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comparison keras_batch_models.xml @ 15:cada91b0c1d1 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author bgruening
date Wed, 09 Aug 2023 12:20:18 +0000
parents 0a3f113397b2
children 9d77b259ef27
comparison
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14:03533fa14e77 15:cada91b0c1d1
1 <tool id="keras_batch_models" name="Build Deep learning Batch Training Models" version="@KERAS_VERSION@" profile="20.05"> 1 <tool id="keras_batch_models" name="Build Deep learning Batch Training Models" version="@VERSION@" profile="@PROFILE@">
2 <description>with online data generator for Genomic/Protein sequences and images</description> 2 <description>with online data generator for Genomic/Protein sequences and images</description>
3 <macros> 3 <macros>
4 <import>main_macros.xml</import> 4 <import>main_macros.xml</import>
5 <import>keras_macros.xml</import> 5 <import>keras_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="python_requirements" /> 7 <expand macro="python_requirements" />
8 <expand macro="macro_stdio" /> 8 <expand macro="macro_stdio" />
9 <version_command>echo "@KERAS_VERSION@"</version_command> 9 <version_command>echo "@VERSION@"</version_command>
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 python '$__tool_directory__/keras_deep_learning.py' 12 python '$__tool_directory__/keras_deep_learning.py'
13 --inputs '$inputs' 13 --inputs '$inputs'
14 --model_json '$mode_selection.infile_json' 14 --model_json '$mode_selection.infile_json'
15 --tool_id 'keras_batch_models' 15 --tool_id 'keras_batch_models'
16 --outfile '$outfile' 16 --outfile '$outfile'
17 #if $get_params
18 --outfile_params '$outfile_params'
19 #end if
20 ]]> 17 ]]>
21 </command> 18 </command>
22 <configfiles> 19 <configfiles>
23 <inputs name="inputs" /> 20 <inputs name="inputs" />
24 </configfiles> 21 </configfiles>
25 <inputs> 22 <inputs>
26 <conditional name="mode_selection"> 23 <conditional name="mode_selection">
27 <param name="mode_type" type="select" label="Choose a building mode"> 24 <param name="mode_type" type="select" label="Choose a building mode">
28 <option value="train_model" selected="true">Build a training model</option> 25 <option value="train_model" selected="true">Build a training model</option>
29 </param> 26 </param>
30 <when value="train_model"> 27 <when value="train_model">
31 <param name="infile_json" type="data" format="json" label="Select the dataset containing model configurations (JSON)" /> 28 <param name="infile_json" type="data" format="json" label="Select the dataset containing model configurations (JSON)" />
32 <param name="learning_type" type="select" label="Select a learning class"> 29 <param name="learning_type" type="select" label="Select a learning class">
33 <option value="KerasGBatchClassifier">KerasGBatchClassifier -- Build a training model with batch data generator</option> 30 <option value="KerasGBatchClassifier">KerasGBatchClassifier -- Build a training model with batch data generator</option>
34 </param> 31 </param>
35 <conditional name="generator_selection"> 32 <conditional name="generator_selection">
36 <param name="generator_type" type="select" label="Select a batch data generator"> 33 <param name="generator_type" type="select" label="Select a batch data generator">
37 <option value="FastaDNABatchGenerator" selected="true">FastaDNABatchGenerator -- Online transformation of DNA sequences</option> 34 <option value="FastaDNABatchGenerator" selected="true">FastaDNABatchGenerator -- Online transformation of DNA sequences</option>
38 <option value="FastaRNABatchGenerator">FastaRNABatchGenerator -- Online transformation of RNA sequences</option> 35 <option value="FastaRNABatchGenerator">FastaRNABatchGenerator -- Online transformation of RNA sequences</option>
39 <option value="FastaProteinBatchGenerator">FastaProteinBatchGenerator -- Online transformation of Protein sequences</option> 36 <option value="FastaProteinBatchGenerator">FastaProteinBatchGenerator -- Online transformation of Protein sequences</option>
40 <option value="GenomicIntervalBatchGenerator">GenomicIntervalBatchGenerator - Online transformation of genomic sequences from a reference genome and intervals</option> 37 <option value="GenomicIntervalBatchGenerator">GenomicIntervalBatchGenerator - Online transformation of genomic sequences from a reference genome and intervals</option>
