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comparison nn_classifier.xml @ 19:a4e183b0b0a4 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
author bgruening
date Tue, 13 Apr 2021 20:57:54 +0000
parents 6cbf023ea0b9
children 11f52f966186
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18:6bdfb232d489 19:a4e183b0b0a4
1 <tool id="sklearn_nn_classifier" name="Nearest Neighbors Classification" version="@VERSION@"> 1 <tool id="sklearn_nn_classifier" name="Nearest Neighbors Classification" version="@VERSION@" profile="20.05">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>main_macros.xml</import> 4 <import>main_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="python_requirements"/> 6 <expand macro="python_requirements" />
7 <expand macro="macro_stdio"/> 7 <expand macro="macro_stdio" />
8 <version_command>echo "@VERSION@"</version_command> 8 <version_command>echo "@VERSION@"</version_command>
9 <command><![CDATA[ 9 <command><![CDATA[
10 python '$nnc_script' '$inputs' 10 python '$nnc_script' '$inputs'
11 ]]> 11 ]]>
12 </command> 12 </command>
13 <configfiles> 13 <configfiles>
14 <inputs name="inputs"/> 14 <inputs name="inputs" />
15 <configfile name="nnc_script"> 15 <configfile name="nnc_script">
16 <![CDATA[ 16 <![CDATA[
17 import sys 17 import sys
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
66 66
67 ]]> 67 ]]>
68 </configfile> 68 </configfile>
69 </configfiles> 69 </configfiles>
70 <inputs> 70 <inputs>
71 <expand macro="sl_Conditional" model="zip"><!--Todo: add sparse to targets--> 71 <expand macro="sl_Conditional" model="zip"> <!--Todo: add sparse to targets-->
72 <param name="selected_algorithm" type="select" label="Classifier type"> 72 <param name="selected_algorithm" type="select" label="Classifier type">
73 <option value="nneighbors">Nearest Neighbors</option> 73 <option value="nneighbors">Nearest Neighbors</option>
74 <option value="ncentroid">Nearest Centroid</option> 74 <option value="ncentroid">Nearest Centroid</option>
75 </param> 75 </param>
76 <when value="nneighbors"> 76 <when value="nneighbors">
77 <expand macro="sl_mixed_input"/> 77 <expand macro="sl_mixed_input" />
78 <conditional name="sampling_methods"> 78 <conditional name="sampling_methods">
79 <param name="sampling_method" type="select" label="Neighbor selection method"> 79 <param name="sampling_method" type="select" label="Neighbor selection method">
80 <option value="KNeighborsClassifier" selected="true">K-nearest neighbors</option> 80 <option value="KNeighborsClassifier" selected="true">K-nearest neighbors</option>
81 <option value="RadiusNeighborsClassifier">Radius-based</option> 81 <option value="RadiusNeighborsClassifier">Radius-based</option>
82 </param> 82 </param>
83 <when value="KNeighborsClassifier"> 83 <when value="KNeighborsClassifier">
84 <expand macro="nn_advanced_options"> 84 <expand macro="nn_advanced_options">
85 <param argument="n_neighbors" type="integer" optional="true" value="5" label="Number of neighbors" help=" "/> 85 <param argument="n_neighbors" type="integer" optional="true" value="5" label="Number of neighbors" help=" " />
86 </expand> 86 </expand>
87 </when> 87 </when>
88 <when value="RadiusNeighborsClassifier"> 88 <when value="RadiusNeighborsClassifier">
89 <expand macro="nn_advanced_options"> 89 <expand macro="nn_advanced_options">
90 <param argument="radius" type="float" optional="true" value="1.0" label="Radius" 90 <param argument="radius" type="float" optional="true" value="1.0" label="Radius" help="Range of parameter space to use by default for :meth ''radius_neighbors'' queries." />
91 help="Range of parameter space to use by default for :meth ''radius_neighbors'' queries."/>
92 </expand> 91 </expand>
93 </when> 92 </when>
94 </conditional> 93 </conditional>
95 </when> 94 </when>
96 <when value="ncentroid"> 95 <when value="ncentroid">
97 <expand macro="sl_mixed_input"/> 96 <expand macro="sl_mixed_input" />
98 <section name="options" title="Advanced Options" expanded="False"> 97 <section name="options" title="Advanced Options" expanded="False">
99 <param argument="metric" type="text" optional="true" value="euclidean" label="Metric" 98 <param argument="metric" type="text" optional="true" value="euclidean" label="Metric" help="The metric to use when calculating distance between instances in a feature array." />
100 help="The metric to use when calculating distance between instances in a feature array."/> 99 <param argument="shrink_threshold" type="float" optional="true" value="" label="Shrink threshold" help="Floating point number for shrinking centroids to remove features." />
101 <param argument="shrink_threshold" type="float" optional="true" value="" label="Shrink threshold"
102 help="Floating point number for shrinking centroids to remove features."/>
103 </section> 100 </section>
104 </when> 101 </when>
105 </expand> 102 </expand>
106 </inputs> 103 </inputs>
107 104
108 <expand macro="output"/> 105 <expand macro="output" />
109 106
110 <tests> 107 <tests>
111 <test> 108 <test>
112 <param name="infile1" value="train_set.tabular" ftype="tabular"/> 109 <param name="infile1" value="train_set.tabular" ftype="tabular" />
113 <param name="infile2" value="train_set.tabular" ftype="tabular"/> 110 <param name="infile2" value="train_set.tabular" ftype="tabular" />
114 <param name="header1" value="True"/> 111 <param name="header1" value="True" />
115 <param name="header2" value="True"/> 112 <param name="header2" value="True" />
