Mercurial > repos > goeckslab > image_learner

annotate image_learner.xml @ 14:94cd9ac4a9b1 draft default tip

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planemo upload for repository https://github.com/goeckslab/gleam.git commit 3188005878e1ad81b0ca59c9c4d4d40dd981acf7
author goeckslab
date Wed, 26 Nov 2025 22:00:32 +0000
parents 1a9c42974a5a
children
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1a9c42974a5a planemo upload for repository https://github.com/goeckslab/gleam.git commit 9f96da4ea7ab3b572af86698ff51b870125cd674
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1 <tool id="image_learner" name="Image Learner" version="0.1.3" profile="22.05">
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2 <description>trains and evaluates an image classification/regression model</description>
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3 <requirements>
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4 <container type="docker">quay.io/goeckslab/galaxy-ludwig-gpu:0.10.1</container>
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5 </requirements>
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6 <required_files>
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7 <include path="constants.py" />
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8 <include path="html_structure.py" />
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9 <include path="image_learner_cli.py" />
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10 <include path="image_workflow.py" />
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11 <include path="ludwig_backend.py" />
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12 <include path="metaformer_setup.py" />
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13 <include path="plotly_plots.py" />
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14 <include path="split_data.py" />
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15 <include path="utils.py" />
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\-_\.]', '_', $input_csv.element_identifier.strip())
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29 ln -sf '$input_csv' "./${sanitized_input_csv}";
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30 #end if
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31
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32 python '$__tool_directory__/image_learner_cli.py'
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33 --csv-file "./${sanitized_input_csv}"
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34 --image-zip "$image_zip"
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35 --model-name "$model_name"
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36 #if $use_pretrained == "true"
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37 --use-pretrained
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38 #if $fine_tune == "true"
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39 --fine-tune
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40 #end if
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41 #end if
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42 #if $customize_defaults == "true"
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43 #if $epochs
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44 --epochs "$epochs"
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45 #end if
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46 #if $early_stop
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47 --early-stop "$early_stop"
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48 #end if
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49 #if $learning_rate_define == "true"
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50 --learning-rate "$learning_rate"
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51 #end if
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52 #if $batch_size_define == "true"
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53 --batch-size "$batch_size"
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54 #end if
2
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55 --split-probabilities "$train_split" "$val_split" "$test_split"
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56 #if $threshold
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57 --threshold "$threshold"
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58 #end if
0
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59 #end if
2
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60 #if $augmentation
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61 --augmentation "$augmentation"
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62 #end if
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63 --image-resize "$image_resize"
2
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64 --random-seed "$random_seed"
0
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65 --output-dir "." &&
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66
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67 mkdir -p '$output_model.extra_files_path' &&
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68 cp -r experiment_run/model/*.json experiment_run/model/model_weights '$output_model.extra_files_path' &&
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69
2
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70 echo "Image Learner Classification Experiment is Done!"
