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comparison keras_batch_models.xml @ 8:8edfc7381344 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
author bgruening
date Tue, 13 Apr 2021 15:58:22 +0000
parents 79efb5472c2e
children 70846a2dd227
comparison
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7:b2494cb1de6d 8:8edfc7381344
1 <tool id="keras_batch_models" name="Build Deep learning Batch Training Models" version="@KERAS_VERSION@"> 1 <tool id="keras_batch_models" name="Build Deep learning Batch Training Models" version="@KERAS_VERSION@" profile="20.05">
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 "@KERAS_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 17 #if $get_params
18 --outfile_params '$outfile_params' 18 --outfile_params '$outfile_params'
19 #end if 19 #end if
20 ]]> 20 ]]>
21 </command> 21 </command>
22 <configfiles> 22 <configfiles>
23 <inputs name="inputs"/> 23 <inputs name="inputs" />
24 </configfiles> 24 </configfiles>
25 <inputs> 25 <inputs>
26 <conditional name="mode_selection"> 26 <conditional name="mode_selection">
27 <param name="mode_type" type="select" label="Choose a building mode"> 27 <param name="mode_type" type="select" label="Choose a building mode">
28 <option value="train_model" selected="true">Build a training model</option> 28 <option value="train_model" selected="true">Build a training model</option>
29 </param> 29 </param>
30 <when value="train_model"> 30 <when value="train_model">
31 <param name="infile_json" type="data" format="json" label="Select the dataset containing model configurations (JSON)"/> 31 <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"> 32 <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> 33 <option value="KerasGBatchClassifier">KerasGBatchClassifier -- Build a training model with batch data generator</option>
34 </param> 34 </param>
35 <conditional name="generator_selection"> 35 <conditional name="generator_selection">
36 <param name="generator_type" type="select" label="Select a batch data generator"> 36 <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> 37 <option value="FastaDNABatchGenerator" selected="true">FastaDNABatchGenerator -- Online transformation of DNA sequences</option>
38 <option value="FastaRNABatchGenerator">FastaRNABatchGenerator -- Online transformation of RNA sequences</option> 38 <option value="FastaRNABatchGenerator">FastaRNABatchGenerator -- Online transformation of RNA sequences</option>
39 <option value="FastaProteinBatchGenerator">FastaProteinBatchGenerator -- Online transformation of Protein sequences</option> 39 <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> 40 <option value="GenomicIntervalBatchGenerator">GenomicIntervalBatchGenerator - Online transformation of genomic sequences from a reference genome and intervals</option>
41 <option value="none">To be determined</option> 41 <option value="none">To be determined</option>
42 </param> 42 </param>
43 <when value="FastaDNABatchGenerator"> 43 <when value="FastaDNABatchGenerator">
44 <expand macro="params_fasta_dna_batch_generator"/> 44 <expand macro="params_fasta_dna_batch_generator" />
45 </when> 45 </when>
46 <when value="FastaRNABatchGenerator"> 46 <when value="FastaRNABatchGenerator">
47 <expand macro="params_fasta_dna_batch_generator"/> 47 <expand macro="params_fasta_dna_batch_generator" />
48 </when> 48 </when>
49 <when value="FastaProteinBatchGenerator"> 49 <when value="FastaProteinBatchGenerator">
50 <expand macro="params_fasta_protein_batch_generator"/> 50 <expand macro="params_fasta_protein_batch_generator" />
51 </when> 51 </when>
52 <when value="GenomicIntervalBatchGenerator"> 52 <when value="GenomicIntervalBatchGenerator">
53 <expand macro="params_genomic_interval_batch_generator"/> 53 <expand macro="params_genomic_interval_batch_generator" />
54 </when> 54 </when>
55 <when value="none"/> 55 <when value="none" />
56 </conditional>
57 <expand macro="keras_compile_params_section" />
58 <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}" />
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`." />
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." />
