Mercurial > repos > goeckslab > image_learner

annotate image_learner.xml @ 2:186424a7eca7 draft

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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
author goeckslab
date Thu, 03 Jul 2025 20:43:24 +0000
parents 39202fe5cf97
children 2c3a3dfaf1a9
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54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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1 <tool id="image_learner" name="Image Learner for Classification" version="0.1.0" profile="22.05">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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2 <description>trains and evaluates a image classification 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="utils.py" />
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8 <include path="image_learner_cli.py" />
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9 </required_files>
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10 <stdio>
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11 <exit_code range="137" level="fatal_oom" description="Out of Memory" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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12 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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13 </stdio>
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14 <command>
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15 <![CDATA[
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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16 #import re
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17
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18 #if $input_csv
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19
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20 #set $sanitized_input_csv = re.sub('[^\w\-_\.]', '_', $input_csv.element_identifier.strip())
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21 ln -sf '$input_csv' "./${sanitized_input_csv}";
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22 #end if
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23
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24 python '$__tool_directory__/image_learner_cli.py'
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25 --csv-file "./${sanitized_input_csv}"
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26 --image-zip "$image_zip"
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27 --model-name "$model_name"
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28 #if $use_pretrained == "true"
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29 --use-pretrained
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30 #if $fine_tune == "true"
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31 --fine-tune
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32 #end if
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33 #end if
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34 #if $customize_defaults == "true"
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35 #if $epochs
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36 --epochs "$epochs"
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37 #end if
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38 #if $early_stop
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39 --early-stop "$early_stop"
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40 #end if
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41 #if $learning_rate_define == "true"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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42 --learning-rate "$learning_rate"
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43 #end if
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44 #if $batch_size_define == "true"
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45 --batch-size "$batch_size"
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46 #end if
2
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47 --split-probabilities "$train_split" "$val_split" "$test_split"
0
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48 #end if
2
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49 #if $augmentation
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50 --augmentation "$augmentation"
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51 #end if
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52 --random-seed "$random_seed"
0
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53 --output-dir "." &&
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54
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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55 mkdir -p '$output_model.extra_files_path' &&
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56 cp -r experiment_run/model/*.json experiment_run/model/model_weights '$output_model.extra_files_path' &&
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57
2
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58 echo "Image Learner Classification Experiment is Done!"
0
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59 ]]>
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60 </command>
2
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61
0
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62 <inputs>
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63 <param argument="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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64 <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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65 <param name="model_name" type="select" optional="false" label="Select a model for your experiment" >
2
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66
0
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67 <option value="resnet18">Resnet18</option>
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68 <option value="resnet34">Resnet34</option>
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69 <option value="resnet50">Resnet50</option>
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70 <option value="resnet101">Resnet101</option>
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71 <option value="resnet152">Resnet152</option>
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72 <option value="resnext50_32x4d">Resnext50_32x4d</option>
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73 <option value="resnext101_32x8d">Resnext101_32x8d</option>
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74 <option value="resnext101_64x4d">Resnext101_64x4d</option>
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75 <option value="resnext152_32x8d">Resnext152_32x8d</option>
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76 <option value="wide_resnet50_2">Wide_resnet50_2</option>
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77 <option value="wide_resnet101_2">Wide_resnet101_2</option>
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78 <option value="wide_resnet103_2">Wide_resnet103_2</option>
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79 <option value="efficientnet_b0">Efficientnet_b0</option>
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80 <option value="efficientnet_b1">Efficientnet_b1</option>
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81 <option value="efficientnet_b2">Efficientnet_b2</option>
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82 <option value="efficientnet_b3">Efficientnet_b3</option>
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83 <option value="efficientnet_b4">Efficientnet_b4</option>
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84 <option value="efficientnet_b5">Efficientnet_b5</option>
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85 <option value="efficientnet_b6">Efficientnet_b6</option>
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86 <option value="efficientnet_b7">Efficientnet_b7</option>
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87 <option value="efficientnet_v2_s">Efficientnet_v2_s</option>
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88 <option value="efficientnet_v2_m">Efficientnet_v2_m</option>
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89 <option value="efficientnet_v2_l">Efficientnet_v2_l</option>
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90 <option value="regnet_y_400mf">Regnet_y_400mf</option>
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91 <option value="regnet_y_800mf">Regnet_y_800mf</option>
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92 <option value="regnet_y_1_6gf">Regnet_y_1_6gf</option>
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93 <option value="regnet_y_3_2gf">Regnet_y_3_2gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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94 <option value="regnet_y_8gf">Regnet_y_8gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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95 <option value="regnet_y_16gf">Regnet_y_16gf</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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96 <option value="regnet_y_32gf">Regnet_y_32gf</option>
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97 <option value="regnet_y_128gf">Regnet_y_128gf</option>
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98 <option value="regnet_x_400mf">Regnet_x_400mf</option>
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99 <option value="regnet_x_800mf">Regnet_x_800mf</option>
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100 <option value="regnet_x_1_6gf">Regnet_x_1_6gf</option>
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101 <option value="regnet_x_3_2gf">Regnet_x_3_2gf</option>
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102 <option value="regnet_x_8gf">Regnet_x_8gf</option>
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103 <option value="regnet_x_16gf">Regnet_x_16gf</option>
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104 <option value="regnet_x_32gf">Regnet_x_32gf</option>
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105 <option value="vgg11">Vgg11</option>
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106 <option value="vgg11_bn">Vgg11_bn</option>
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107 <option value="vgg13">Vgg13</option>
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108 <option value="vgg13_bn">Vgg13_bn</option>
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109 <option value="vgg16">Vgg16</option>
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110 <option value="vgg16_bn">Vgg16_bn</option>
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111 <option value="vgg19">Vgg19</option>
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112 <option value="vgg19_bn">Vgg19_bn</option>
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113 <option value="shufflenet_v2_x0_5">Shufflenet_v2_x0_5</option>
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114 <option value="shufflenet_v2_x1_0">Shufflenet_v2_x1_0</option>
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115 <option value="shufflenet_v2_x1_5">Shufflenet_v2_x1_5</option>
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116 <option value="shufflenet_v2_x2_0">Shufflenet_v2_x2_0</option>
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117 <option value="squeezenet1_0">Squeezenet1_0</option>
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118 <option value="squeezenet1_1">Squeezenet1_1</option>
