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comparison keras_batch_models.xml @ 0:f59a4f7c47f9 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
author bgruening
date Fri, 09 Aug 2019 06:26:30 -0400
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children 79efb5472c2e
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1 <tool id="keras_batch_models" name="Build Deep learning Batch Training Models" version="@KERAS_VERSION@">
2 <description>with online data generator for Genomic/Protein sequences and images</description>
3 <macros>
4 <import>main_macros.xml</import>
5 <import>keras_macros.xml</import>
6 </macros>
7 <expand macro="python_requirements"/>
8 <expand macro="macro_stdio"/>
9 <version_command>echo "@KERAS_VERSION@"</version_command>
10 <command>
11 <![CDATA[
12 python '$__tool_directory__/keras_deep_learning.py'
13 --inputs '$inputs'
14 --model_json '$mode_selection.infile_json'
15 --tool_id 'keras_batch_models'
16 --outfile '$outfile'
17 #if $get_params
18 --outfile_params '$outfile_params'
19 #end if
20 ]]>
21 </command>
22 <configfiles>
23 <inputs name="inputs"/>
24 </configfiles>
25 <inputs>
26 <conditional name="mode_selection">
27 <param name="mode_type" type="select" label="Choose a building mode">
28 <option value="train_model" selected="true">Build a training model</option>
29 </param>
30 <when value="train_model">
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">
33 <option value="KerasGBatchClassifier">KerasGBatchClassifier -- Build a training model with batch data generator</option>
34 </param>
35 <conditional name="generator_selection">
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>
38 <option value="FastaRNABatchGenerator">FastaRNABatchGenerator -- Online transformation of RNA 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>
41 <!--option value="ImageBatchGenerator">ImageBatchGenerator - Online transformation of images</option-->
42 </param>
43 <when value="FastaDNABatchGenerator">
44 <expand macro="params_fasta_dna_batch_generator"/>
45 </when>
46 <when value="FastaRNABatchGenerator">
47 <expand macro="params_fasta_dna_batch_generator"/>
48 </when>
49 <when value="FastaProteinBatchGenerator">
50 <expand macro="params_fasta_protein_batch_generator"/>
51 </when>
52 <when value="GenomicIntervalBatchGenerator">
53 <expand macro="params_genomic_interval_batch_generator"/>
54 </when>
55 <!--when value="ImageBatchGenerator">
56 <expand macro="params_image_batch_generator"/>
57 </when-->
58 </conditional>
59 <expand macro="keras_compile_params_section"/>
60 <expand macro="keras_fit_params_section"/>
61 <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}"/>
62 <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`."/>
63 <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."/>
64 </when>
65 </conditional>
66 <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."/>
67 </inputs>
68 <outputs>
69 <data format="zip" name="outfile" label="Keras Batch Classifier on ${on_string}"/>
70 <data format="tabular" name="outfile_params" label="get_params for Keras Batch Classifier on ${on_string}">
71 <filter>get_params</filter>
72 </data>
73 </outputs>
74 <tests>
75 <test>
76 <conditional name="mode_selection">
77 <param name="infile_json" value="deepsear_1feature.json" ftype="json"/>
78 <param name="learning_type" value="KerasGBatchClassifier"/>
79 <conditional name="generator_selection">
80 <param name="generator_type" value="GenomicIntervalBatchGenerator"/>
81 <param name="seed" value="999"/>
82 </conditional>
83 <section name="fit_params">
84 <param name="epochs" value="100"/>
85 </section>
86 </conditional>
87 <output name="outfile" file="keras_batch_model03" compare="sim_size" delta="5"/>
88 </test>
89 <test>
90 <conditional name="mode_selection">
91 <param name="infile_json" value="keras01.json" ftype="json"/>