0
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71 ]]>
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72 </command>
2
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73
0
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74 <inputs>
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75 <param name="input_csv" type="data" format="csv" optional="false" label="the metadata csv containing image_path column, label column and optional split column" />
0
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76 <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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77 <param name="model_name" type="select" optional="false" label="Select a model for your experiment" >
2
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78
0
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79 <option value="resnet18">Resnet18</option>
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80 <option value="resnet34">Resnet34</option>
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81 <option value="resnet50">Resnet50</option>
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82 <option value="resnet101">Resnet101</option>
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83 <option value="resnet152">Resnet152</option>
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84 <option value="resnext50_32x4d">Resnext50_32x4d</option>
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85 <option value="resnext101_32x8d">Resnext101_32x8d</option>
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86 <option value="resnext101_64x4d">Resnext101_64x4d</option>
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87 <option value="resnext152_32x8d">Resnext152_32x8d</option>
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88 <option value="wide_resnet50_2">Wide_resnet50_2</option>
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89 <option value="wide_resnet101_2">Wide_resnet101_2</option>
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90 <option value="wide_resnet103_2">Wide_resnet103_2</option>
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91 <option value="efficientnet_b0">Efficientnet_b0</option>
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92 <option value="efficientnet_b1">Efficientnet_b1</option>
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93 <option value="efficientnet_b2">Efficientnet_b2</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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94 <option value="efficientnet_b3">Efficientnet_b3</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
95 <option value="efficientnet_b4">Efficientnet_b4</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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96 <option value="efficientnet_b5">Efficientnet_b5</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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97 <option value="efficientnet_b6">Efficientnet_b6</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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98 <option value="efficientnet_b7">Efficientnet_b7</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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99 <option value="efficientnet_v2_s">Efficientnet_v2_s</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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100 <option value="efficientnet_v2_m">Efficientnet_v2_m</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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101 <option value="efficientnet_v2_l">Efficientnet_v2_l</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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102 <option value="regnet_y_400mf">Regnet_y_400mf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
103 <option value="regnet_y_800mf">Regnet_y_800mf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
104 <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:
diff changeset
105 <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:
diff changeset
106 <option value="regnet_y_8gf">Regnet_y_8gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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107 <option value="regnet_y_16gf">Regnet_y_16gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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108 <option value="regnet_y_32gf">Regnet_y_32gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
109 <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
110 <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
111 <option value="regnet_x_800mf">Regnet_x_800mf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
112 <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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113 <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
114 <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
115 <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
116 <option value="regnet_x_32gf">Regnet_x_32gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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117 <option value="vgg11">Vgg11</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
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118 <option value="vgg11_bn">Vgg11_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
119 <option value="vgg13">Vgg13</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
120 <option value="vgg13_bn">Vgg13_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
121 <option value="vgg16">Vgg16</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
122 <option value="vgg16_bn">Vgg16_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
123 <option value="vgg19">Vgg19</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
124 <option value="vgg19_bn">Vgg19_bn</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
125 <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
126 <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
127 <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
128 <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
129 <option value="squeezenet1_0">Squeezenet1_0</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
130 <option value="squeezenet1_1">Squeezenet1_1</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
131 <option value="swin_t">Swin_t</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
132 <option value="swin_s">Swin_s</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
133 <option value="swin_b">Swin_b</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
134 <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
135 <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
136 <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
137 <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
138 <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
139 <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
140 <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
141 <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
142 <option value="convnext_tiny">Convnext_tiny</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
143 <option value="convnext_small">Convnext_small</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
144 <option value="convnext_base">Convnext_base</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
145 <option value="convnext_large">Convnext_large</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
