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comparison multimodal_learner.xml @ 3:25bb80df7c0c draft default tip

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planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
author goeckslab
date Sat, 17 Jan 2026 22:53:42 +0000
parents b708d0e210e6
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2:b708d0e210e6 3:25bb80df7c0c
1 <tool id="multimodal_learner" name="Multimodal Learner" version="0.1.1" profile="22.01"> 1 <tool id="multimodal_learner" name="Multimodal Learner" version="0.1.2" profile="22.01">
2 <description>Train and evaluate an AutoGluon Multimodal model (tabular + image + text)</description> 2 <description>Train and evaluate an AutoGluon Multimodal model (tabular + image + text)</description>
3 3
4 <requirements> 4 <requirements>
5 <container type='docker'>quay.io/goeckslab/multimodal-learner:1.4.0</container> 5 <container type='docker'>quay.io/goeckslab/multimodal-learner:1.4.0</container>
6 </requirements> 6 </requirements>
41 ln -sf '$input_csv' 'train_input.csv'; 41 ln -sf '$input_csv' 'train_input.csv';
42 #if $test_dataset_conditional.has_test_dataset == "yes" 42 #if $test_dataset_conditional.has_test_dataset == "yes"
43 ln -sf '$test_dataset_conditional.input_test' 'test_input.csv'; 43 ln -sf '$test_dataset_conditional.input_test' 'test_input.csv';
44 #end if 44 #end if
45 45
46 python '$__tool_directory__/multimodal_learner.py' 46 python '$__tool_directory__/multimodal_learner.py'
47 --input_csv_train 'train_input.csv' 47 --input_csv_train 'train_input.csv'
48 #if $test_dataset_conditional.has_test_dataset == "yes" 48 #if $test_dataset_conditional.has_test_dataset == "yes"
49 --input_csv_test 'test_input.csv' 49 --input_csv_test 'test_input.csv'
50 #end if 50 #end if
51 --target_column '$target_column' 51 --target_column '$target_column'
52 #if $sample_id_selector.use_sample_id == "yes"
53 --sample_id_column '$sample_id_selector.sample_id_column'
54 #end if
52 55
53 #if $use_images_conditional.use_images == "yes" 56 #if $use_images_conditional.use_images == "yes"
54 #if $images_zip_cli 57 #if $images_zip_cli
55 --images_zip $images_zip_cli 58 --images_zip $images_zip_cli
56 #end if 59 #end if
109 ]]></command> 112 ]]></command>
110 113
111 <inputs> 114 <inputs>
112 <param name="input_csv" type="data" format="csv,tsv" label="Training dataset (CSV/TSV)" help="Must contain the target column and optional image paths"/> 115 <param name="input_csv" type="data" format="csv,tsv" label="Training dataset (CSV/TSV)" help="Must contain the target column and optional image paths"/>
113 <param name="target_column" type="data_column" data_ref="input_csv" numerical="false" use_header_names="true" label="Target / Label column"/> 116 <param name="target_column" type="data_column" data_ref="input_csv" numerical="false" use_header_names="true" label="Target / Label column"/>
117 <conditional name="sample_id_selector">
118 <param name="use_sample_id" type="select" label="Use a sample ID column for leakage-aware splitting?" help="Select yes to choose a column that groups related records (e.g., patient_id or slide_id).">
119 <option value="no" selected="true">No column selected</option>
120 <option value="yes">Yes</option>
121 </param>
122 <when value="yes">
123 <param name="sample_id_column" type="data_column" data_ref="input_csv" use_header_names="true" label="Sample ID column" help="All rows with the same ID stay in the same split or fold to reduce leakage. Used for internal train/val/test splits and group-aware CV folds." />
124 </when>
125 <when value="no"/>
126 </conditional>
114 127
115 <conditional name="test_dataset_conditional"> 128 <conditional name="test_dataset_conditional">
116 <param name="has_test_dataset" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Provide separate test dataset?"/> 129 <param name="has_test_dataset" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Provide separate test dataset?"/>
117 <when value="yes"> 130 <when value="yes">
118 <param name="input_test" type="data" format="csv,tsv" optional="true" label="Test dataset (CSV/TSV)"/> 131 <param name="input_test" type="data" format="csv,tsv" optional="true" label="Test dataset (CSV/TSV)"/>