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comparison svm.xml @ 19:d67dcd63f6cb 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 17:32:55 +0000
parents 2df8f5c30edc
children b878e4cdd63a
comparison
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18:02d2be90dedb 19:d67dcd63f6cb
1 <tool id="sklearn_svm_classifier" name="Support vector machines (SVMs)" version="@VERSION@"> 1 <tool id="sklearn_svm_classifier" name="Support vector machines (SVMs)" version="@VERSION@" profile="20.05">
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>
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><![CDATA[ 10 <command><![CDATA[
11 python '$svc_script' '$inputs' 11 python '$svc_script' '$inputs'
12 ]]> 12 ]]>
13 </command> 13 </command>
14 <configfiles> 14 <configfiles>
15 <inputs name="inputs"/> 15 <inputs name="inputs" />
16 <configfile name="svc_script"> 16 <configfile name="svc_script">
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 import pickle
70 <option value="SVC">C-Support Vector Classification</option> 70 <option value="SVC">C-Support Vector Classification</option>
71 <option value="NuSVC">Nu-Support Vector Classification</option> 71 <option value="NuSVC">Nu-Support Vector Classification</option>
72 <option value="LinearSVC">Linear Support Vector Classification</option> 72 <option value="LinearSVC">Linear Support Vector Classification</option>
73 </param> 73 </param>
74 <when value="SVC"> 74 <when value="SVC">
75 <expand macro="sl_mixed_input"/> 75 <expand macro="sl_mixed_input" />
76 <expand macro="svc_advanced_options"> 76 <expand macro="svc_advanced_options">
77 <expand macro="C"/> 77 <expand macro="C" />
78 </expand> 78 </expand>
79 </when> 79 </when>
80 <when value="NuSVC"> 80 <when value="NuSVC">
81 <expand macro="sl_mixed_input"/> 81 <expand macro="sl_mixed_input" />
82 <expand macro="svc_advanced_options"> 82 <expand macro="svc_advanced_options">
83 <param argument="nu" type="float" optional="true" value="0.5" label="Nu control parameter" help="Controls the number of support vectors. Should be in the interval (0, 1]. "/> 83 <param argument="nu" type="float" optional="true" value="0.5" label="Nu control parameter" help="Controls the number of support vectors. Should be in the interval (0, 1]. " />
84 </expand> 84 </expand>
85 </when> 85 </when>
86 <when value="LinearSVC"> 86 <when value="LinearSVC">
87 <expand macro="sl_mixed_input"/> 87 <expand macro="sl_mixed_input" />
88 <section name="options" title="Advanced Options" expanded="False"> 88 <section name="options" title="Advanced Options" expanded="False">
89 <expand macro="C"/> 89 <expand macro="C" />
90 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/> 90 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. " />
91 <expand macro="random_state" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data for probability estimation. A fixed seed allows reproducible results."/> 91 <expand macro="random_state" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data for probability estimation. A fixed seed allows reproducible results." />
92 <!--expand macro="class_weight"/--> 92 <!--expand macro="class_weight"/-->
93 <param argument="max_iter" type="integer" optional="true" value="1000" label="Maximum number of iterations" help="The maximum number of iterations to be run."/> 93 <param argument="max_iter" type="integer" optional="true" value="1000" label="Maximum number of iterations" help="The maximum number of iterations to be run." />
94 <param argument="loss" type="select" label="Loss function" help="Specifies the loss function. ''squared_hinge'' is the square of the hinge loss."> 94 <param argument="loss" type="select" label="Loss function" help="Specifies the loss function. ''squared_hinge'' is the square of the hinge loss.">
95 <option value="squared_hinge" selected="true">Squared hinge</option> 95 <option value="squared_hinge" selected="true">Squared hinge</option>
96 <option value="hinge">Hinge</option> 96 <option value="hinge">Hinge</option>
97 </param> 97 </param>
98 <param argument="penalty" type="select" label="Penalization norm" help=" "> 98 <param argument="penalty" type="select" label="Penalization norm" help=" ">
99 <option value="l1" >l1</option> 99 <option value="l1">l1</option>