146 <option value="maxvit_t">Maxvit_t</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
147 <option value="alexnet">Alexnet</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
148 <option value="googlenet">Googlenet</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
149 <option value="inception_v3">Inception_v3</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
150 <option value="mobilenet_v2">Mobilenet_v2</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
151 <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
152 <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
153 <!-- MetaFormer Models -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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diff changeset
154 <option value="identityformer_s12">IdentityFormer S12</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
155 <option value="identityformer_s24">IdentityFormer S24</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
156 <option value="identityformer_s36">IdentityFormer S36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
157 <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
158 <option value="identityformer_m48">IdentityFormer M48</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
159 <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
160 <option value="randformer_s24">RandFormer S24</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
161 <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
162 <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
163 <option value="randformer_m48">RandFormer M48</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
164 <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
165 <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
166 <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
167 <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
168 <option value="poolformerv2_m48">PoolFormerV2 M48</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
169 <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
170 <option value="convformer_s18_384">ConvFormer S18 384</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
171 <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
172 <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
173 <option value="convformer_s18_in21k">ConvFormer S18 ImageNet21k Pretrained</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
174 <option value="convformer_s36">ConvFormer S36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
175 <option value="convformer_s36_384">ConvFormer S36 384</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 9
diff changeset
176 <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
177 <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
178 <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
179 <option value="convformer_m36">ConvFormer M36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
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180 <option value="convformer_m36_384">ConvFormer M36 384</option>
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181 <option value="convformer_m36_in21ft1k">ConvFormer M36 ImageNet21k</option>
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182 <option value="convformer_m36_384_in21ft1k">ConvFormer M36 384 ImageNet21k</option>
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183 <option value="convformer_m36_in21k">ConvFormer M36 ImageNet21k Pretrained</option>
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184 <option value="convformer_b36">ConvFormer B36</option>
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185 <option value="convformer_b36_384">ConvFormer B36 384</option>
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186 <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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187 <option value="convformer_b36_384_in21ft1k">ConvFormer B36 384 ImageNet21k</option>
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188 <option value="convformer_b36_in21k">ConvFormer B36 ImageNet21k Pretrained</option>
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189 <option value="caformer_s18">CAFormer S18</option>
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190 <option value="caformer_s18_384">CAFormer S18 384</option>
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191 <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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192 <option value="caformer_s18_384_in21ft1k">CAFormer S18 384 ImageNet21k</option>
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193 <option value="caformer_s18_in21k">CAFormer S18 ImageNet21k Pretrained</option>
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194 <option value="caformer_s36">CAFormer S36</option>
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195 <option value="caformer_s36_384">CAFormer S36 384</option>
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196 <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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197 <option value="caformer_s36_384_in21ft1k">CAFormer S36 384 ImageNet21k</option>
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198 <option value="caformer_s36_in21k">CAFormer S36 ImageNet21k Pretrained</option>
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199 <option value="caformer_m36">CAFormer M36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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200 <option value="caformer_m36_384">CAFormer M36 384</option>
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201 <option value="caformer_m36_in21ft1k">CAFormer M36 ImageNet21k</option>
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202 <option value="caformer_m36_384_in21ft1k">CAFormer M36 384 ImageNet21k</option>
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203 <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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204 <option value="caformer_b36">CAFormer B36</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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205 <option value="caformer_b36_384">CAFormer B36 384</option>
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206 <option value="caformer_b36_in21ft1k">CAFormer B36 ImageNet21k</option>
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207 <option value="caformer_b36_384_in21ft1k">CAFormer B36 384 ImageNet21k</option>
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208 <option value="caformer_b36_in21k">CAFormer B36 ImageNet21k Pretrained</option>
0
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209 </param>
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210
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211 <conditional name="scratch_fine_tune">
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212 <param name="use_pretrained" type="select"
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213 label="Use pretrained weights?"
9
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214 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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215 <option value="false">No</option>
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216 <option value="true" selected="true">Yes</option>
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217 </param>
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218 <when value="true">
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219 <param name="fine_tune" type="select" label="Fine tune the encoder?"
