
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128 <option value="loss">Loss</option>
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129 </param>
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130 </when>
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131 <when value="regression">
20
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132 <param name="validation_metric_regression" type="select" optional="true" label="Validation metric (regression)" help="Metrics accepted by Ludwig 0.10.1 for regression outputs.">
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133 <option value="" selected="true">Auto (use task default)</option>
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134 <option value="mean_squared_error">Mean Squared Error</option>
18
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135 <option value="mean_absolute_error">Mean Absolute Error</option>
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136 <option value="root_mean_squared_error">Root Mean Squared Error</option>
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137 <option value="root_mean_squared_percentage_error">Root Mean Squared Percentage Error</option>
15
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138 <option value="loss">Loss</option>
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139 </param>
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140 </when>
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141 <when value="auto">
20
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142 <param name="validation_metric_auto" type="select" optional="true" label="Validation metric (auto)" help="Auto defers to the inferred task and picks the best default metric; use this only to override the choice.">
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143 <option value="" selected="true"></option>
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144 </param>
15
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145 </when>
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146 </conditional>
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147 <conditional name="column_override">
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148 <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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149 <option value="false" selected="true">No</option>
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150 <option value="true">Yes</option>
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151 </param>
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152 <when value="true">
20
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153 <param name="target_column" type="data_column" data_ref="input_csv" use_header_names="true" optional="true" label="Target/label column name" help="Overrides the default 'label' column name in the metadata CSV." />
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154 <param name="image_column" type="data_column" data_ref="input_csv" use_header_names="true" optional="true" label="Image column name" help="Overrides the default 'image_path' column name in the metadata CSV." />
15
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155 </when>
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156 <when value="false">
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157 <!-- No additional parameters -->
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158 </when>
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159 </conditional>
20
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160 <param name="sample_id_column" type="data_column" data_ref="input_csv" use_header_names="true" optional="true" label="Sample ID column (optional)" help="Optional column used to group samples during splitting to prevent data leakage (e.g., patient_id or slide_id). Only used when no split column is provided." />
0
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161 <param name="model_name" type="select" optional="false" label="Select a model for your experiment" >
2
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162
0
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163 <option value="resnet18">Resnet18</option>
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164 <option value="resnet34">Resnet34</option>
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165 <option value="resnet50">Resnet50</option>
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166 <option value="resnet101">Resnet101</option>
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167 <option value="resnet152">Resnet152</option>
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168 <option value="resnext50_32x4d">Resnext50_32x4d</option>
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169 <option value="resnext101_32x8d">Resnext101_32x8d</option>
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170 <option value="resnext101_64x4d">Resnext101_64x4d</option>
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171 <option value="resnext152_32x8d">Resnext152_32x8d</option>
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172 <option value="wide_resnet50_2">Wide_resnet50_2</option>
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173 <option value="wide_resnet101_2">Wide_resnet101_2</option>
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174 <option value="wide_resnet103_2">Wide_resnet103_2</option>
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175 <option value="efficientnet_b0">Efficientnet_b0</option>
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176 <option value="efficientnet_b1">Efficientnet_b1</option>
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177 <option value="efficientnet_b2">Efficientnet_b2</option>
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178 <option value="efficientnet_b3">Efficientnet_b3</option>
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179 <option value="efficientnet_b4">Efficientnet_b4</option>
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180 <option value="efficientnet_b5">Efficientnet_b5</option>
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181 <option value="efficientnet_b6">Efficientnet_b6</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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182 <option value="efficientnet_b7">Efficientnet_b7</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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183 <option value="efficientnet_v2_s">Efficientnet_v2_s</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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184 <option value="efficientnet_v2_m">Efficientnet_v2_m</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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185 <option value="efficientnet_v2_l">Efficientnet_v2_l</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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186 <option value="regnet_y_400mf">Regnet_y_400mf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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187 <option value="regnet_y_800mf">Regnet_y_800mf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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188 <option value="regnet_y_1_6gf">Regnet_y_1_6gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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189 <option value="regnet_y_3_2gf">Regnet_y_3_2gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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190 <option value="regnet_y_8gf">Regnet_y_8gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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191 <option value="regnet_y_16gf">Regnet_y_16gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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192 <option value="regnet_y_32gf">Regnet_y_32gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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193 <option value="regnet_y_128gf">Regnet_y_128gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
194 <option value="regnet_x_400mf">Regnet_x_400mf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
195 <option value="regnet_x_800mf">Regnet_x_800mf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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196 <option value="regnet_x_1_6gf">Regnet_x_1_6gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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197 <option value="regnet_x_3_2gf">Regnet_x_3_2gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
198 <option value="regnet_x_8gf">Regnet_x_8gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
199 <option value="regnet_x_16gf">Regnet_x_16gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
200 <option value="regnet_x_32gf">Regnet_x_32gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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201 <option value="vgg11">Vgg11</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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202 <option value="vgg11_bn">Vgg11_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
203 <option value="vgg13">Vgg13</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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204 <option value="vgg13_bn">Vgg13_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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205 <option value="vgg16">Vgg16</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