41 <option value="none">To be determined</option> 38 <option value="none">To be determined</option>
42 </param> 39 </param>
43 <when value="FastaDNABatchGenerator"> 40 <when value="FastaDNABatchGenerator">
44 <expand macro="params_fasta_dna_batch_generator" /> 41 <expand macro="params_fasta_dna_batch_generator" />
45 </when> 42 </when>
46 <when value="FastaRNABatchGenerator"> 43 <when value="FastaRNABatchGenerator">
47 <expand macro="params_fasta_dna_batch_generator" /> 44 <expand macro="params_fasta_dna_batch_generator" />
48 </when> 45 </when>
49 <when value="FastaProteinBatchGenerator"> 46 <when value="FastaProteinBatchGenerator">
50 <expand macro="params_fasta_protein_batch_generator" /> 47 <expand macro="params_fasta_protein_batch_generator" />
51 </when> 48 </when>
52 <when value="GenomicIntervalBatchGenerator"> 49 <when value="GenomicIntervalBatchGenerator">
53 <expand macro="params_genomic_interval_batch_generator" /> 50 <expand macro="params_genomic_interval_batch_generator" />
54 </when> 51 </when>
55 <when value="none" /> 52 <when value="none" />
56 </conditional> 53 </conditional>
57 <expand macro="keras_compile_params_section" /> 54 <expand macro="keras_compile_params_section" />
58 <expand macro="keras_fit_params_section" /> 55 <expand macro="keras_fit_params_section" />
59 <param name="class_positive_factor" type="float" value="1" optional="true" label="class_positive_factor" help="For binary classification only. If int, like 5, will convert to class_weight {0: 1, 1: 5}. If float, 0.2, corresponds to class_weight {0: 1/0.2, 1: 1}" /> 56 <param name="class_positive_factor" type="float" value="1" optional="true" label="class_positive_factor" help="For binary classification only. If int, like 5, will convert to class_weight {0: 1, 1: 5}. If float, 0.2, corresponds to class_weight {0: 1/0.2, 1: 1}" />
60 <param name="prediction_steps" type="integer" value="" optional="true" label="prediction_steps" help="Prediction steps. Optional. If None, it equals number of samples divided by `batch_size`." /> 57 <param name="prediction_steps" type="integer" value="" optional="true" label="prediction_steps" help="Prediction steps. Optional. If None, it equals number of samples divided by `batch_size`." />
61 <param name="random_seed" type="integer" value="" optional="true" label="Random Seed" help="Integer or blank for None. Warning: when random seed is set to an integer, training will be running in single thread mode, which may cause slowness." /> 58 <param name="random_seed" type="integer" value="" optional="true" label="Random Seed" help="Integer or blank for None. Warning: when random seed is set to an integer, training will be running in single thread mode, which may cause slowness." />
62 </when> 59 </when>
63 </conditional> 60 </conditional>
64 <param name="get_params" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Output parameters for searchCV?" help="Optional. Tunable parameters could be obtained through `estimator_attributes` tool." /> 61 </inputs>
65 </inputs> 62 <outputs>
66 <outputs> 63 <data format="h5mlm" name="outfile" label="Keras Batch Classifier on ${on_string}" />
67 <data format="zip" name="outfile" label="Keras Batch Classifier on ${on_string}" /> 64 </outputs>
68 <data format="tabular" name="outfile_params" label="get_params for Keras Batch Classifier on ${on_string}"> 65 <tests>
69 <filter>get_params</filter> 66 <test>
70 </data> 67 <conditional name="mode_selection">
71 </outputs> 68 <param name="infile_json" value="keras05.json" ftype="json" />
72 <tests> 69 <param name="learning_type" value="KerasGBatchClassifier" />
73 <test> 70 <conditional name="generator_selection">
74 <conditional name="mode_selection"> 71 <param name="generator_type" value="none" />
75 <param name="infile_json" value="keras01.json" ftype="json" /> 72 </conditional>
76 <param name="learning_type" value="KerasGBatchClassifier" /> 73 <section name="compile_params">
77 <conditional name="generator_selection"> 74 <param name="loss" value="categorical_crossentropy" />
78 <param name="generator_type" value="none" /> 75 <conditional name="optimizer_selection">
