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comparison svm.xml @ 25:b878e4cdd63a draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author bgruening
date Wed, 09 Aug 2023 12:24:57 +0000
parents d67dcd63f6cb
children
comparison
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24:b7c3e9a3b954 25:b878e4cdd63a
1 <tool id="sklearn_svm_classifier" name="Support vector machines (SVMs)" version="@VERSION@" profile="20.05"> 1 <tool id="sklearn_svm_classifier" name="Support vector machines (SVMs)" version="@VERSION@" profile="@PROFILE@">
2 <description>for classification</description> 2 <description>for classification</description>
3 <macros> 3 <macros>
4 <import>main_macros.xml</import> 4 <import>main_macros.xml</import>
5 <!-- macro name="class_weight" argument="class_weight"--> 5 <!-- macro name="class_weight" argument="class_weight"-->
6 </macros> 6 </macros>
17 <![CDATA[ 17 <![CDATA[
18 import sys 18 import sys
19 import json 19 import json
20 import sklearn.svm 20 import sklearn.svm
21 import pandas 21 import pandas
22 import pickle 22
23 23 from galaxy_ml.model_persist import dump_model_to_h5, load_model_from_h5
24 from galaxy_ml.utils import load_model, get_X_y 24 from galaxy_ml.utils import clean_params, get_X_y
25 25
26 26
27 input_json_path = sys.argv[1] 27 input_json_path = sys.argv[1]
28 with open(input_json_path, "r") as param_handler: 28 with open(input_json_path, "r") as param_handler:
29 params = json.load(param_handler) 29 params = json.load(param_handler)
31 #if $selected_tasks.selected_task == "load": 31 #if $selected_tasks.selected_task == "load":
32 32
33 header = 'infer' if params["selected_tasks"]["header"] else None 33 header = 'infer' if params["selected_tasks"]["header"] else None
34 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None) 34 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None)
35 35
36 with open("$infile_model", 'rb') as model_handler: 36 classifier_object = load_model_from_h5('$infile_model')
37 classifier_object = load_model(model_handler) 37 classifier_object = clean_params(classifier_object)
38 38
39 prediction = classifier_object.predict(data) 39 prediction = classifier_object.predict(data)
40 prediction_df = pandas.DataFrame(prediction) 40 prediction_df = pandas.DataFrame(prediction)
41 res = pandas.concat([data, prediction_df], axis=1) 41 res = pandas.concat([data, prediction_df], axis=1)
42 res.to_csv(path_or_buf = "$outfile_predict", sep="\t", index=False) 42 res.to_csv(path_or_buf = "$outfile_predict", sep="\t", index=False)
54 54
55 my_class = getattr(sklearn.svm, selected_algorithm) 55 my_class = getattr(sklearn.svm, selected_algorithm)
56 classifier_object = my_class(**options) 56 classifier_object = my_class(**options)
57 classifier_object.fit(X, y) 57 classifier_object.fit(X, y)
58 58
59 with open("$outfile_fit", 'wb') as out_handler: 59 dump_model_to_h5(classifier_object, '$outfile_fit')
60 pickle.dump(classifier_object, out_handler)
61 60
62 #end if 61 #end if
63 62
64 ]]> 63 ]]>
65 </configfile> 64 </configfile>
66 </configfiles> 65 </configfiles>
67 <inputs> 66 <inputs>
68 <expand macro="sl_Conditional" model="zip"> 67 <expand macro="sl_Conditional" model="h5mlm">
69 <param name="selected_algorithm" type="select" label="Classifier type"> 68 <param name="selected_algorithm" type="select" label="Classifier type">
70 <option value="SVC">C-Support Vector Classification</option> 69 <option value="SVC">C-Support Vector Classification</option>
71 <option value="NuSVC">Nu-Support Vector Classification</option> 70 <option value="NuSVC">Nu-Support Vector Classification</option>
72 <option value="LinearSVC">Linear Support Vector Classification</option> 71 <option value="LinearSVC">Linear Support Vector Classification</option>
73 </param> 72 </param>
147 <param name="selected_algorithm" value="LinearSVC" /> 146 <param name="selected_algorithm" value="LinearSVC" />
148 <param name="random_state" value="5" /> 147 <param name="random_state" value="5" />
149 <output name="outfile_fit" file="svc_model03" compare="sim_size" /> 148 <output name="outfile_fit" file="svc_model03" compare="sim_size" />
150 </test> 149 </test>
151 <test> 150 <test>
152 <param name="infile_model" value="svc_model01" ftype="zip" /> 151 <param name="infile_model" value="svc_model01" ftype="h5mlm" />
153 <param name="infile_data" value="test_set.tabular" ftype="tabular" /> 152 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
154 <param name="header" value="True" /> 153 <param name="header" value="True" />
155 <param name="selected_task" value="load" /> 154 <param name="selected_task" value="load" />
156 <output name="outfile_predict" file="svc_prediction_result01.tabular" /> 155 <output name="outfile_predict" file="svc_prediction_result01.tabular" />
157 </test> 156 </test>
158 <test> 157 <test>
159 <param name="infile_model" value="svc_model02" ftype="zip" /> 158 <param name="infile_model" value="svc_model02" ftype="h5mlm" />
160 <param name="infile_data" value="test_set.tabular" ftype="tabular" /> 159 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
161 <param name="header" value="True" /> 160 <param name="header" value="True" />
162 <param name="selected_task" value="load" /> 161 <param name="selected_task" value="load" />
163 <output name="outfile_predict" file="svc_prediction_result02.tabular" /> 162 <output name="outfile_predict" file="svc_prediction_result02.tabular" />
164 </test> 163 </test>
165 <test> 164 <test>
166 <param name="infile_model" value="svc_model03" ftype="zip" /> 165 <param name="infile_model" value="svc_model03" ftype="h5mlm" />
167 <param name="infile_data" value="test_set.tabular" ftype="tabular" /> 166 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
168 <param name="header" value="True" />
169 <param name="selected_task" value="load" /> 167 <param name="selected_task" value="load" />
170 <output name="outfile_predict" file="svc_prediction_result03.tabular" /> 168 <output name="outfile_predict" file="svc_prediction_result03.tabular" />
171 </test> 169 </test>
172 <!-- The following test is expected to fail, it is testing the whitelist/blacklist filtering. 170 <!-- The following test is expected to fail, it is testing the whitelist/blacklist filtering.
173 It loads a pickle with malicious content that we do not accept. --> 171 It loads a pickle with malicious content that we do not accept. -->
174 <test expect_failure="true"> 172 <test expect_failure="true">
175 <param name="infile_model" value="pickle_blacklist" ftype="zip" /> 173 <param name="infile_model" value="unsafe_model.h5mlm" />
176 <param name="infile_data" value="test_set.tabular" ftype="tabular" /> 174 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
177 <param name="header" value="True" /> 175 <param name="header" value="True" />
178 <param name="selected_task" value="load" /> 176 <param name="selected_task" value="load" />
179 </test> 177 </test>
180 </tests> 178 </tests>