206 <option value="vgg16_bn">Vgg16_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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207 <option value="vgg19">Vgg19</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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208 <option value="vgg19_bn">Vgg19_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
209 <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
parents:
diff changeset
210 <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
211 <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
212 <option value="shufflenet_v2_x2_0">Shufflenet_v2_x2_0</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
213 <option value="squeezenet1_0">Squeezenet1_0</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
214 <option value="squeezenet1_1">Squeezenet1_1</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
215 <option value="swin_t">Swin_t</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
216 <option value="swin_s">Swin_s</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
217 <option value="swin_b">Swin_b</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
218 <option value="swin_v2_t">Swin_v2_t</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
219 <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
220 <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
221 <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
222 <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
223 <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
224 <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
225 <option value="vit_h_14">Vit_h_14</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
226 <option value="convnext_tiny">Convnext_tiny</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
227 <option value="convnext_small">Convnext_small</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
228 <option value="convnext_base">Convnext_base</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
229 <option value="convnext_large">Convnext_large</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
230 <option value="maxvit_t">Maxvit_t</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
231 <option value="alexnet">Alexnet</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
232 <option value="googlenet">Googlenet</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
233 <option value="inception_v3">Inception_v3</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
234 <option value="mobilenet_v2">Mobilenet_v2</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
235 <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
236 <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
237 <!-- MetaFormer Models -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
238 <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
239 <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
240 <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
241 <option value="identityformer_m36">IdentityFormer M36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
242 <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
243 <option value="randformer_s12">RandFormer S12</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
244 <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
245 <option value="randformer_s36">RandFormer S36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
246 <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
247 <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
248 <option value="poolformerv2_s12">PoolFormerV2 S12</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
249 <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
250 <option value="poolformerv2_s36">PoolFormerV2 S36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
251 <option value="poolformerv2_m36">PoolFormerV2 M36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
252 <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
253 <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
254 <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
255 <option value="convformer_s18_in21ft1k">ConvFormer S18 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
256 <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
257 <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
258 <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
259 <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
260 <option value="convformer_s36_in21ft1k">ConvFormer S36 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
261 <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
parents: 9
diff changeset
262 <option value="convformer_s36_in21k">ConvFormer S36 ImageNet21k Pretrained</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
263 <option value="convformer_m36">ConvFormer M36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
264 <option value="convformer_m36_384">ConvFormer M36 384</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
265 <option value="convformer_m36_in21ft1k">ConvFormer M36 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
266 <option value="convformer_m36_384_in21ft1k">ConvFormer M36 384 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
267 <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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268 <option value="convformer_b36">ConvFormer B36</option>
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269 <option value="convformer_b36_384">ConvFormer B36 384</option>
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270 <option value="convformer_b36_in21ft1k">ConvFormer B36 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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271 <option value="convformer_b36_384_in21ft1k">ConvFormer B36 384 ImageNet21k</option>
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272 <option value="convformer_b36_in21k">ConvFormer B36 ImageNet21k Pretrained</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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273 <option value="caformer_s18">CAFormer S18</option>
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274 <option value="caformer_s18_384">CAFormer S18 384</option>
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275 <option value="caformer_s18_in21ft1k">CAFormer S18 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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276 <option value="caformer_s18_384_in21ft1k">CAFormer S18 384 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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277 <option value="caformer_s18_in21k">CAFormer S18 ImageNet21k Pretrained</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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278 <option value="caformer_s36">CAFormer S36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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279 <option value="caformer_s36_384">CAFormer S36 384</option>
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280 <option value="caformer_s36_in21ft1k">CAFormer S36 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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281 <option value="caformer_s36_384_in21ft1k">CAFormer S36 384 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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282 <option value="caformer_s36_in21k">CAFormer S36 ImageNet21k Pretrained</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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283 <option value="caformer_m36">CAFormer M36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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284 <option value="caformer_m36_384">CAFormer M36 384</option>
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285 <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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286 <option value="caformer_m36_384_in21ft1k">CAFormer M36 384 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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287 <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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288 <option value="caformer_b36">CAFormer B36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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289 <option value="caformer_b36_384">CAFormer B36 384</option>
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290 <option value="caformer_b36_in21ft1k">CAFormer B36 ImageNet21k</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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291 <option value="caformer_b36_384_in21ft1k">CAFormer B36 384 ImageNet21k</option>
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292 <option value="caformer_b36_in21k">CAFormer B36 ImageNet21k Pretrained</option>
0
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293 </param>
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294
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295 <conditional name="scratch_fine_tune">
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296 <param name="use_pretrained" type="select"
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297 label="Use pretrained weights?"