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119 <option value="swin_t">Swin_t</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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120 <option value="swin_s">Swin_s</option>
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121 <option value="swin_b">Swin_b</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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122 <option value="swin_v2_t">Swin_v2_t</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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123 <option value="swin_v2_s">Swin_v2_s</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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124 <option value="swin_v2_b">Swin_v2_b</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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125 <option value="vit_b_16">Vit_b_16</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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126 <option value="vit_b_32">Vit_b_32</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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127 <option value="vit_l_16">Vit_l_16</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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128 <option value="vit_l_32">Vit_l_32</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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129 <option value="vit_h_14">Vit_h_14</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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130 <option value="convnext_tiny">Convnext_tiny</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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131 <option value="convnext_small">Convnext_small</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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132 <option value="convnext_base">Convnext_base</option>
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133 <option value="convnext_large">Convnext_large</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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134 <option value="maxvit_t">Maxvit_t</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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135 <option value="alexnet">Alexnet</option>
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136 <option value="googlenet">Googlenet</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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137 <option value="inception_v3">Inception_v3</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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138 <option value="mobilenet_v2">Mobilenet_v2</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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139 <option value="mobilenet_v3_large">Mobilenet_v3_large</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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140 <option value="mobilenet_v3_small">Mobilenet_v3_small</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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141 </param>
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142
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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143 <conditional name="scratch_fine_tune">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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144 <param name="use_pretrained" type="select"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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145 label="Use pretrained weights?"
2
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146 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
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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147 <option value="false">No</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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148 <option value="true" selected="true">Yes</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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149 </param>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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150 <when value="true">
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151 <param name="fine_tune" type="select" label="Fine tune the encoder?"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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152 help="Whether to fine tune the encoder(combiner and decoder will be fine-tued anyway)" >
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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153 <option value="false" >No</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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154 <option value="true" selected="true">Yes</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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155 </param>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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156 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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157 <when value="false">
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158 <!-- No additional parameters to show if the user selects 'No' -->
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159 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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160 </conditional>
2
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161 <param argument="augmentation"
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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162 name="augmentation"
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163 type="select"
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164 multiple="true"
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165 display="checkboxes"
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166 label="Image Augmentation"
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167 help="Pick any combination of augmentations to apply">
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168 <option value="random_horizontal_flip">Random Horizontal Flip</option>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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169 <option value="random_vertical_flip">Random Vertical Flip</option>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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170 <option value="random_rotate">Random Rotate</option>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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171 <option value="random_blur">Random Blur</option>
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172 <option value="random_brightness">Random Brightness</option>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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173 <option value="random_contrast">Random Contrast</option>
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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174 </param>
0
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175 <param argument="random_seed" type="integer" value="42" optional="true" label="Random seed (set for reproducibility)" min="0" max="999999"/>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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176 <conditional name="advanced_settings">
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177 <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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178 <option value="false" selected="true">No</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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179 <option value="true">Yes</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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180 </param>
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181 <when value="true">
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182 <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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183 <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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184 <conditional name="learning_rate_condition">
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185 <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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186 <option value="false" selected="true" >No</option>
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187 <option value="true">Yes</option>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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188 </param>
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189 <when value="true">
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190 <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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191 </when>
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192 <when value="false">
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193 <!-- No additional parameters to show if the user selects 'No' -->
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194 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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195 </conditional>
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196 <conditional name="batch_size_condition">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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197 <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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198 <option value="false" selected="true" >No</option>
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199 <option value="true">Yes</option>
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200 </param>
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201 <when value="true">
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202 <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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203 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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204 <when value="false">
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205 <!-- 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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206 </when>
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207 </conditional>
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208 <param name="train_split" type="float"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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209 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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210 value="0.7"
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211 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
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212 <param name="val_split" type="float"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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213 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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214 value="0.1"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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215 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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216 <param name="test_split" type="float"
