Mercurial > repos > bgruening > sklearn_discriminant_classifier

comparison discriminant.xml @ 13:f46da2feb233 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
author bgruening
date Mon, 09 Jul 2018 14:33:25 -0400
parents e0067d9baffc
children fb232caca397
comparison
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12:cb14b6827f70 13:f46da2feb233
20 import numpy as np 20 import numpy as np
21 import sklearn.discriminant_analysis 21 import sklearn.discriminant_analysis
22 import pandas 22 import pandas
23 import pickle 23 import pickle
24 24
25 @COLUMNS_FUNCTION@
26 @GET_X_y_FUNCTION@
27
25 input_json_path = sys.argv[1] 28 input_json_path = sys.argv[1]
26 params = json.load(open(input_json_path, "r")) 29 params = json.load(open(input_json_path, "r"))
27 30
28 31
29 #if $selected_tasks.selected_task == "load": 32 #if $selected_tasks.selected_task == "load":
30 33
31 classifier_object = pickle.load(open("$infile_model", 'r')) 34 classifier_object = pickle.load(open("$infile_model", 'r'))
32 35
33 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=0, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False ) 36 header = 'infer' if params["selected_tasks"]["header"] else None
37 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False)
34 prediction = classifier_object.predict(data) 38 prediction = classifier_object.predict(data)
35 prediction_df = pandas.DataFrame(prediction) 39 prediction_df = pandas.DataFrame(prediction)
36 res = pandas.concat([data, prediction_df], axis=1) 40 res = pandas.concat([data, prediction_df], axis=1)
37 res.to_csv(path_or_buf = "$outfile_predict", sep="\t", index=False) 41 res.to_csv(path_or_buf = "$outfile_predict", sep="\t", index=False)
38 42
39 #else: 43 #else:
40 44
41 data_train = pandas.read_csv("$selected_tasks.infile_train", sep='\t', header=0, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False ) 45 X, y = get_X_y(params, "$selected_tasks.selected_algorithms.input_options.infile1" ,"$selected_tasks.selected_algorithms.input_options.infile2")
42
43 data = data_train.ix[:,0:len(data_train.columns)-1]
44 labels = np.array(data_train[data_train.columns[len(data_train.columns)-1]])
45 46
46 options = params["selected_tasks"]["selected_algorithms"]["options"] 47 options = params["selected_tasks"]["selected_algorithms"]["options"]
47 selected_algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"] 48 selected_algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"]
48 49
49 my_class = getattr(sklearn.discriminant_analysis, selected_algorithm) 50 my_class = getattr(sklearn.discriminant_analysis, selected_algorithm)
50 classifier_object = my_class(**options) 51 classifier_object = my_class(**options)
51 classifier_object.fit(data,labels) 52 classifier_object.fit(X, y)
52 pickle.dump(classifier_object,open("$outfile_fit", 'w+'), pickle.HIGHEST_PROTOCOL) 53 pickle.dump(classifier_object,open("$outfile_fit", 'w+'), pickle.HIGHEST_PROTOCOL)
53 54
54 #end if 55 #end if
55 ]]> 56 ]]>
56 </configfile> 57 </configfile>
57 </configfiles> 58 </configfiles>
58 <inputs> 59 <inputs>
59 <expand macro="train_loadConditional" model="zip"> 60 <expand macro="sl_Conditional" model="zip">
60 <param name="selected_algorithm" type="select" label="Classifier type"> 61 <param name="selected_algorithm" type="select" label="Classifier type">
61 <option value="LinearDiscriminantAnalysis" selected="true">Linear Discriminant Classifier</option> 62 <option value="LinearDiscriminantAnalysis" selected="true">Linear Discriminant Classifier</option>
62 <option value="QuadraticDiscriminantAnalysis">Quadratic Discriminant Classifier</option> 63 <option value="QuadraticDiscriminantAnalysis">Quadratic Discriminant Classifier</option>
63 </param> 64 </param>
64 <when value="LinearDiscriminantAnalysis"> 65 <when value="LinearDiscriminantAnalysis">
66 <expand macro="sl_mixed_input"/>
65 <section name="options" title="Advanced Options" expanded="False"> 67 <section name="options" title="Advanced Options" expanded="False">
66 <param argument="solver" type="select" optional="true" label="Solver" help=""> 68 <param argument="solver" type="select" optional="true" label="Solver" help="">
67 <option value="svd" selected="true">Singular Value Decomposition</option> 69 <option value="svd" selected="true">Singular Value Decomposition</option>
68 <option value="lsqr">Least Squares Solution</option> 70 <option value="lsqr">Least Squares Solution</option>
69 <option value="eigen">Eigenvalue Decomposition</option> 71 <option value="eigen">Eigenvalue Decomposition</option>
76 <param argument="store_covariance" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" 78 <param argument="store_covariance" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false"
77 label="Store covariance" help="Compute class covariance matrix."/> 79 label="Store covariance" help="Compute class covariance matrix."/>
78 </section> 80 </section>
79 </when> 81 </when>
80 <when value="QuadraticDiscriminantAnalysis"> 82 <when value="QuadraticDiscriminantAnalysis">
83 <expand macro="sl_mixed_input"/>
81 <section name="options" title="Advanced Options" expanded="False"> 84 <section name="options" title="Advanced Options" expanded="False">
82 <!--expand macro="priors"/--> 85 <!--expand macro="priors"/-->