8
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220 help="Whether to fine tune the encoder(combiner and decoder will be fine-tuned anyway)" >
0
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221 <option value="false" >No</option>
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222 <option value="true" selected="true">Yes</option>
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223 </param>
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224 </when>
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225 <when value="false">
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226 <!-- No additional parameters to show if the user selects 'No' -->
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227 </when>
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228 </conditional>
14
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229 <param name="image_resize"
11
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230 type="select"
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231 label="Image Resize"
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232 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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233 <option value="original" selected="true">Original Size (No Resize)</option>
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234 <option value="96x96">96x96</option>
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235 <option value="128x128">128x128</option>
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236 <option value="160x160">160x160</option>
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237 <option value="192x192">192x192</option>
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238 <option value="220x220">220x220</option>
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239 <option value="224x224">224x224</option>
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240 <option value="256x256">256x256</option>
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241 <option value="299x299">299x299</option>
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242 <option value="320x320">320x320</option>
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243 <option value="384x384">384x384</option>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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244 <option value="448x448">448x448</option>
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245 <option value="512x512">512x512</option>
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246 </param>
14
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247 <param name="augmentation"
2
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248 type="select"
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249 multiple="true"
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250 display="checkboxes"
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251 label="Image Augmentation"
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252 help="Pick any combination of augmentations to apply">
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253 <option value="random_horizontal_flip">Random Horizontal Flip</option>
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254 <option value="random_vertical_flip">Random Vertical Flip</option>
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255 <option value="random_rotate">Random Rotate</option>
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256 <option value="random_blur">Random Blur</option>
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257 <option value="random_brightness">Random Brightness</option>
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258 <option value="random_contrast">Random Contrast</option>
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259 </param>
0
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260 <param argument="random_seed" type="integer" value="42" optional="true" label="Random seed (set for reproducibility)" min="0" max="999999"/>
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261 <conditional name="advanced_settings">
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262 <param name="customize_defaults" type="select" label="Customize Default Settings?" help="Select yes if you want to customize the default settings of the experiment.">
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263 <option value="false" selected="true">No</option>
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264 <option value="true">Yes</option>
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265 </param>
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266 <when value="true">
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267 <param name="epochs" type="integer" value="10" min="1" max="99999" label="Epochs" help="Total number of full passes through the training dataset. Higher values may improve accuracy but increase training time. Default: 10." />
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268 <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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269 <conditional name="learning_rate_condition">
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270 <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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271 <option value="false" selected="true" >No</option>
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272 <option value="true">Yes</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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273 </param>
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274 <when value="true">
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275 <param name="learning_rate" type="float" value="0.001" min="0.0001" max="1.0" label="Learning Rate" help="Initial learning rate for the optimizer. Default: 0.001." />
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276 </when>
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277 <when value="false">
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278 <!-- No additional parameters to show if the user selects 'No' -->
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279 </when>
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280 </conditional>
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281 <conditional name="batch_size_condition">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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282 <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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283 <option value="false" selected="true" >No</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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284 <option value="true">Yes</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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285 </param>
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286 <when value="true">
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287 <param name="batch_size" type="integer" value="32" min="1" max="99999" label="Batch Size" help="Number of samples per gradient update. Default: 32." />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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288 </when>
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289 <when value="false">
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290 <!-- No additional parameters to show if the user selects 'No' -->
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291 </when>
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292 </conditional>
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293 <param name="train_split" type="float"
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294 label="Training split proportion (only works if no split column in the metadata csv)"
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295 value="0.7"
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296 help="Fraction of data for training (e.g., 0.7). train split + val split + test split should = 1"/>
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297 <param name="val_split" type="float"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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298 label="Validation split proportion (only works if no split column in the metadata csv)"
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299 value="0.1"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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300 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
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301 <param name="test_split" type="float"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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302 label="Test split proportion (only works if no split column in the metadata csv)"
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303 value="0.2"
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304 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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305 <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
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306 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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307 <when value="false">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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308 <!-- No additional parameters to show if the user selects 'No' -->
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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309 </when>
2
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310 </conditional>
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311 </inputs>
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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312 <outputs>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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313 <data format="ludwig_model" name="output_model" label="${tool.name} trained model on ${on_string}" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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314 <data format="html" name="output_report" from_work_dir="image_classification_results_report.html" label="${tool.name} report on ${on_string}" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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315 <collection type="list" name="output_pred_csv" label="${tool.name} predictions CSVs/experiment stats/plots on ${on_string}" >
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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316 <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
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317 <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
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318 <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
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319 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" format="png" directory="experiment_run/visualizations/test" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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320 </collection>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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321 </outputs>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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322 <tests>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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323 <test expect_num_outputs="3">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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324 <param name="input_csv" value="mnist_subset.csv" ftype="csv" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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325 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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326 <param name="model_name" value="resnet18" />