92 <param name="learning_type" value="KerasGBatchClassifier"/>
93 <conditional name="generator_selection">
94 <param name="generator_type" value="FastaDNABatchGenerator"/>
95 <param name="seed" value="999"/>
96 </conditional>
97 <section name="fit_params">
98 <param name="epochs" value="100"/>
99 <repeat name="callbacks">
100 <conditional name="callback_selection">
101 <param name="callback_type" value="EarlyStopping"/>
102 <param name="monitor" value="val_loss"/>
103 </conditional>
104 </repeat>
105 </section>
106 </conditional>
107 <output name="outfile" file="keras_batch_model02" compare="sim_size" delta="5"/>
108 </test>
109 <test>
110 <conditional name="mode_selection">
111 <param name="infile_json" value="keras01.json" ftype="json"/>
112 <param name="learning_type" value="KerasGBatchClassifier"/>
113 <conditional name="generator_selection">
114 <param name="generator_type" value="FastaDNABatchGenerator"/>
115 <param name="seed" value="999"/>
116 </conditional>
117 <section name="fit_params">
118 <param name="epochs" value="100"/>
119 <repeat name="callbacks">
120 <conditional name="callback_selection">
121 <param name="callback_type" value="None"/>
122 </conditional>
123 </repeat>
124 </section>
125 </conditional>
126 <param name="get_params" value="true" />
127 <output name="outfile" file="keras_batch_model01" compare="sim_size" delta="5"/>
128 <output name="outfile_params" file="keras_batch_params01.tabular" />
129 </test>
130 </tests>
131 <help>
132 <![CDATA[
133 **What does this tool do?**
134
135 This tool builds deep learning training models using API `galaxy_ml.keras_galaxy_model.KerasGBatchClassifier`_, which takes parameters in FIVE categories.
136
137 - a JSON file that contains layer information for a deep learning model.
138
139 - a data batch generator that converts raw data, such as images and genomic sequences, into numerical data to be able to fit the deep learning model. That the cycle of `batch conversion - fitting` occur in stream mode, also called on-line transformation, guarantees the training to be CPU and memory efficient. Reference: `galaxy_ml.preprocessors.FastaDNABatchGenerator`_, `galaxy_ml.preprocessors.FastaRNABatchGenerator`_, `galaxy_ml.preprocessors.FastaProteinBatchGenerator`_, `galaxy_ml.preprocessors.GenomicIntervalBatchGenerator`_.
140
141 - compile parameters, are mainly composed of loss function and optimizer.
142
143 - fit parameters, a group of variables that control the training process, referring to `galaxy_ml.keras_galaxy_model.KerasGBatchClassifier`_ and `keras.io`_.
144
145 - other parameters, including `class_positive_factor`, `prediction_steps`, `seed` (random seed) and so on.
146
147
148 **Output**
149
150 A zipped model file that could be used in `model_validation` tool or `hyperparameter search` tool.
151
152 .. _`galaxy_ml.keras_galaxy_model.KerasGBatchClassifier`: https://goeckslab.github.io/Galaxy-ML/APIs/keras-galaxy-models/#kerasgbatchclassifier
153
154 .. _`galaxy_ml.preprocessors.FastaDNABatchGenerator`: https://goeckslab.github.io/Galaxy-ML/APIs/keras-galaxy-models/#FastaDNABatchGenerator
155
156 .. _`galaxy_ml.preprocessors.FastaRNABatchGenerator`: https://goeckslab.github.io/Galaxy-ML/APIs/keras-galaxy-models/#FastaRNABatchGenerator
157
158 .. _`galaxy_ml.preprocessors.FastaProteinBatchGenerator`: https://goeckslab.github.io/Galaxy-ML/APIs/keras-galaxy-models/#FastaProteinBatchGenerator
159
160 .. _`galaxy_ml.preprocessors.GenomicIntervalBatchGenerator`: https://goeckslab.github.io/Galaxy-ML/APIs/keras-galaxy-models/#GenomicIntervalBatchGenerator
161
162 .. _`keras.io`: https://keras.io/models/model/#fit_generator
163
164 ]]>
165 </help>
166 <citations>
167 <expand macro="keras_citation"/>
168 <expand macro="tensorflow_citation"/>
169 </citations>
170 </tool>