9
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298 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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299 <option value="false">No</option>
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300 <option value="true" selected="true">Yes</option>
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301 </param>
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302 <when value="true">
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303 <param name="fine_tune" type="select" label="Fine tune the encoder?"
8
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304 help="Whether to fine tune the encoder(combiner and decoder will be fine-tuned anyway)" >
0
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305 <option value="false" >No</option>
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306 <option value="true" selected="true">Yes</option>
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307 </param>
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308 </when>
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309 <when value="false">
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310 <!-- No additional parameters to show if the user selects 'No' -->
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311 </when>
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312 </conditional>
14
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313 <param name="image_resize"
11
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314 type="select"
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315 label="Image Resize"
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316 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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317 <option value="original" selected="true">Original Size (No Resize)</option>
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318 <option value="96x96">96x96</option>
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319 <option value="128x128">128x128</option>
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320 <option value="160x160">160x160</option>
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321 <option value="192x192">192x192</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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322 <option value="220x220">220x220</option>
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323 <option value="224x224">224x224</option>
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324 <option value="256x256">256x256</option>
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325 <option value="299x299">299x299</option>
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326 <option value="320x320">320x320</option>
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327 <option value="384x384">384x384</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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328 <option value="448x448">448x448</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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329 <option value="512x512">512x512</option>
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330 </param>
14
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331 <param name="augmentation"
2
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332 type="select"
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333 multiple="true"
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334 display="checkboxes"
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335 label="Image Augmentation"
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336 help="Pick any combination of augmentations to apply">
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337 <option value="random_horizontal_flip">Random Horizontal Flip</option>
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338 <option value="random_vertical_flip">Random Vertical Flip</option>
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339 <option value="random_rotate">Random Rotate</option>
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340 <option value="random_blur">Random Blur</option>
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341 <option value="random_brightness">Random Brightness</option>
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342 <option value="random_contrast">Random Contrast</option>
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343 </param>
0
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344 <param argument="random_seed" type="integer" value="42" optional="true" label="Random seed (set for reproducibility)" min="0" max="999999"/>
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345 <conditional name="advanced_settings">
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346 <param name="customize_defaults" type="select" label="Customize Default Settings?" help="Select yes if you want to customize the default settings of the experiment.">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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347 <option value="false" selected="true">No</option>
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348 <option value="true">Yes</option>
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349 </param>
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350 <when value="true">
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351 <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." />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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352 <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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353 <conditional name="learning_rate_condition">
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354 <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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355 <option value="false" selected="true" >No</option>
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356 <option value="true">Yes</option>
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357 </param>
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358 <when value="true">
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359 <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." />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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360 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
361 <when value="false">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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362 <!-- No additional parameters to show if the user selects 'No' -->
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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363 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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364 </conditional>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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365 <conditional name="batch_size_condition">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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366 <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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367 <option value="false" selected="true" >No</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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368 <option value="true">Yes</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
369 </param>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
370 <when value="true">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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371 <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
goeckslab
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372 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
373 <when value="false">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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374 <!-- No additional parameters to show if the user selects 'No' -->
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
375 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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376 </conditional>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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377 <param name="train_split" type="float"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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378 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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379 value="0.7"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
380 help="Fraction of data for training (e.g., 0.7). train split + val split + test split should = 1"/>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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diff changeset
381 <param name="val_split" type="float"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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382 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
383 value="0.1"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
384 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
385 <param name="test_split" type="float"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
386 label="Test split proportion (only works if no split column in the metadata csv)"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
387 value="0.2"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff changeset
388 help="Fraction of data for testing (e.g., 0.2) train split + val split + test split should = 1."/>
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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parents: 5
diff changeset
389 <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
390 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
391 <when value="false">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
392 <!-- 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
393 </when>
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
394 </conditional>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
395 </inputs>
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
396 <outputs>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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397 <data format="ludwig_model" name="output_model" label="${tool.name} trained model on ${on_string}" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
398 <data format="html" name="output_report" from_work_dir="image_classification_results_report.html" label="${tool.name} report on ${on_string}" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
399 <collection type="list" name="output_pred_csv" label="${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
400 <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
401 <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
