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comparison model_prediction.xml @ 9:4aa701f5a393 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 18:00:54 +0000
parents 6efb9bc6bf32
children 3bb1b688b0e4
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8:83228baae3c5 9:4aa701f5a393
1 <tool id="model_prediction" name="Model Prediction" version="@VERSION@"> 1 <tool id="model_prediction" name="Model Prediction" version="@VERSION@" profile="20.05">
2 <description>predicts on new data using a preffited model</description> 2 <description>predicts on new data using a preffited model</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 '$__tool_directory__/model_prediction.py' 13 python '$__tool_directory__/model_prediction.py'
27 </command> 27 </command>
28 <configfiles> 28 <configfiles>
29 <inputs name="inputs" /> 29 <inputs name="inputs" />
30 </configfiles> 30 </configfiles>
31 <inputs> 31 <inputs>
32 <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing pipeline/estimator object"/> 32 <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing pipeline/estimator object" />
33 <param name="infile_weights" type="data" format="h5" optional="true" label="Choose the dataset containing weights for the estimator above" help="Optional. For deep learning only."/> 33 <param name="infile_weights" type="data" format="h5" optional="true" label="Choose the dataset containing weights for the estimator above" help="Optional. For deep learning only." />
34 <param argument="method" type="select" label="Select invocation method"> 34 <param argument="method" type="select" label="Select invocation method">
35 <option value="predict" selected="true">predict</option> 35 <option value="predict" selected="true">predict</option>
36 <option value="predict_proba">predict_proba</option> 36 <option value="predict_proba">predict_proba</option>
37 </param> 37 </param>
38 <conditional name="input_options"> 38 <conditional name="input_options">
41 <option value="sparse">sparse matrix</option> 41 <option value="sparse">sparse matrix</option>
42 <option value="seq_fasta">sequnences in a fasta file</option> 42 <option value="seq_fasta">sequnences in a fasta file</option>
43 <option value="variant_effect">reference genome and variant call file</option> 43 <option value="variant_effect">reference genome and variant call file</option>
44 </param> 44 </param>
45 <when value="tabular"> 45 <when value="tabular">
46 <param name="infile1" type="data" format="tabular" label="Training samples dataset:"/> 46 <param name="infile1" type="data" format="tabular" label="Training samples dataset:" />
47 <param name="header1" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> 47 <param name="header1" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
48 <conditional name="column_selector_options_1"> 48 <conditional name="column_selector_options_1">
49 <expand macro="samples_column_selector_options" multiple="true"/> 49 <expand macro="samples_column_selector_options" multiple="true" />
50 </conditional> 50 </conditional>
51 </when> 51 </when>
52 <when value="sparse"> 52 <when value="sparse">
53 <param name="infile1" type="data" format="txt" label="Select a sparse matrix" help=""/> 53 <param name="infile1" type="data" format="txt" label="Select a sparse matrix" help="" />
54 </when> 54 </when>
55 <when value="seq_fasta"> 55 <when value="seq_fasta">
56 <param name="fasta_path" type="data" format="fasta" label="Dataset containing fasta genomic/protein sequences" help="Sequences will be one-hot encoded to arrays."/> 56 <param name="fasta_path" type="data" format="fasta" label="Dataset containing fasta genomic/protein sequences" help="Sequences will be one-hot encoded to arrays." />
57 <param name="seq_type" type="select" label="Sequence type"> 57 <param name="seq_type" type="select" label="Sequence type">
58 <option value="FastaDNABatchGenerator">DNA</option> 58 <option value="FastaDNABatchGenerator">DNA</option>
59 <option value="FastaRNABatchGenerator">RNA</option> 59 <option value="FastaRNABatchGenerator">RNA</option>
60 <option value="FastaProteinBatchGenerator">Protein</option> 60 <option value="FastaProteinBatchGenerator">Protein</option>
61 </param> 61 </param>
62 </when> 62 </when>
63 <when value="variant_effect"> 63 <when value="variant_effect">