100 <option value="l2" selected="true">l2</option> 100 <option value="l2" selected="true">l2</option>
101 </param> 101 </param>
102 <param argument="dual" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use the shrinking heuristic" help="Select the algorithm to either solve the dual or primal optimization problem. Prefer dual=False when n_samples > n_features."/> 102 <param argument="dual" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use the shrinking heuristic" help="Select the algorithm to either solve the dual or primal optimization problem. Prefer dual=False when n_samples > n_features." />
103 <param argument="multi_class" type="select" label="Multi-class strategy" help="Determines the multi-class strategy if y contains more than two classes."> 103 <param argument="multi_class" type="select" label="Multi-class strategy" help="Determines the multi-class strategy if y contains more than two classes.">
104 <option value="ovr" selected="true">ovr</option> 104 <option value="ovr" selected="true">ovr</option>
105 <option value="crammer_singer" >crammer_singer</option> 105 <option value="crammer_singer">crammer_singer</option>
106 </param> 106 </param>
107 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Calculate the intercept for this model" help="If set to false, data is expected to be already centered."/> 107 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Calculate the intercept for this model" help="If set to false, data is expected to be already centered." />
108 <param argument="intercept_scaling" type="float" optional="true" value="1" label="Add synthetic feature to the instance vector" help=" "/> 108 <param argument="intercept_scaling" type="float" optional="true" value="1" label="Add synthetic feature to the instance vector" help=" " />
109 </section> 109 </section>
110 </when> 110 </when>
111 </expand> 111 </expand>
112 </inputs> 112 </inputs>
113 <expand macro="output"/> 113 <expand macro="output" />
114 <tests> 114 <tests>
115 <test> 115 <test>
116 <param name="infile1" value="train_set.tabular" ftype="tabular"/> 116 <param name="infile1" value="train_set.tabular" ftype="tabular" />
117 <param name="infile2" value="train_set.tabular" ftype="tabular"/> 117 <param name="infile2" value="train_set.tabular" ftype="tabular" />
118 <param name="header1" value="True"/> 118 <param name="header1" value="True" />
119 <param name="header2" value="True"/> 119 <param name="header2" value="True" />
120 <param name="col1" value="1,2,3,4"/> 120 <param name="col1" value="1,2,3,4" />
121 <param name="col2" value="5"/> 121 <param name="col2" value="5" />
122 <param name="selected_task" value="train"/> 122 <param name="selected_task" value="train" />
123 <param name="selected_algorithm" value="SVC"/> 123 <param name="selected_algorithm" value="SVC" />
124 <param name="random_state" value="5"/> 124 <param name="random_state" value="5" />
125 <output name="outfile_fit" file="svc_model01" compare="sim_size"/> 125 <output name="outfile_fit" file="svc_model01" compare="sim_size" />
126 </test> 126 </test>
127 <test> 127 <test>
128 <param name="infile1" value="train_set.tabular" ftype="tabular"/> 128 <param name="infile1" value="train_set.tabular" ftype="tabular" />
129 <param name="infile2" value="train_set.tabular" ftype="tabular"/> 129 <param name="infile2" value="train_set.tabular" ftype="tabular" />
130 <param name="header1" value="True"/> 130 <param name="header1" value="True" />
131 <param name="header2" value="True"/> 131 <param name="header2" value="True" />
132 <param name="col1" value="1,2,3,4"/> 132 <param name="col1" value="1,2,3,4" />
133 <param name="col2" value="5"/> 133 <param name="col2" value="5" />
134 <param name="selected_task" value="train"/> 134 <param name="selected_task" value="train" />
135 <param name="selected_algorithm" value="NuSVC"/> 135 <param name="selected_algorithm" value="NuSVC" />
136 <param name="random_state" value="5"/> 136 <param name="random_state" value="5" />
137 <output name="outfile_fit" file="svc_model02" compare="sim_size"/> 137 <output name="outfile_fit" file="svc_model02" compare="sim_size" />
138 </test> 138 </test>
139 <test> 139 <test>
140 <param name="infile1" value="train_set.tabular" ftype="tabular"/> 140 <param name="infile1" value="train_set.tabular" ftype="tabular" />