402 <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
403 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" format="png" directory="experiment_run/visualizations/test" />
19
c460abae83eb planemo upload for repository https://github.com/goeckslab/gleam.git commit b47f0fd63d8d5d18d602d45bb21ebbe36ba4fcfe
goeckslab
parents: 18
diff changeset
404 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" format="png" directory="experiment_run/feature_importance_examples" />
c460abae83eb planemo upload for repository https://github.com/goeckslab/gleam.git commit b47f0fd63d8d5d18d602d45bb21ebbe36ba4fcfe
goeckslab
parents: 18
diff changeset
405 <discover_datasets pattern="(?P&lt;designation&gt;feature_importance_examples\.zip)" format="zip" directory="experiment_run" />
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
406 </collection>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
407 </outputs>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
408 <tests>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
409 <test expect_num_outputs="3">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
410 <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
411 <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
412 <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
413 <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
414 <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
415 <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
416 <output name="output_report">
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
417 <assert_contents>
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 14
diff changeset
418 <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
419 <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
420 <has_text text="Test Results" />
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 </output>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
423
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
424 <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
425 <element name="predictions.csv" >
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
426 <assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
427 <has_n_columns n="1" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
428 </assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
429 </element>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
430 </output_collection>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
431 </test>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
432 <test expect_num_outputs="3">
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
433 <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
434 <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
435 <param name="model_name" value="resnet18" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
436 <output name="output_report">
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
437 <assert_contents>
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 14
diff changeset
438 <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
439 <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
440 <has_text text="Test Results" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
441 </assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
442 </output>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
443 <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
444 <element name="predictions.csv" >
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
445 <assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
446 <has_n_columns n="1" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
447 </assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
448 </element>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
449 </output_collection>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
450 </test>
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
451 <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
452 <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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453 <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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454 <param name="model_name" value="caformer_s18" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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455 <output name="output_report">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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456 <assert_contents>
15
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457 <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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458 <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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459 <has_text text="Test Results" />
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 </output>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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462
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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463 <output_collection name="output_pred_csv" type="list" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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464 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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465 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
466 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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467 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
468 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
469 </output_collection>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
470 </test>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
471 <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
472 <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
473 <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
474 <param name="model_name" value="randformer_s12" />
14
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diff changeset
475 <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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diff changeset
476 <param name="advanced_settings|epochs" value="5" />
11
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diff changeset
477 <output name="output_report">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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478 <assert_contents>
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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479 <has_text text="Test Performance Summary" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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diff changeset
480 <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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diff changeset
481 <has_text text="Test Results" />
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 </output>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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484
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
485 <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
486 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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487 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
488 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
489 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
490 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
491 </output_collection>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
492 </test>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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493 <!-- Test 7: MetaFormer with 384x384 input - verifies model correctly handles non-224x224 dimensions -->
16
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diff changeset
494 <!-- <test expect_num_outputs="3">
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
495 <param name="input_csv" value="mnist_subset.csv" ftype="csv" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
496 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
497 <param name="model_name" value="caformer_s18_384" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
498 <param name="image_resize" value="384x384" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
499 <output name="output_report">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
500 <assert_contents>
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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diff changeset
501 <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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diff changeset
502 <has_text text="Training and Validation Results" />
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
503 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
504 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
505 </output>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
506 <output_collection name="output_pred_csv" type="list" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
507 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
508 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
509 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
510 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
511 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
512 <element name="description" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
513 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
514 <has_text text="384" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
515 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
516 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
517 </output_collection>
16
8729f69e9207 planemo upload for repository https://github.com/goeckslab/gleam.git commit bb4bcdc888d73bbfd85d78ce8999a1080fe813ff
goeckslab
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diff changeset
518 </test> -->
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
519 <!-- Test 8: Binary classification with custom threshold - verifies ROC curve generation for binary tasks; need to find a test dataset -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
520 <!-- <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
521 <param name="input_csv" value="binary_classification.csv" ftype="csv" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
522 <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
523 <param name="model_name" value="resnet18" />
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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parents: 14
diff changeset
524 <param name="advanced_settings|customize_defaults" value="true" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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diff changeset
525 <param name="advanced_settings|threshold" value="0.6" />
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