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217 label="Test split proportion (only works if no split column in the metadata csv)"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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218 value="0.2"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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219 help="Fraction of data for testing (e.g., 0.2) 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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220 </when>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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221 <when value="false">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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222 <!-- 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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223 </when>
2
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224 </conditional>
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225 </inputs>
0
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226 <outputs>
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227 <data format="ludwig_model" name="output_model" label="${tool.name} trained model on ${on_string}" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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228 <data format="html" name="output_report" from_work_dir="image_classification_results_report.html" label="${tool.name} report on ${on_string}" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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229 <collection type="list" name="output_pred_csv" label="${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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230 <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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231 <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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232 <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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233 <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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234 </collection>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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235 </outputs>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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236 <tests>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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237 <test expect_num_outputs="3">
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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238 <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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239 <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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240 <param name="model_name" value="resnet18" />
1
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241 <output name="output_report">
0
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242 <assert_contents>
1
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243 <has_text text="Results Summary" />
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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244 <has_text text="Train/Validation Results" />
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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245 <has_text text="Test Results" />
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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246 </assert_contents>
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247 </output>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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248
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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249 <output_collection name="output_pred_csv" type="list" >
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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250 <element name="predictions.csv" >
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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251 <assert_contents>
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252 <has_n_columns n="1" />
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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253 </assert_contents>
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254 </element>
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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255 </output_collection>
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256 </test>
2
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257 <test expect_num_outputs="3">
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258 <param name="input_csv" value="mnist_subset.csv" ftype="csv" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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259 <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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260 <param name="model_name" value="resnet18" />
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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261 <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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262 <output name="output_report">
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263 <assert_contents>
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264 <has_text text="Results Summary" />
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265 <has_text text="Train/Validation Results" />
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266 <has_text text="Test Results" />
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267 </assert_contents>
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268 </output>
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269
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270 <output_collection name="output_pred_csv" type="list" >
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271 <element name="predictions.csv" >
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272 <assert_contents>
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273 <has_n_columns n="1" />
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274 </assert_contents>
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275 </element>
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276 </output_collection>
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277 </test>
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278 <test expect_num_outputs="3">
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279 <param name="input_csv" value="utkface_labels.csv" ftype="csv" />
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280 <param name="image_zip" value="age_regression.zip" ftype="zip" />
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281 <param name="model_name" value="resnet18" />
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282 <output name="output_report">
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283 <assert_contents>
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284 <has_text text="Results Summary" />
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285 <has_text text="Train/Validation Results" />
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286 <has_text text="Test Results" />
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287 </assert_contents>
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288 </output>
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289 <output name="output_report" file="expected_regression.html" compare="sim_size"/>
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290
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291 <output_collection name="output_pred_csv" type="list" >
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292 <element name="predictions.csv" >
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293 <assert_contents>
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294 <has_n_columns n="1" />
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295 </assert_contents>
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296 </element>
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297 </output_collection>
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298 </test>
0
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299 </tests>
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300 <help>
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301 <![CDATA[
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302 **What it does**
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303 Image Learner for Classification: trains and evaluates a image classification model.
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304 It uses the metadata csv to find the image paths and labels.
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305 The metadata csv should contain a column with the name 'image_path' and a column with the name 'label'.
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306 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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307 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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308
2
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309 **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).**
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310
0
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311
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312 **Outputs**
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313 The tool will output a trained model in the form of a ludwig_model file,
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314 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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315 The html report will contain metrics&experiment setup parameters, train&val plots and test plots.
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316
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317 ]]>
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318 </help>
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319 <citations>
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320 <citation type="bibtex">
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321 @misc{https://doi.org/10.48550/arxiv.1909.07930,
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322 doi = {10.48550/ARXIV.1909.07930},
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323 url = {https://arxiv.org/abs/1909.07930},
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324 author = {Molino, Piero and Dudin, Yaroslav and Miryala, Sai Sumanth},
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325 title = {Ludwig: a type-based declarative deep learning toolbox},
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326 publisher = {arXiv},
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327 year = {2019},
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328 copyright = {arXiv.org perpetual, non-exclusive license}
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329 }
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330 </citation>
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331 </citations>
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332 </tool>