Mercurial > repos > bgruening > sklearn_model_fit
comparison simple_model_fit.xml @ 6:26decbf4bdb8 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
author | bgruening |
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date | Tue, 13 Apr 2021 17:56:21 +0000 |
parents | 734c66aa945a |
children | f903c8cf1455 |
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5:1c25f305db70 | 6:26decbf4bdb8 |
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1 <tool id="sklearn_model_fit" name="Fit a Pipeline, Ensemble" version="@VERSION@"> | 1 <tool id="sklearn_model_fit" name="Fit a Pipeline, Ensemble" version="@VERSION@" profile="20.05"> |
2 <description>or other models using a labeled dataset</description> | 2 <description>or other models using a labeled dataset</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 "@VERSION@"</version_command> | 9 <version_command>echo "@VERSION@"</version_command> |
10 <command> | 10 <command> |
11 <![CDATA[ | 11 <![CDATA[ |
12 export HDF5_USE_FILE_LOCKING='FALSE'; | 12 export HDF5_USE_FILE_LOCKING='FALSE'; |
13 python '$__tool_directory__/simple_model_fit.py' | 13 python '$__tool_directory__/simple_model_fit.py' |
23 </command> | 23 </command> |
24 <configfiles> | 24 <configfiles> |
25 <inputs name="inputs" /> | 25 <inputs name="inputs" /> |
26 </configfiles> | 26 </configfiles> |
27 <inputs> | 27 <inputs> |
28 <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing pipeline/estimator"/> | 28 <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing pipeline/estimator" /> |
29 <param name="is_deep_learning" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Is the estimator a deep learning model?"/> | 29 <param name="is_deep_learning" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Is the estimator a deep learning model?" /> |
30 <conditional name="input_options"> | 30 <conditional name="input_options"> |
31 <expand macro="data_input_options"/> | 31 <expand macro="data_input_options" /> |
32 <when value="tabular"> | 32 <when value="tabular"> |
33 <expand macro="samples_tabular" label1="Choose the training dataset containing features" multiple1="true" multiple2="false"/> | 33 <expand macro="samples_tabular" label1="Choose the training dataset containing features" multiple1="true" multiple2="false" /> |
34 </when> | 34 </when> |
35 <when value="sparse"> | 35 <when value="sparse"> |
36 <expand macro="sparse_target"/> | 36 <expand macro="sparse_target" /> |
37 </when> | 37 </when> |
38 </conditional> | 38 </conditional> |
39 </inputs> | 39 </inputs> |
40 <outputs> | 40 <outputs> |
41 <data format="zip" name="out_object" label="Fitted model (skeleton) on $(on_string)"/> | 41 <data format="zip" name="out_object" label="Fitted model (skeleton) on $(on_string)" /> |
42 <data format="h5" name="out_weights" label="Weights trained on ${on_string}"> | 42 <data format="h5" name="out_weights" label="Weights trained on ${on_string}"> |
43 <filter>is_deep_learning</filter> | 43 <filter>is_deep_learning</filter> |
44 </data> | 44 </data> |
45 </outputs> | 45 </outputs> |
46 <tests> | 46 <tests> |
47 <test> | 47 <test> |
48 <param name="infile_estimator" value="pipeline05" ftype="zip"/> | 48 <param name="infile_estimator" value="pipeline05" ftype="zip" /> |
49 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> | 49 <param name="infile1" value="regression_X.tabular" ftype="tabular" /> |
50 <param name="header1" value="true" /> | 50 <param name="header1" value="true" /> |
51 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> | 51 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" /> |
52 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> | 52 <param name="infile2" value="regression_y.tabular" ftype="tabular" /> |
53 <param name="header2" value="true"/> | 53 <param name="header2" value="true" /> |
54 <param name="col2" value="1"/> | 54 <param name="col2" value="1" /> |
55 <output name="out_object" file="model_fit01" compare="sim_size" delta="50"/> | 55 <output name="out_object" file="model_fit01" compare="sim_size" delta="50" /> |
56 </test> | 56 </test> |
57 <test> | 57 <test> |
58 <param name="infile_estimator" value="keras_model04"/> | 58 <param name="infile_estimator" value="keras_model04" /> |
59 <param name="is_deep_learning" value="true"/> | 59 <param name="is_deep_learning" value="true" /> |
60 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> | 60 <param name="infile1" value="regression_X.tabular" ftype="tabular" /> |
61 <param name="header1" value="true" /> | 61 <param name="header1" value="true" /> |
62 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> | 62 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" /> |
63 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> | 63 <param name="infile2" value="regression_y.tabular" ftype="tabular" /> |
64 <param name="header2" value="true"/> | 64 <param name="header2" value="true" /> |
65 <param name="col2" value="1"/> | 65 <param name="col2" value="1" /> |
66 <output name="out_object" file="model_fit02" compare="sim_size" delta="10"/> | 66 <output name="out_object" file="model_fit02" compare="sim_size" delta="50" /> |
67 <output name="out_weights" file="model_fit02.h5" compare="sim_size" delta="10"/> | 67 <output name="out_weights" file="model_fit02.h5" compare="sim_size" delta="50" /> |
68 </test> | 68 </test> |
69 </tests> | 69 </tests> |
70 <help> | 70 <help> |
71 <![CDATA[ | 71 <![CDATA[ |
72 **What it does** | 72 **What it does** |
86 - optional hdf5 file containing weights for deep learning models. | 86 - optional hdf5 file containing weights for deep learning models. |
87 | 87 |
88 ]]> | 88 ]]> |
89 </help> | 89 </help> |
90 <expand macro="sklearn_citation"> | 90 <expand macro="sklearn_citation"> |
91 <expand macro="keras_citation"/> | 91 <expand macro="keras_citation" /> |
92 <expand macro="selene_citation"/> | 92 <expand macro="selene_citation" /> |
93 </expand> | 93 </expand> |
94 </tool> | 94 </tool> |