83 <param argument="reg_param" type="float" optional="true" value="0.0" label="Regularization coefficient" help="Covariance estimate regularizer."/> 86 <param argument="reg_param" type="float" optional="true" value="0.0" label="Regularization coefficient" help="Covariance estimate regularizer."/>
84 <expand macro="tol" default_value="0.00001" help_text="Rank estimation threshold used in SVD solver."/> 87 <expand macro="tol" default_value="0.00001" help_text="Rank estimation threshold used in SVD solver."/>
85 <param argument="store_covariances" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" 88 <param argument="store_covariances" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false"
89 </expand> 92 </expand>
90 </inputs> 93 </inputs>
91 <expand macro="output"/> 94 <expand macro="output"/>
92 <tests> 95 <tests>
93 <test> 96 <test>
94 <param name="infile_train" value="train.tabular" ftype="tabular"/> 97 <param name="infile1" value="train.tabular" ftype="tabular"/>
98 <param name="infile2" value="train.tabular" ftype="tabular"/>
99 <param name="header1" value="True"/>
100 <param name="header2" value="True"/>
101 <param name="col1" value="1,2,3,4"/>
102 <param name="col2" value="5"/>
95 <param name="selected_task" value="train"/> 103 <param name="selected_task" value="train"/>
96 <param name="selected_algorithm" value="LinearDiscriminantAnalysis"/> 104 <param name="selected_algorithm" value="LinearDiscriminantAnalysis"/>
97 <param name="solver" value="svd" /> 105 <param name="solver" value="svd" />
98 <param name="store_covariances" value="True"/> 106 <param name="store_covariances" value="True"/>
99 <output name="outfile_fit" file="lda_model01" compare="sim_size" delta="500"/> 107 <output name="outfile_fit" file="lda_model01" compare="sim_size" delta="500"/>
100 </test> 108 </test>
101 <test> 109 <test>
102 <param name="infile_train" value="train.tabular" ftype="tabular"/> 110 <param name="infile1" value="train.tabular" ftype="tabular"/>
111 <param name="infile2" value="train.tabular" ftype="tabular"/>
112 <param name="header1" value="True"/>
113 <param name="header2" value="True"/>
114 <param name="col1" value="1,2,3,4"/>
115 <param name="col2" value="5"/>
103 <param name="selected_task" value="train"/> 116 <param name="selected_task" value="train"/>
104 <param name="selected_algorithm" value="LinearDiscriminantAnalysis"/> 117 <param name="selected_algorithm" value="LinearDiscriminantAnalysis"/>
105 <param name="solver" value="lsqr"/> 118 <param name="solver" value="lsqr"/>
106 <output name="outfile_fit" file="lda_model02" compare="sim_size" delta="500"/> 119 <output name="outfile_fit" file="lda_model02" compare="sim_size" delta="500"/>
107 </test> 120 </test>
108 <test> 121 <test>
109 <param name="infile_train" value="train.tabular" ftype="tabular"/> 122 <param name="infile1" value="train.tabular" ftype="tabular"/>
123 <param name="infile2" value="train.tabular" ftype="tabular"/>
124 <param name="header1" value="True"/>
125 <param name="header2" value="True"/>
126 <param name="col1" value="1,2,3,4"/>
127 <param name="col2" value="5"/>
110 <param name="selected_task" value="train"/> 128 <param name="selected_task" value="train"/>
111 <param name="selected_algorithm" value="QuadraticAnalysis"/> 129 <param name="selected_algorithm" value="QuadraticDiscriminantAnalysis"/>
112 <output name="outfile_fit" file="qda_model01" compare="sim_size" delta="500"/> 130 <output name="outfile_fit" file="qda_model01" compare="sim_size" delta="500"/>
113 </test> 131 </test>
114 <test> 132 <test>
115 <param name="infile_model" value="lda_model01" ftype="zip"/> 133 <param name="infile_model" value="lda_model01" ftype="zip"/>
116 <param name="infile_data" value="test.tabular" ftype="tabular"/> 134 <param name="infile_data" value="test.tabular" ftype="tabular"/>
135 <param name="header" value="True"/>
117 <param name="selected_task" value="load"/> 136 <param name="selected_task" value="load"/>
118 <output name="outfile_predict" file="lda_prediction_result01.tabular"/> 137 <output name="outfile_predict" file="lda_prediction_result01.tabular"/>
119 </test> 138 </test>
120 <test> 139 <test>
121 <param name="infile_model" value="lda_model02" ftype="zip"/> 140 <param name="infile_model" value="lda_model02" ftype="zip"/>
122 <param name="infile_data" value="test.tabular" ftype="tabular"/> 141 <param name="infile_data" value="test.tabular" ftype="tabular"/>
142 <param name="header" value="True"/>
123 <param name="selected_task" value="load"/> 143 <param name="selected_task" value="load"/>
124 <output name="outfile_predict" file="lda_prediction_result02.tabular"/> 144 <output name="outfile_predict" file="lda_prediction_result02.tabular"/>
125 </test> 145 </test>
126 <test> 146 <test>
127 <param name="infile_model" value="qda_model01" ftype="zip"/> 147 <param name="infile_model" value="qda_model01" ftype="zip"/>
128 <param name="infile_data" value="test.tabular" ftype="tabular"/> 148 <param name="infile_data" value="test.tabular" ftype="tabular"/>
149 <param name="header" value="True"/>
129 <param name="selected_task" value="load"/> 150 <param name="selected_task" value="load"/>
130 <output name="outfile_predict" file="qda_prediction_result01.tabular"/> 151 <output name="outfile_predict" file="qda_prediction_result01.tabular"/>
131 </test> 152 </test>
132 </tests> 153 </tests>
133 <help><![CDATA[ 154 <help><![CDATA[