526 <output name="output_report">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
527 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
528 <has_text text="Results Summary" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
529 <has_text text="Train/Validation Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
530 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
531 <has_text text="ROC-AUC Curves" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
532 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
533 </output>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
534 <output_collection name="output_pred_csv" type="list" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
535 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
536 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
537 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
538 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
539 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
540 <element name="test_statistics.json" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
541 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
542 <has_text text="roc_auc" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
543 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
544 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
545 </output_collection>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
546 </test> -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
547 <!-- Test 9: PoolFormerV2 model configuration - verifies custom_model parameter persists in config -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
548 <!-- Test 10: Multi-class classification with ROC curves - verifies robust ROC-AUC plot generation -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
549 <!-- <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
550 <param name="input_csv" value="mnist_subset.csv" ftype="csv" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
551 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
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552 <param name="model_name" value="resnet18" />
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553 <param name="advanced_settings|customize_defaults" value="true" />
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554 <param name="advanced_settings|epochs" value="3" />
11
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555 <output name="output_report">
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556 <assert_contents>
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557 <has_text text="Results Summary" />
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558 <has_text text="Train/Validation Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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559 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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560 <has_text text="ROC-AUC Curves" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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561 <has_text text="Micro-average ROC" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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562 </assert_contents>
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563 </output>
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564 <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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565 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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566 <assert_contents>
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567 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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568 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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diff changeset
569 </element>
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570 </output_collection>
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571 </test> -->
12
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572 <test expect_num_outputs="3">
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573 <param name="input_csv" value="mnist_subset_binary.csv" ftype="csv" />
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574 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
bcfa2e234a80 planemo upload for repository https://github.com/goeckslab/gleam.git commit 96bab8325992d16fcaad8e0a4dc4c62b00e2abc2
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575 <param name="model_name" value="resnet18" />
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576 <param name="advanced_settings|customize_defaults" value="true" />
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577 <param name="advanced_settings|threshold" value="0.6" />
15
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578 <param name="task_selection|task" value="classification" />
20
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579 <param name="task_selection|validation_metric_multiclass" value="accuracy" />
12
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580 <output name="output_report">
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581 <assert_contents>
15
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582 <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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583 <has_text text="Training and Validation Results" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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584 <has_text text="Test Results" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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585 <has_text text="Threshold" />
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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586 <has_text text="0.60" />
12
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587 </assert_contents>
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588 </output>
bcfa2e234a80 planemo upload for repository https://github.com/goeckslab/gleam.git commit 96bab8325992d16fcaad8e0a4dc4c62b00e2abc2
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589 <output_collection name="output_pred_csv" type="list" >
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590 <element name="predictions.csv" >
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591 <assert_contents>
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592 <has_n_columns n="1" />
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593 </assert_contents>
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594 </element>
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595 </output_collection>
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596 </test>
9
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597 </tests>
0
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598 <help>
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599 <![CDATA[
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600 **What it does**
9
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601 Image Learner for Classification/regression: trains and evaluates a image classification/regression model.
0
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602 It uses the metadata csv to find the image paths and labels.
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603 The metadata csv should contain a column with the name 'image_path' and a column with the name 'label'.
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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604 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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605 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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606 You can optionally specify a sample ID column to keep related samples in the same split and prevent data leakage.
0
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607
11
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608 **Models Available**
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609 This tool supports a wide range of state-of-the-art image classification models including:
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610 - Traditional CNNs (ResNet, EfficientNet, VGG, etc.)
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611 - Vision Transformers (ViT, Swin Transformer)
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612 - Modern architectures (ConvNeXt, MaxViT)
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613 - MetaFormer family models (IdentityFormer, RandFormer, PoolFormerV2, ConvFormer, CAFormer)
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614
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615 **MetaFormer Models**
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616 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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617
9
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618 **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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619
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620 **Outputs**
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621 The tool will output a trained model in the form of a ludwig_model file,
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622 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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623 The html report will contain metrics&experiment setup parameters, train&val plots and test plots.
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624
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625 ]]>
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626 </help>
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627 <citations>
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628 <citation type="bibtex">
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629 @misc{https://doi.org/10.48550/arxiv.1909.07930,
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630 doi = {10.48550/ARXIV.1909.07930},
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631 url = {https://arxiv.org/abs/1909.07930},
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632 author = {Molino, Piero and Dudin, Yaroslav and Miryala, Sai Sumanth},
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633 title = {Ludwig: a type-based declarative deep learning toolbox},
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634 publisher = {arXiv},
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635 year = {2019},
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636 copyright = {arXiv.org perpetual, non-exclusive license}
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637 }
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638 </citation>
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639 </citations>
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640 </tool>