Mercurial > repos > goeckslab > ludwig_visualize

comparison ludwig_macros.xml @ 0:dceb8493730d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
author goeckslab
date Tue, 07 Jan 2025 22:44:54 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:dceb8493730d
1 <macros>
2 <token name="@LUDWIG_VERSION@">0.10.1</token>
3
4 <token name="@SUFFIX@">0</token>
5
6 <token name="@VERSION@">@LUDWIG_VERSION@+@SUFFIX@</token>
7
8 <token name="@PROFILE@">21.05</token>
9
10 <xml name="python_requirements_gpu">
11 <requirements>
12 <container type="docker">quay.io/goeckslab/galaxy-ludwig-gpu:latest</container>
13 </requirements>
14 </xml>
15
16 <xml name="python_requirements">
17 <requirements>
18 <container type="docker">quay.io/goeckslab/galaxy-ludwig:0.10.3</container>
19 </requirements>
20 </xml>
21
22 <xml name="macro_stdio">
23 <stdio>
24 <exit_code range="137" level="fatal_oom" description="Out of Memory" />
25 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
26 </stdio>
27 </xml>
28
29 <xml name="macro_citations">
30 <citations>
31 <citation type="bibtex">
32 @misc{https://doi.org/10.48550/arxiv.1909.07930,
33 doi = {10.48550/ARXIV.1909.07930},
34 url = {https://arxiv.org/abs/1909.07930},
35 author = {Molino, Piero and Dudin, Yaroslav and Miryala, Sai Sumanth},
36 title = {Ludwig: a type-based declarative deep learning toolbox},
37 publisher = {arXiv},
38 year = {2019},
39 copyright = {arXiv.org perpetual, non-exclusive license}
40 }
41 </citation>
42 </citations>
43 </xml>
44
45 <xml name="encoder_parameters">
46 <param argument="name" type="text" value="" label="Name of the column containing the input feature" />
47 <param argument="norm" type="select" label="Select the norm mode">
48 <option value="none" selected="true">Null</option>
49 <option value="batch">batch</option>
50 <option value="layer">layer</option>
51 </param>
52 <param argument="tied_weights" type="text" value="" optional="true" label="Name of the input feature to tie the weights of the encoder with" help="It needs to be the name of a feature of the same type and with the same encoder parameters. Optional" />
53 <yield />
54 </xml>
55
56 <xml name="visualize_file_format">
57 <param type="select" name="file_format" label="Choose the output format">
58 <option value="pdf" selected="true">pdf</option>
59 <option value="png">png</option>
60 </param>
61 </xml>
62
63 <xml name="visualize_output_feature_name">
64 <param argument="output_feature_name" type="text" value="" optional="true" label="Name of the output feature" help="If `None`, use all output features." />
65 </xml>
66
67 <xml name="visualize_training_statistics">
68 <param argument="training_statistics" type="data" format="html,json" multiple="true" label="Training statistics" />
69 </xml>
70
71 <xml name="visualize_test_statistics">
72 <param argument="test_statistics" type="data" format="html,json" multiple="true" label="Choose experiment test statistics file(s)" />
73 </xml>
74
75 <xml name="visualize_hyperopt_stats_path">
76 <param argument="hyperopt_stats_path" type="data" format="json" label="Select the hyperopt result (JSON)" />
77 </xml>
78
79 <xml name="visualize_model_names">
80 <param argument="model_names" type="text" value="" optional="true" label="Model name(s) to use as labels" help="Comma delimited for multiple." />
81 </xml>
82
83 <xml name="visualize_probabilities">
84 <param argument="probabilities" type="data" format="html" multiple="true" label="Choose the prediction results to extract probabilities from" />
85 </xml>
86
87 <xml name="visualize_ground_truth_metadata">
88 <param argument="ground_truth_metadata" type="data" format="ludwig_model,json" label="Choose the file containing feature metadata json file created during training" />
89 </xml>
90
91 <xml name="visualize_split_file">
92 <param argument="split_file" type="data" format="csv" optional="true" label="Choose the file containing split values" />
93 </xml>
94
95 <xml name="visualize_ground_truth_split">
96 <param argument="ground_truth_split" type="select" label="Select the ground truth split" >
97 <option value="0">0 -- training</option>
98 <option value="1">1 -- validation</option>
99 <option value="2">2 -- test</option>
100 </param>
101 </xml>
102
103 <xml name="visualize_ground_truth">
104 <param argument="ground_truth" type="text" value="" label="Choose the ground truth file" />
105 </xml>
106
107 <xml name="visualize_predictions">
108 <param argument="predictions" type="data" format="html" multiple="true" label="Choose the prediction result files" />
109 </xml>
110
111 <xml name="visualize_top_n_classes">
112 <param argument="top_n_classes" type="text" value="" label="Type in the list containing numbers of classes to plot" />
113 </xml>
114
115 <xml name="visualize_threshold_output_feature_names">
116 <param argument="threshold_output_feature_names" type="text" value="" label="Type in the list containing two output feature names for visualization" />
117 </xml>
118
119 <xml name="visualize_labels_limit">
120 <param argument="labels_limit" type="integer" value="" optional="true" label="Set the upper limit on the numeric encoded label value" help="Encoded numeric label values in dataset that are higher than `label_limit` are considered to be 'rare' labels." min="1" max="1000"/>
121 </xml>
122
123 <xml name="visualize_metrics">
124 <param argument="metrics" type="select" multiple="true" label="Select the metrics to display" >
125 <option value="f1" selected="true">f1</option>
126 <option value="precision">precision</option>
127 <option value="recall">recall</option>
128 <option value="accuracy">accuracy</option>
129 </param>
130 </xml>
131
132 <xml name="visualize_positive_label">
133 <param argument="positive_label" type="integer" value="1" label="Numeric encoded value for the positive class" min="1" max="1000" />
134 </xml>
135
136 <xml name="visualize_ground_truth_apply_idx">
137 <param argument="ground_truth_apply_idx" type="boolean" checked="true" label="Whether to use metadata['str2idx'] in np.vectorize?" />
138 </xml>
139
140 <xml name="visualize_normalize">
141 <param argument="normalize" type="boolean" checked="false" label="Whether to normalize rows in confusion matrix?" />
142 </xml>
143 </macros>