116 <param name="col1" value="1,2,3,4"/> 113 <param name="col1" value="1,2,3,4" />
117 <param name="col2" value="5"/> 114 <param name="col2" value="5" />
118 <param name="selected_task" value="train"/> 115 <param name="selected_task" value="train" />
119 <param name="selected_algorithm" value="nneighbors"/> 116 <param name="selected_algorithm" value="nneighbors" />
120 <param name="sampling_method" value="KNeighborsClassifier" /> 117 <param name="sampling_method" value="KNeighborsClassifier" />
121 <param name="algorithm" value="brute" /> 118 <param name="algorithm" value="brute" />
122 <output name="outfile_fit" file="nn_model01" compare="sim_size" delta="5"/> 119 <output name="outfile_fit" file="nn_model01" compare="sim_size" delta="5" />
123 </test> 120 </test>
124 <test> 121 <test>
125 <param name="infile1" value="train_set.tabular" ftype="tabular"/> 122 <param name="infile1" value="train_set.tabular" ftype="tabular" />
126 <param name="infile2" value="train_set.tabular" ftype="tabular"/> 123 <param name="infile2" value="train_set.tabular" ftype="tabular" />
127 <param name="header1" value="True"/> 124 <param name="header1" value="True" />
128 <param name="header2" value="True"/> 125 <param name="header2" value="True" />
129 <param name="col1" value="1,2,3,4"/> 126 <param name="col1" value="1,2,3,4" />
130 <param name="col2" value="5"/> 127 <param name="col2" value="5" />
131 <param name="selected_task" value="train"/> 128 <param name="selected_task" value="train" />
132 <param name="selected_algorithm" value="nneighbors"/> 129 <param name="selected_algorithm" value="nneighbors" />
133 <param name="sampling_method" value="RadiusNeighborsClassifier" /> 130 <param name="sampling_method" value="RadiusNeighborsClassifier" />
134 <output name="outfile_fit" file="nn_model02" compare="sim_size" delta="5"/> 131 <output name="outfile_fit" file="nn_model02" compare="sim_size" delta="5" />
135 </test> 132 </test>
136 <test> 133 <test>
137 <param name="infile1" value="train_set.tabular" ftype="tabular"/> 134 <param name="infile1" value="train_set.tabular" ftype="tabular" />
138 <param name="infile2" value="train_set.tabular" ftype="tabular"/> 135 <param name="infile2" value="train_set.tabular" ftype="tabular" />
139 <param name="header1" value="True"/> 136 <param name="header1" value="True" />
140 <param name="header2" value="True"/> 137 <param name="header2" value="True" />
141 <param name="col1" value="1,2,3,4"/> 138 <param name="col1" value="1,2,3,4" />
142 <param name="col2" value="5"/> 139 <param name="col2" value="5" />
143 <param name="selected_task" value="train"/> 140 <param name="selected_task" value="train" />
144 <param name="selected_algorithm" value="ncentroid"/> 141 <param name="selected_algorithm" value="ncentroid" />
145 <output name="outfile_fit" file="nn_model03" compare="sim_size" delta="5"/> 142 <output name="outfile_fit" file="nn_model03" compare="sim_size" delta="5" />
146 </test> 143 </test>
147 <test> 144 <test>
148 <param name="infile_model" value="nn_model01" ftype="zip"/> 145 <param name="infile_model" value="nn_model01" ftype="zip" />
149 <param name="infile_data" value="test_set.tabular" ftype="tabular"/> 146 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
150 <param name="header" value="True"/> 147 <param name="header" value="True" />
151 <param name="selected_task" value="load"/> 148 <param name="selected_task" value="load" />
152 <output name="outfile_predict" file="nn_prediction_result01.tabular"/> 149 <output name="outfile_predict" file="nn_prediction_result01.tabular" />
153 </test> 150 </test>
154 <test> 151 <test>
155 <param name="infile_model" value="nn_model02" ftype="zip"/> 152 <param name="infile_model" value="nn_model02" ftype="zip" />
156 <param name="infile_data" value="test_set.tabular" ftype="tabular"/> 153 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
157 <param name="header" value="True"/> 154 <param name="header" value="True" />
158 <param name="selected_task" value="load"/> 155 <param name="selected_task" value="load" />
159 <output name="outfile_predict" file="nn_prediction_result02.tabular"/> 156 <output name="outfile_predict" file="nn_prediction_result02.tabular" />
160 </test> 157 </test>
161 <test> 158 <test>
162 <param name="infile_model" value="nn_model03" ftype="zip"/> 159 <param name="infile_model" value="nn_model03" ftype="zip" />
163 <param name="infile_data" value="test_set.tabular" ftype="tabular"/> 160 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
164 <param name="header" value="True"/> 161 <param name="header" value="True" />
165 <param name="selected_task" value="load"/> 162 <param name="selected_task" value="load" />
166 <output name="outfile_predict" file="nn_prediction_result03.tabular"/> 163 <output name="outfile_predict" file="nn_prediction_result03.tabular" />
167 </test> 164 </test>
168 </tests> 165 </tests>
169 <help><![CDATA[ 166 <help><![CDATA[
170 **What it does** 167 **What it does**
171 This module implements the k-nearest neighbors classification algorithms. 168 This module implements the k-nearest neighbors classification algorithms.
172 For more information check http://scikit-learn.org/stable/modules/neighbors.html 169 For more information check http://scikit-learn.org/stable/modules/neighbors.html
173 ]]></help> 170 ]]> </help>
174 <expand macro="sklearn_citation"/> 171 <expand macro="sklearn_citation" />
175 </tool> 172 </tool>