141 <param name="infile2" value="train_set.tabular" ftype="tabular"/> 141 <param name="infile2" value="train_set.tabular" ftype="tabular" />
142 <param name="header1" value="True"/> 142 <param name="header1" value="True" />
143 <param name="header2" value="True"/> 143 <param name="header2" value="True" />
144 <param name="col1" value="1,2,3,4"/> 144 <param name="col1" value="1,2,3,4" />
145 <param name="col2" value="5"/> 145 <param name="col2" value="5" />
146 <param name="selected_task" value="train"/> 146 <param name="selected_task" value="train" />
147 <param name="selected_algorithm" value="LinearSVC"/> 147 <param name="selected_algorithm" value="LinearSVC" />
148 <param name="random_state" value="5"/> 148 <param name="random_state" value="5" />
149 <output name="outfile_fit" file="svc_model03" compare="sim_size"/> 149 <output name="outfile_fit" file="svc_model03" compare="sim_size" />
150 </test> 150 </test>
151 <test> 151 <test>
152 <param name="infile_model" value="svc_model01" ftype="zip"/> 152 <param name="infile_model" value="svc_model01" ftype="zip" />
153 <param name="infile_data" value="test_set.tabular" ftype="tabular"/> 153 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
154 <param name="header" value="True"/> 154 <param name="header" value="True" />
155 <param name="selected_task" value="load"/> 155 <param name="selected_task" value="load" />
156 <output name="outfile_predict" file="svc_prediction_result01.tabular"/> 156 <output name="outfile_predict" file="svc_prediction_result01.tabular" />
157 </test> 157 </test>
158 <test> 158 <test>
159 <param name="infile_model" value="svc_model02" ftype="zip"/> 159 <param name="infile_model" value="svc_model02" ftype="zip" />
160 <param name="infile_data" value="test_set.tabular" ftype="tabular"/> 160 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
161 <param name="header" value="True"/> 161 <param name="header" value="True" />
162 <param name="selected_task" value="load"/> 162 <param name="selected_task" value="load" />
163 <output name="outfile_predict" file="svc_prediction_result02.tabular"/> 163 <output name="outfile_predict" file="svc_prediction_result02.tabular" />
164 </test> 164 </test>
165 <test> 165 <test>
166 <param name="infile_model" value="svc_model03" ftype="zip"/> 166 <param name="infile_model" value="svc_model03" ftype="zip" />
167 <param name="infile_data" value="test_set.tabular" ftype="tabular"/> 167 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
168 <param name="header" value="True"/> 168 <param name="header" value="True" />
169 <param name="selected_task" value="load"/> 169 <param name="selected_task" value="load" />
170 <output name="outfile_predict" file="svc_prediction_result03.tabular"/> 170 <output name="outfile_predict" file="svc_prediction_result03.tabular" />
171 </test> 171 </test>
172 <!-- The following test is expected to fail, it is testing the whitelist/blacklist filtering. 172 <!-- 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. --> 173 It loads a pickle with malicious content that we do not accept. -->
174 <test expect_failure="true"> 174 <test expect_failure="true">
175 <param name="infile_model" value="pickle_blacklist" ftype="zip"/> 175 <param name="infile_model" value="pickle_blacklist" ftype="zip" />
176 <param name="infile_data" value="test_set.tabular" ftype="tabular"/> 176 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
177 <param name="header" value="True"/> 177 <param name="header" value="True" />
178 <param name="selected_task" value="load"/> 178 <param name="selected_task" value="load" />
179 </test> 179 </test>
180 </tests> 180 </tests>
181 <help><![CDATA[ 181 <help><![CDATA[
182 **What it does** 182 **What it does**
183 This module implements the Support Vector Machine (SVM) classification algorithms. 183 This module implements the Support Vector Machine (SVM) classification algorithms.
201 201
202 For more information check http://scikit-learn.org/stable/modules/neighbors.html 202 For more information check http://scikit-learn.org/stable/modules/neighbors.html
203 203
204 ]]> 204 ]]>
205 </help> 205 </help>
206 <expand macro="sklearn_citation"/> 206 <expand macro="sklearn_citation" />
207 </tool> 207 </tool>