Mercurial > repos > bgruening > sklearn_nn_classifier
comparison nn_classifier.xml @ 7:5072ac474cd5 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
author | bgruening |
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date | Sat, 29 Sep 2018 07:29:02 -0400 |
parents | e972a913e61a |
children | ed7b1654e841 |
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6:e972a913e61a | 7:5072ac474cd5 |
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18 import json | 18 import json |
19 import numpy as np | 19 import numpy as np |
20 import sklearn.neighbors | 20 import sklearn.neighbors |
21 import pandas | 21 import pandas |
22 | 22 |
23 execfile("$__tool_directory__/sk_whitelist.py") | 23 with open("$__tool_directory__/sk_whitelist.json", "r") as f: |
24 execfile("$__tool_directory__/utils.py", globals()) | 24 sk_whitelist = json.load(f) |
25 exec(open("$__tool_directory__/utils.py").read(), globals()) | |
25 | 26 |
26 input_json_path = sys.argv[1] | 27 input_json_path = sys.argv[1] |
27 with open(input_json_path, "r") as param_handler: | 28 with open(input_json_path, "r") as param_handler: |
28 params = json.load(param_handler) | 29 params = json.load(param_handler) |
29 | 30 |
30 #if $selected_tasks.selected_task == "load": | 31 #if $selected_tasks.selected_task == "load": |
31 | 32 |
32 with open("$infile_model", 'rb') as model_handler: | 33 with open("$infile_model", 'rb') as model_handler: |
33 classifier_object = SafePickler.load(model_handler) | 34 classifier_object = load_model(model_handler) |
34 | 35 |
35 header = 'infer' if params["selected_tasks"]["header"] else None | 36 header = 'infer' if params["selected_tasks"]["header"] else None |
36 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False) | 37 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False) |
37 prediction = classifier_object.predict(data) | 38 prediction = classifier_object.predict(data) |
38 prediction_df = pandas.DataFrame(prediction) | 39 prediction_df = pandas.DataFrame(prediction) |
116 <param name="col2" value="5"/> | 117 <param name="col2" value="5"/> |
117 <param name="selected_task" value="train"/> | 118 <param name="selected_task" value="train"/> |
118 <param name="selected_algorithm" value="nneighbors"/> | 119 <param name="selected_algorithm" value="nneighbors"/> |
119 <param name="sampling_method" value="KNeighborsClassifier" /> | 120 <param name="sampling_method" value="KNeighborsClassifier" /> |
120 <param name="algorithm" value="brute" /> | 121 <param name="algorithm" value="brute" /> |
121 <output name="outfile_fit" file="nn_model01.txt"/> | 122 <output name="outfile_fit" file="nn_model01"/> |
122 </test> | 123 </test> |
123 <test> | 124 <test> |
124 <param name="infile1" value="train_set.tabular" ftype="tabular"/> | 125 <param name="infile1" value="train_set.tabular" ftype="tabular"/> |
125 <param name="infile2" value="train_set.tabular" ftype="tabular"/> | 126 <param name="infile2" value="train_set.tabular" ftype="tabular"/> |
126 <param name="header1" value="True"/> | 127 <param name="header1" value="True"/> |
127 <param name="header2" value="True"/> | 128 <param name="header2" value="True"/> |
128 <param name="col1" value="1,2,3,4"/> | 129 <param name="col1" value="1,2,3,4"/> |
129 <param name="col2" value="5"/> | 130 <param name="col2" value="5"/> |
130 <param name="selected_task" value="train"/> | 131 <param name="selected_task" value="train"/> |
131 <param name="selected_algorithm" value=""/> | |
132 <param name="selected_algorithm" value="nneighbors"/> | 132 <param name="selected_algorithm" value="nneighbors"/> |
133 <param name="sampling_method" value="RadiusNeighborsClassifier" /> | 133 <param name="sampling_method" value="RadiusNeighborsClassifier" /> |
134 <output name="outfile_fit" file="nn_model02.txt"/> | 134 <output name="outfile_fit" file="nn_model02"/> |
135 </test> | 135 </test> |
136 <test> | 136 <test> |
137 <param name="infile1" value="train_set.tabular" ftype="tabular"/> | 137 <param name="infile1" value="train_set.tabular" ftype="tabular"/> |
138 <param name="infile2" value="train_set.tabular" ftype="tabular"/> | 138 <param name="infile2" value="train_set.tabular" ftype="tabular"/> |
139 <param name="header1" value="True"/> | 139 <param name="header1" value="True"/> |
140 <param name="header2" value="True"/> | 140 <param name="header2" value="True"/> |
141 <param name="col1" value="1,2,3,4"/> | 141 <param name="col1" value="1,2,3,4"/> |
142 <param name="col2" value="5"/> | 142 <param name="col2" value="5"/> |
143 <param name="selected_task" value="train"/> | 143 <param name="selected_task" value="train"/> |
144 <param name="selected_algorithm" value="ncentroid"/> | 144 <param name="selected_algorithm" value="ncentroid"/> |
145 <output name="outfile_fit" file="nn_model03.txt"/> | 145 <output name="outfile_fit" file="nn_model03"/> |
146 </test> | 146 </test> |
147 <test> | 147 <test> |
148 <param name="infile_model" value="nn_model01.txt" ftype="txt"/> | 148 <param name="infile_model" value="nn_model01" ftype="zip"/> |
149 <param name="infile_data" value="test_set.tabular" ftype="tabular"/> | 149 <param name="infile_data" value="test_set.tabular" ftype="tabular"/> |
150 <param name="header" value="True"/> | 150 <param name="header" value="True"/> |
151 <param name="selected_task" value="load"/> | 151 <param name="selected_task" value="load"/> |
152 <output name="outfile_predict" file="nn_prediction_result01.tabular"/> | 152 <output name="outfile_predict" file="nn_prediction_result01.tabular"/> |
153 </test> | 153 </test> |
154 <test> | 154 <test> |
155 <param name="infile_model" value="nn_model02.txt" ftype="txt"/> | 155 <param name="infile_model" value="nn_model02" ftype="zip"/> |
156 <param name="infile_data" value="test_set.tabular" ftype="tabular"/> | 156 <param name="infile_data" value="test_set.tabular" ftype="tabular"/> |
157 <param name="header" value="True"/> | 157 <param name="header" value="True"/> |
158 <param name="selected_task" value="load"/> | 158 <param name="selected_task" value="load"/> |
159 <output name="outfile_predict" file="nn_prediction_result02.tabular"/> | 159 <output name="outfile_predict" file="nn_prediction_result02.tabular"/> |
160 </test> | 160 </test> |
161 <test> | 161 <test> |
162 <param name="infile_model" value="nn_model03.txt" ftype="txt"/> | 162 <param name="infile_model" value="nn_model03" ftype="zip"/> |
163 <param name="infile_data" value="test_set.tabular" ftype="tabular"/> | 163 <param name="infile_data" value="test_set.tabular" ftype="tabular"/> |
164 <param name="header" value="True"/> | 164 <param name="header" value="True"/> |
165 <param name="selected_task" value="load"/> | 165 <param name="selected_task" value="load"/> |
166 <output name="outfile_predict" file="nn_prediction_result03.tabular"/> | 166 <output name="outfile_predict" file="nn_prediction_result03.tabular"/> |
167 </test> | 167 </test> |