62 </when>
56 </conditional> 63 </conditional>
57 <expand macro="keras_compile_params_section"/> 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." />
58 <expand macro="keras_fit_params_section"/> 65 </inputs>
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}"/> 66 <outputs>
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`."/> 67 <data format="zip" name="outfile" label="Keras Batch Classifier on ${on_string}" />
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."/> 68 <data format="tabular" name="outfile_params" label="get_params for Keras Batch Classifier on ${on_string}">
62 </when> 69 <filter>get_params</filter>
63 </conditional> 70 </data>
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."/> 71 </outputs>
65 </inputs> 72 <tests>
66 <outputs> 73 <test>
67 <data format="zip" name="outfile" label="Keras Batch Classifier on ${on_string}"/> 74 <conditional name="mode_selection">
68 <data format="tabular" name="outfile_params" label="get_params for Keras Batch Classifier on ${on_string}"> 75 <param name="infile_json" value="keras01.json" ftype="json" />
69 <filter>get_params</filter> 76 <param name="learning_type" value="KerasGBatchClassifier" />
70 </data> 77 <conditional name="generator_selection">
71 </outputs> 78 <param name="generator_type" value="none" />
72 <tests> 79 </conditional>
73 <test> 80 <section name="fit_params">
74 <conditional name="mode_selection"> 81 <param name="epochs" value="100" />
75 <param name="infile_json" value="keras01.json" ftype="json"/> 82 <repeat name="callbacks">
76 <param name="learning_type" value="KerasGBatchClassifier"/> 83 <conditional name="callback_selection">
77 <conditional name="generator_selection"> 84 <param name="callback_type" value="None" />
78 <param name="generator_type" value="none"/> 85 </conditional>
79 </conditional> 86 </repeat>
80 <section name="fit_params"> 87 </section>
81 <param name="epochs" value="100"/>
82 <repeat name="callbacks">
83 <conditional name="callback_selection">
84 <param name="callback_type" value="None"/>
85 </conditional> 88 </conditional>
86 </repeat> 89 <param name="get_params" value="true" />
87 </section> 90 <output name="outfile" file="keras_batch_model04" compare="sim_size" delta="30" />
88 </conditional> 91 <output name="outfile_params" file="keras_batch_params04.tabular" />
89 <param name="get_params" value="true" /> 92 </test>
90 <output name="outfile" file="keras_batch_model04" compare="sim_size" delta="5"/> 93 <test>
91 <output name="outfile_params" file="keras_batch_params04.tabular" /> 94 <conditional name="mode_selection">
92 </test> 95 <param name="infile_json" value="deepsear_1feature.json" ftype="json" />
93 <test> 96 <param name="learning_type" value="KerasGBatchClassifier" />
94 <conditional name="mode_selection"> 97 <conditional name="generator_selection">
95 <param name="infile_json" value="deepsear_1feature.json" ftype="json"/> 98 <param name="generator_type" value="GenomicIntervalBatchGenerator" />
96 <param name="learning_type" value="KerasGBatchClassifier"/> 99 <param name="seed" value="999" />
97 <conditional name="generator_selection"> 100 </conditional>
98 <param name="generator_type" value="GenomicIntervalBatchGenerator"/> 101 <section name="fit_params">
99 <param name="seed" value="999"/> 102 <param name="epochs" value="100" />
100 </conditional> 103 </section>
101 <section name="fit_params">
102 <param name="epochs" value="100"/>
103 </section>
104 </conditional>
105 <output name="outfile" file="keras_batch_model03" compare="sim_size" delta="5"/>
106 </test>
107 <test>
108 <conditional name="mode_selection">
109 <param name="infile_json" value="keras01.json" ftype="json"/>
110 <param name="learning_type" value="KerasGBatchClassifier"/>
111 <conditional name="generator_selection">
112 <param name="generator_type" value="FastaDNABatchGenerator"/>
113 <param name="seed" value="999"/>
114 </conditional>
115 <section name="fit_params">
116 <param name="epochs" value="100"/>
117 <repeat name="callbacks">
118 <conditional name="callback_selection">
119 <param name="callback_type" value="EarlyStopping"/>