64 <param name="ref_genome_file" type="data" format="fasta" label="Dataset containing reference genomic sequence" help="fasta"/> 64 <param name="ref_genome_file" type="data" format="fasta" label="Dataset containing reference genomic sequence" help="fasta" />
65 <param name="blacklist_regions" type="select" label="blacklist regioins" help="A pre-loaded list of blacklisted intervals.Refer to `selene` for details."> 65 <param name="blacklist_regions" type="select" label="blacklist regioins" help="A pre-loaded list of blacklisted intervals.Refer to `selene` for details.">
66 <option value="none" selected="true">None</option> 66 <option value="none" selected="true">None</option>
67 <option value="hg38">hg38</option> 67 <option value="hg38">hg38</option>
68 <option value="hg19">hg19</option> 68 <option value="hg19">hg19</option>
69 </param> 69 </param>
70 <param name="vcf_file" type="data" format="vcf" label="Dataset containing sequence variations" help="vcf"/> 70 <param name="vcf_file" type="data" format="vcf" label="Dataset containing sequence variations" help="vcf" />
71 <param name="seq_length" type="integer" value="1000" label="Encoding seqence length" help="A stretch of sequence surrounding the variation position on the reference genome."/> 71 <param name="seq_length" type="integer" value="1000" label="Encoding seqence length" help="A stretch of sequence surrounding the variation position on the reference genome." />
72 <param name="output_reference" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Predict the reference sequence?" help="If False, predict on the variant sequence."/> 72 <param name="output_reference" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Predict the reference sequence?" help="If False, predict on the variant sequence." />
73 </when> 73 </when>
74 </conditional> 74 </conditional>
75 </inputs> 75 </inputs>
76 <outputs> 76 <outputs>
77 <data format="tabular" name="outfile_predict"/> 77 <data format="tabular" name="outfile_predict" />
78 </outputs> 78 </outputs>
79 <tests> 79 <tests>
80 <test> 80 <test>
81 <param name="infile_estimator" value="best_estimator_.zip" ftype="zip"/> 81 <param name="infile_estimator" value="best_estimator_.zip" ftype="zip" />
82 <param name="method" value="predict"/> 82 <param name="method" value="predict" />
83 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> 83 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
84 <param name="header1" value="true" /> 84 <param name="header1" value="true" />
85 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> 85 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
86 <output name="outfile_predict" file="model_pred01.tabular"/> 86 <output name="outfile_predict" file="model_pred01.tabular" />
87 </test> 87 </test>
88 <test> 88 <test>
89 <param name="infile_estimator" value="keras_model04" ftype="zip"/> 89 <param name="infile_estimator" value="keras_model04" ftype="zip" />
90 <param name="infile_weights" value="train_test_eval_weights02.h5" ftype="h5"/> 90 <param name="infile_weights" value="train_test_eval_weights02.h5" ftype="h5" />
91 <param name="method" value="predict"/> 91 <param name="method" value="predict" />
92 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> 92 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
93 <param name="header1" value="true" /> 93 <param name="header1" value="true" />
94 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> 94 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
95 <output name="outfile_predict" > 95 <output name="outfile_predict">
96 <assert_contents> 96 <assert_contents>
97 <has_n_columns n="1"/> 97 <has_n_columns n="1" />
98 <has_text text="70.2"/> 98 <has_text text="70.2" />
99 <has_text text="61.2"/> 99 <has_text text="61.2" />
100 <has_text text="74.2"/> 100 <has_text text="74.2" />
101 <has_text text="65.9"/> 101 <has_text text="65.9" />
102 <has_text text="52.9"/> 102 <has_text text="52.9" />
103 </assert_contents> 103 </assert_contents>
104 </output> 104 </output>
105 </test> 105 </test>
106 </tests> 106 </tests>
107 <help> 107 <help>
121 - reference genome and variant call file 121 - reference genome and variant call file
122 122
123 ]]> 123 ]]>
124 </help> 124 </help>
125 <expand macro="sklearn_citation"> 125 <expand macro="sklearn_citation">
126 <expand macro="keras_citation"/> 126 <expand macro="keras_citation" />
127 <expand macro="selene_citation"/> 127 <expand macro="selene_citation" />
128 </expand> 128 </expand>
129 </tool> 129 </tool>