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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327 <param name="augmentation" value="random_horizontal_flip,random_vertical_flip,random_rotate" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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328 <output name="output_report">
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329 <assert_contents>
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330 <has_text text="Results Summary" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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331 <has_text text="Train/Validation Results" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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332 <has_text text="Test Results" />
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333 </assert_contents>
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334 </output>
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335
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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336 <output_collection name="output_pred_csv" type="list" >
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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337 <element name="predictions.csv" >
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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338 <assert_contents>
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339 <has_n_columns n="1" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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340 </assert_contents>
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341 </element>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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342 </output_collection>
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343 </test>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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344 <test expect_num_outputs="3">
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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345 <param name="input_csv" value="utkface_labels.csv" ftype="csv" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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346 <param name="image_zip" value="age_regression.zip" ftype="zip" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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347 <param name="model_name" value="resnet18" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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348 <output name="output_report">
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349 <assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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350 <has_text text="Results Summary" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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351 <has_text text="Train/Validation Results" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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352 <has_text text="Test Results" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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353 </assert_contents>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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354 </output>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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355 <output_collection name="output_pred_csv" type="list" >
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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356 <element name="predictions.csv" >
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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357 <assert_contents>
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358 <has_n_columns n="1" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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359 </assert_contents>
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diff changeset
360 </element>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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361 </output_collection>
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362 </test>
11
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363 <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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364 <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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365 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
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366 <param name="model_name" value="caformer_s18" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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367 <output name="output_report">
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368 <assert_contents>
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369 <has_text text="Results Summary" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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370 <has_text text="Train/Validation Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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371 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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372 </assert_contents>
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373 </output>
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374
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375 <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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376 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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377 <assert_contents>
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378 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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379 </assert_contents>
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380 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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381 </output_collection>
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382 </test>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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383 <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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384 <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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385 <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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386 <param name="model_name" value="randformer_s12" />
14
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387 <param name="advanced_settings|customize_defaults" value="true" />
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388 <param name="advanced_settings|epochs" value="5" />
11
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389 <output name="output_report">
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390 <assert_contents>
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391 <has_text text="Results Summary" />
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392 <has_text text="Train/Validation Results" />
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393 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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394 </assert_contents>
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395 </output>
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396
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397 <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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398 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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399 <assert_contents>
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400 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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401 </assert_contents>
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402 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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403 </output_collection>
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404 </test>
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405 <!-- Test 7: MetaFormer with 384x384 input - verifies model correctly handles non-224x224 dimensions -->
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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406 <test expect_num_outputs="3">
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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407 <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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408 <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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409 <param name="model_name" value="caformer_s18_384" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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410 <param name="image_resize" value="384x384" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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411 <output name="output_report">
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412 <assert_contents>
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413 <has_text text="Results Summary" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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414 <has_text text="Train/Validation Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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415 <has_text text="Test Results" />
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416 </assert_contents>
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417 </output>
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418 <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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419 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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420 <assert_contents>
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421 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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422 </assert_contents>
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423 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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424 <element name="description" >
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425 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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426 <has_text text="384" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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427 </assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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428 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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429 </output_collection>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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430 </test>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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431 <!-- Test 8: Binary classification with custom threshold - verifies ROC curve generation for binary tasks; need to find a test dataset -->