120 <param name="monitor" value="val_loss"/>
121 </conditional> 104 </conditional>
122 </repeat> 105 <output name="outfile" file="keras_batch_model03" compare="sim_size" delta="30" />
123 </section> 106 </test>
124 </conditional> 107 <test>
125 <output name="outfile" file="keras_batch_model02" compare="sim_size" delta="5"/> 108 <conditional name="mode_selection">
126 </test> 109 <param name="infile_json" value="keras01.json" ftype="json" />
127 <test> 110 <param name="learning_type" value="KerasGBatchClassifier" />
128 <conditional name="mode_selection"> 111 <conditional name="generator_selection">
129 <param name="infile_json" value="keras01.json" ftype="json"/> 112 <param name="generator_type" value="FastaDNABatchGenerator" />
130 <param name="learning_type" value="KerasGBatchClassifier"/> 113 <param name="seed" value="999" />
131 <conditional name="generator_selection"> 114 </conditional>
132 <param name="generator_type" value="FastaDNABatchGenerator"/> 115 <section name="fit_params">
133 <param name="seed" value="999"/> 116 <param name="epochs" value="100" />
134 </conditional> 117 <repeat name="callbacks">
135 <section name="fit_params"> 118 <conditional name="callback_selection">
136 <param name="epochs" value="100"/> 119 <param name="callback_type" value="EarlyStopping" />
137 <repeat name="callbacks"> 120 <param name="monitor" value="val_loss" />
138 <conditional name="callback_selection"> 121 </conditional>
139 <param name="callback_type" value="None"/> 122 </repeat>
123 </section>
140 </conditional> 124 </conditional>
141 </repeat> 125 <output name="outfile" file="keras_batch_model02" compare="sim_size" delta="30" />
142 </section> 126 </test>
143 </conditional> 127 <test>
144 <param name="get_params" value="true" /> 128 <conditional name="mode_selection">
145 <output name="outfile" file="keras_batch_model01" compare="sim_size" delta="5"/> 129 <param name="infile_json" value="keras01.json" ftype="json" />
146 <output name="outfile_params" file="keras_batch_params01.tabular" /> 130 <param name="learning_type" value="KerasGBatchClassifier" />
147 </test> 131 <conditional name="generator_selection">
148 </tests> 132 <param name="generator_type" value="FastaDNABatchGenerator" />
149 <help> 133 <param name="seed" value="999" />
150 <![CDATA[ 134 </conditional>
135 <section name="fit_params">
136 <param name="epochs" value="100" />
137 <repeat name="callbacks">
138 <conditional name="callback_selection">
139 <param name="callback_type" value="None" />
140 </conditional>
141 </repeat>
142 </section>
143 </conditional>
144 <param name="get_params" value="true" />
145 <output name="outfile" file="keras_batch_model01" compare="sim_size" delta="30" />
146 <output name="outfile_params" file="keras_batch_params01.tabular" />
147 </test>
148 </tests>
149 <help>
150 <![CDATA[
151 **What does this tool do?** 151 **What does this tool do?**
152 152
153 This tool builds deep learning training models using API `galaxy_ml.keras_galaxy_model.KerasGBatchClassifier`_, which takes parameters in FIVE categories. 153 This tool builds deep learning training models using API `galaxy_ml.keras_galaxy_model.KerasGBatchClassifier`_, which takes parameters in FIVE categories.
154 154
155 - a JSON file that contains layer information for a deep learning model. 155 - a JSON file that contains layer information for a deep learning model.
178 .. _`galaxy_ml.preprocessors.GenomicIntervalBatchGenerator`: https://goeckslab.github.io/Galaxy-ML/APIs/keras-galaxy-models/#GenomicIntervalBatchGenerator 178 .. _`galaxy_ml.preprocessors.GenomicIntervalBatchGenerator`: https://goeckslab.github.io/Galaxy-ML/APIs/keras-galaxy-models/#GenomicIntervalBatchGenerator
179 179
180 .. _`keras.io`: https://keras.io/models/model/#fit_generator 180 .. _`keras.io`: https://keras.io/models/model/#fit_generator
181 181
182 ]]> 182 ]]>
183 </help> 183 </help>
184 <citations> 184 <citations>
185 <expand macro="keras_citation"/> 185 <expand macro="keras_citation" />
186 <expand macro="tensorflow_citation"/> 186 <expand macro="tensorflow_citation" />
187 </citations> 187 </citations>
188 </tool> 188 </tool>