79 </conditional> 76 <param name="optimizer_type" value="RMSprop" />
80 <section name="fit_params"> 77 <section name="optimizer_options">
81 <param name="epochs" value="100" /> 78 <param name="lr" value="0.0001" />
82 <repeat name="callbacks"> 79 <param name="decay" value="0.000001" />
83 <conditional name="callback_selection"> 80 </section>
84 <param name="callback_type" value="None" /> 81 </conditional>
85 </conditional> 82 <param name="metrics" value="acc,categorical_accuracy" />
86 </repeat> 83 </section>
87 </section> 84 <section name="fit_params">
88 </conditional> 85 <param name="epochs" value="100" />
89 <param name="get_params" value="true" /> 86 <repeat name="callbacks">
90 <output name="outfile" file="keras_batch_model04" compare="sim_size" delta="30" /> 87 <conditional name="callback_selection">
91 <output name="outfile_params" file="keras_batch_params04.tabular" /> 88 <param name="callback_type" value="None" />
92 </test> 89 </conditional>
93 <test> 90 </repeat>
94 <conditional name="mode_selection"> 91 </section>
95 <param name="infile_json" value="deepsear_1feature.json" ftype="json" /> 92 </conditional>
96 <param name="learning_type" value="KerasGBatchClassifier" /> 93 <output name="outfile" file="keras_batch_model05" compare="sim_size" delta="5" />
97 <conditional name="generator_selection"> 94 </test>
98 <param name="generator_type" value="GenomicIntervalBatchGenerator" /> 95 <test>
99 <param name="seed" value="999" /> 96 <conditional name="mode_selection">
100 </conditional> 97 <param name="infile_json" value="keras01.json" ftype="json" />
101 <section name="fit_params"> 98 <param name="learning_type" value="KerasGBatchClassifier" />
102 <param name="epochs" value="100" /> 99 <conditional name="generator_selection">
103 </section> 100 <param name="generator_type" value="none" />
104 </conditional> 101 </conditional>
105 <output name="outfile" file="keras_batch_model03" compare="sim_size" delta="30" /> 102 <section name="fit_params">
106 </test> 103 <param name="epochs" value="100" />
107 <test> 104 <repeat name="callbacks">
108 <conditional name="mode_selection"> 105 <conditional name="callback_selection">
109 <param name="infile_json" value="keras01.json" ftype="json" /> 106 <param name="callback_type" value="None" />
110 <param name="learning_type" value="KerasGBatchClassifier" /> 107 </conditional>
111 <conditional name="generator_selection"> 108 </repeat>
112 <param name="generator_type" value="FastaDNABatchGenerator" /> 109 </section>
113 <param name="seed" value="999" /> 110 </conditional>
114 </conditional> 111 <output name="outfile" file="keras_batch_model04" compare="sim_size" delta="20" />
115 <section name="fit_params"> 112 </test>
116 <param name="epochs" value="100" /> 113 <test>
117 <repeat name="callbacks"> 114 <conditional name="mode_selection">
118 <conditional name="callback_selection"> 115 <param name="infile_json" value="deepsear_1feature.json" ftype="json" />
119 <param name="callback_type" value="EarlyStopping" /> 116 <param name="learning_type" value="KerasGBatchClassifier" />
120 <param name="monitor" value="val_loss" /> 117 <conditional name="generator_selection">
121 </conditional> 118 <param name="generator_type" value="GenomicIntervalBatchGenerator" />
122 </repeat> 119 <param name="seed" value="999" />
123 </section> 120 </conditional>
124 </conditional> 121 <section name="fit_params">
125 <output name="outfile" file="keras_batch_model02" compare="sim_size" delta="30" /> 122 <param name="epochs" value="100" />
126 </test> 123 </section>
127 <test> 124 </conditional>
128 <conditional name="mode_selection"> 125 <output name="outfile" file="keras_batch_model03" compare="sim_size" delta="20" />
129 <param name="infile_json" value="keras01.json" ftype="json" /> 126 </test>
130 <param name="learning_type" value="KerasGBatchClassifier" /> 127 <test>
131 <conditional name="generator_selection"> 128 <conditional name="mode_selection">
132 <param name="generator_type" value="FastaDNABatchGenerator" /> 129 <param name="infile_json" value="keras01.json" ftype="json" />
133 <param name="seed" value="999" /> 130 <param name="learning_type" value="KerasGBatchClassifier" />