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432 <!-- <test expect_num_outputs="3">
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433 <param name="input_csv" value="binary_classification.csv" ftype="csv" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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434 <param name="image_zip" value="binary_images.zip" ftype="zip" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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435 <param name="model_name" value="resnet18" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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436 <param name="customize_defaults" value="true" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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437 <param name="threshold" value="0.6" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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438 <output name="output_report">
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439 <assert_contents>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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440 <has_text text="Results Summary" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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441 <has_text text="Train/Validation Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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442 <has_text text="Test Results" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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443 <has_text text="ROC-AUC Curves" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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444 </assert_contents>
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445 </output>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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446 <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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447 <element name="predictions.csv" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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448 <assert_contents>
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449 <has_n_columns n="1" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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450 </assert_contents>
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451 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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452 <element name="test_statistics.json" >
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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453 <assert_contents>
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454 <has_text text="roc_auc" />
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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455 </assert_contents>
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456 </element>
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
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457 </output_collection>
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458 </test> -->
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459 <!-- Test 9: PoolFormerV2 model configuration - verifies custom_model parameter persists in config -->
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460 <!-- Test 10: Multi-class classification with ROC curves - verifies robust ROC-AUC plot generation -->
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461 <!-- <test expect_num_outputs="3">
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462 <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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463 <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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464 <param name="model_name" value="resnet18" />
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465 <param name="customize_defaults" value="true" />
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466 <param name="epochs" value="3" />
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467 <output name="output_report">
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468 <assert_contents>
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469 <has_text text="Results Summary" />
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470 <has_text text="Train/Validation Results" />
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471 <has_text text="Test Results" />
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472 <has_text text="ROC-AUC Curves" />
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473 <has_text text="Micro-average ROC" />
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474 </assert_contents>
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475 </output>
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476 <output_collection name="output_pred_csv" type="list" >
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477 <element name="predictions.csv" >
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478 <assert_contents>
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479 <has_n_columns n="1" />
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480 </assert_contents>
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481 </element>
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482 </output_collection>
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483 </test> -->
12
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484 <test expect_num_outputs="3">
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485 <param name="input_csv" value="mnist_subset_binary.csv" ftype="csv" />
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486 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
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487 <param name="model_name" value="resnet18" />
14
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488 <param name="advanced_settings|customize_defaults" value="true" />
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489 <param name="advanced_settings|threshold" value="0.6" />
12
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490 <output name="output_report">
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491 <assert_contents>
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492 <has_text text="Accuracy" />
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493 <has_text text="Precision" />
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494 <has_text text="Learning Curves Label Accuracy" />
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495 </assert_contents>
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496 </output>
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497 <output_collection name="output_pred_csv" type="list" >
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498 <element name="predictions.csv" >
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499 <assert_contents>
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500 <has_n_columns n="1" />
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501 </assert_contents>
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502 </element>
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503 </output_collection>
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504 </test>
9
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505 </tests>
0
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506 <help>
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507 <![CDATA[
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508 **What it does**
9
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509 Image Learner for Classification/regression: trains and evaluates a image classification/regression model.
0
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510 It uses the metadata csv to find the image paths and labels.
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511 The metadata csv should contain a column with the name 'image_path' and a column with the name 'label'.
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512 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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513 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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514
11
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515 **Models Available**
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516 This tool supports a wide range of state-of-the-art image classification models including:
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517 - Traditional CNNs (ResNet, EfficientNet, VGG, etc.)
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518 - Vision Transformers (ViT, Swin Transformer)
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519 - Modern architectures (ConvNeXt, MaxViT)
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520 - MetaFormer family models (IdentityFormer, RandFormer, PoolFormerV2, ConvFormer, CAFormer)
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521
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522 **MetaFormer Models**
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523 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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524
9
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525 **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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526
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527 **Outputs**
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528 The tool will output a trained model in the form of a ludwig_model file,
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529 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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530 The html report will contain metrics&experiment setup parameters, train&val plots and test plots.
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531
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532 ]]>
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533 </help>
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534 <citations>
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535 <citation type="bibtex">
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536 @misc{https://doi.org/10.48550/arxiv.1909.07930,
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537 doi = {10.48550/ARXIV.1909.07930},
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538 url = {https://arxiv.org/abs/1909.07930},
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539 author = {Molino, Piero and Dudin, Yaroslav and Miryala, Sai Sumanth},
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540 title = {Ludwig: a type-based declarative deep learning toolbox},
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541 publisher = {arXiv},
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542 year = {2019},
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543 copyright = {arXiv.org perpetual, non-exclusive license}
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544 }
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545 </citation>
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546 </citations>
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547 </tool>