134 </conditional> 131 <conditional name="generator_selection">
135 <section name="fit_params"> 132 <param name="generator_type" value="FastaDNABatchGenerator" />
136 <param name="epochs" value="100" /> 133 <param name="seed" value="999" />
137 <repeat name="callbacks"> 134 </conditional>
138 <conditional name="callback_selection"> 135 <section name="fit_params">
139 <param name="callback_type" value="None" /> 136 <param name="epochs" value="100" />
140 </conditional> 137 <repeat name="callbacks">
141 </repeat> 138 <conditional name="callback_selection">
142 </section> 139 <param name="callback_type" value="EarlyStopping" />
143 </conditional> 140 <param name="monitor" value="val_loss" />
144 <param name="get_params" value="true" /> 141 </conditional>
145 <output name="outfile" file="keras_batch_model01" compare="sim_size" delta="30" /> 142 </repeat>
146 <output name="outfile_params" file="keras_batch_params01.tabular" /> 143 </section>
147 </test> 144 </conditional>
148 </tests> 145 <output name="outfile" file="keras_batch_model02" compare="sim_size" delta="20" />
149 <help> 146 </test>
150 <![CDATA[ 147 <test>
148 <conditional name="mode_selection">
149 <param name="infile_json" value="keras01.json" ftype="json" />
150 <param name="learning_type" value="KerasGBatchClassifier" />
151 <conditional name="generator_selection">
152 <param name="generator_type" value="FastaDNABatchGenerator" />
153 <param name="seed" value="999" />
154 </conditional>
155 <section name="fit_params">
156 <param name="epochs" value="100" />
157 <repeat name="callbacks">
158 <conditional name="callback_selection">
159 <param name="callback_type" value="None" />
160 </conditional>
161 </repeat>
162 </section>
163 </conditional>
164 <output name="outfile" file="keras_batch_model01" compare="sim_size" delta="5" />
165 </test>
166 </tests>
167 <help>
168 <![CDATA[
151 **What does this tool do?** 169 **What does this tool do?**
152 170
153 This tool builds deep learning training models using API `galaxy_ml.keras_galaxy_model.KerasGBatchClassifier`_, which takes parameters in FIVE categories. 171 This tool builds deep learning training models using API `galaxy_ml.keras_galaxy_model.KerasGBatchClassifier`_, which takes parameters in FIVE categories.
154 172
155 - a JSON file that contains layer information for a deep learning model. 173 - a JSON file that contains layer information for a deep learning model.
163 - other parameters, including `class_positive_factor`, `prediction_steps`, `seed` (random seed) and so on. 181 - other parameters, including `class_positive_factor`, `prediction_steps`, `seed` (random seed) and so on.
164 182
165 183
166 **Output** 184 **Output**
167 185
168 A zipped model file that could be used in `model_validation` tool or `hyperparameter search` tool. 186 A model file that could be used in `model_validation` tool or `hyperparameter search` tool.
169 187
170 .. _`galaxy_ml.keras_galaxy_model.KerasGBatchClassifier`: https://goeckslab.github.io/Galaxy-ML/APIs/keras-galaxy-models/#kerasgbatchclassifier 188 .. _`galaxy_ml.keras_galaxy_model.KerasGBatchClassifier`: https://goeckslab.github.io/Galaxy-ML/APIs/keras-galaxy-models/#kerasgbatchclassifier
171 189
172 .. _`galaxy_ml.preprocessors.FastaDNABatchGenerator`: https://goeckslab.github.io/Galaxy-ML/APIs/keras-galaxy-models/#FastaDNABatchGenerator 190 .. _`galaxy_ml.preprocessors.FastaDNABatchGenerator`: https://goeckslab.github.io/Galaxy-ML/APIs/keras-galaxy-models/#FastaDNABatchGenerator
173 191
178 .. _`galaxy_ml.preprocessors.GenomicIntervalBatchGenerator`: https://goeckslab.github.io/Galaxy-ML/APIs/keras-galaxy-models/#GenomicIntervalBatchGenerator 196 .. _`galaxy_ml.preprocessors.GenomicIntervalBatchGenerator`: https://goeckslab.github.io/Galaxy-ML/APIs/keras-galaxy-models/#GenomicIntervalBatchGenerator
179 197
180 .. _`keras.io`: https://keras.io/models/model/#fit_generator 198 .. _`keras.io`: https://keras.io/models/model/#fit_generator
181 199
182 ]]> 200 ]]>
183 </help> 201 </help>
184 <citations> 202 <citations>
185 <expand macro="keras_citation" /> 203 <expand macro="keras_citation" />
186 <expand macro="tensorflow_citation" /> 204 <expand macro="tensorflow_citation" />
187 </citations> 205 </citations>
188 </tool> 206 </tool>