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comparison pca.xml @ 1:132805688fa3 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 18:49:35 +0000
parents 2d7016b3ae92
children c16818ce0424
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0:2d7016b3ae92 1:132805688fa3
1 <tool id="sklearn_pca" name="Principal component analysis" version="@VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="sklearn_pca" name="Principal component analysis" version="@VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
2 <description>with scikit-learn</description> 2 <description>with scikit-learn</description>
3 <macros> 3 <macros>
4 <import>main_macros.xml</import> 4 <import>main_macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token> 5 <token name="@GALAXY_VERSION@">0</token>
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 detect_errors="exit_code"> 10 <command detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 python '$__tool_directory__/pca.py' 12 python '$__tool_directory__/pca.py'
13 -i '$infile' 13 -i '$infile'
59 #end if 59 #end if
60 -o '$outfile' 60 -o '$outfile'
61 ]]> 61 ]]>
62 </command> 62 </command>
63 <inputs> 63 <inputs>
64 <param name="infile" type="data" format="tabular" label="Input file"/> 64 <param name="infile" type="data" format="tabular" label="Input file" />
65 <param name="header" type="boolean" label="Exclude Header" truevalue="--header" falsevalue="" help="If present, exclude the header row from the dataset"/> 65 <param name="header" type="boolean" label="Exclude Header" truevalue="--header" falsevalue="" help="If present, exclude the header row from the dataset" />
66 <conditional name="column_selector_options"> 66 <conditional name="column_selector_options">
67 <expand macro="samples_column_selector_options" multiple="true" column_option="selected_column_selector_option" col_name="col1" infile="infile"/> 67 <expand macro="samples_column_selector_options" multiple="true" column_option="selected_column_selector_option" col_name="col1" infile="infile" />
68 </conditional> 68 </conditional>
69 <conditional name="select_pca_type"> 69 <conditional name="select_pca_type">
70 <param name="select_pca_opts" type="select" label="Select PCA Type" help="Choose which flavour of PCA to use"> 70 <param name="select_pca_opts" type="select" label="Select PCA Type" help="Choose which flavour of PCA to use">
71 <option value="classical" selected="true">Classical PCA</option> 71 <option value="classical" selected="true">Classical PCA</option>
72 <option value="incremental">Incremental PCA</option> 72 <option value="incremental">Incremental PCA</option>
73 <option value="kernel">Kernel PCA</option> 73 <option value="kernel">Kernel PCA</option>
74 </param> 74 </param>
75 <when value="classical"> 75 <when value="classical">
76 <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept"/> 76 <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept" />
77 <param name="whiten" type="boolean" label="Whiten Components" truevalue="--whiten" falsevalue="" help="Setting this option will reduce the redundancy and correlations between the features"/> 77 <param name="whiten" type="boolean" label="Whiten Components" truevalue="--whiten" falsevalue="" help="Setting this option will reduce the redundancy and correlations between the features" />
78 <conditional name="select_solver_type"> 78 <conditional name="select_solver_type">
79 <param name="svd_solver_opts" type="select" label="SVD Solver" help="Method to perform the singular value decomposition"> 79 <param name="svd_solver_opts" type="select" label="SVD Solver" help="Method to perform the singular value decomposition">
80 <option value="auto" selected="true">auto</option> 80 <option value="auto" selected="true">auto</option>
81 <option value="full">full</option> 81 <option value="full">full</option>
82 <option value="arpack">arpack</option> 82 <option value="arpack">arpack</option>
83 <option value="randomized">randomized</option> 83 <option value="randomized">randomized</option>
84 </param> 84 </param>
85 <when value="arpack"> 85 <when value="arpack">
86 <param name="tolerance" type="float" value="0.0" label="Tolerance" help="Convergence tolerance for arpack. If 0, optimal value will be chosen by arpack"/> 86 <param name="tolerance" type="float" value="0.0" label="Tolerance" help="Convergence tolerance for arpack. If 0, optimal value will be chosen by arpack" />
87 </when> 87 </when>
88 <when value="auto"/> 88 <when value="auto" />
89 <when value="full"/> 89 <when value="full" />
90 <when value="randomized"/> 90 <when value="randomized" />
91 </conditional> 91 </conditional>
92 </when> 92 </when>
93 <when value="incremental"> 93 <when value="incremental">
94 <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept"/> 94 <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept" />
95 <param name="whiten" type="boolean" label="Whiten Components" truevalue="--whiten" falsevalue=""/> 95 <param name="whiten" type="boolean" label="Whiten Components" truevalue="--whiten" falsevalue="" />
96 <param name="batch_size" type="integer" optional="true" label="Batch Size" help="The number of samples to use for each batch"/> 96 <param name="batch_size" type="integer" optional="true" label="Batch Size" help="The number of samples to use for each batch" />
97 </when> 97 </when>
98 <when value="kernel"> 98 <when value="kernel">
99 <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept"/> 99 <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept" />
100 <conditional name="select_kernel_opts"> 100 <conditional name="select_kernel_opts">
101 <param name="kernel_opts" type="select" label="Kernel Type"> 101 <param name="kernel_opts" type="select" label="Kernel Type">
102 <option value="linear" selected="true">linear</option> 102 <option value="linear" selected="true">linear</option>
103 <option value="poly">poly</option> 103 <option value="poly">poly</option>
104 <option value="rbf">rbf</option> 104 <option value="rbf">rbf</option>
105 <option value="sigmoid">sigmoid</option> 105 <option value="sigmoid">sigmoid</option>
106 <option value="cosine">cosine</option> 106 <option value="cosine">cosine</option>
107 <option value="precomputed">precomputed</option> 107 <option value="precomputed">precomputed</option>
108 </param> 108 </param>
109 <when value="poly"> 109 <when value="poly">
110 <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels"/> 110 <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels" />
111 <param name="degree" type="integer" value="3" label="Degree of the polynomial" help="Degree for poly kernels. Ignored by other kernels"/> 111 <param name="degree" type="integer" value="3" label="Degree of the polynomial" help="Degree for poly kernels. Ignored by other kernels" />
112 <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels"/> 112 <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels" />
113 </when> 113 </when>
114 <when value="sigmoid"> 114 <when value="sigmoid">
115 <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels"/> 115 <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels" />
116 <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels"/> 116 <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels" />
117 </when> 117 </when>
118 <when value="rbf"> 118 <when value="rbf">
119 <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels"/> 119 <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels" />
120 </when> 120 </when>
121 <when value="linear"/> 121 <when value="linear" />
122 <when value="cosine"/> 122 <when value="cosine" />
123 <when value="precomputed"/> 123 <when value="precomputed" />
124 </conditional> 124 </conditional>
125 <conditional name="select_solver_type"> 125 <conditional name="select_solver_type">
126 <param name="eigen_solver_opts" type="select" label="Eigen Solver"> 126 <param name="eigen_solver_opts" type="select" label="Eigen Solver">
127 <option value="auto" selected="true">auto</option> 127 <option value="auto" selected="true">auto</option>
128 <option value="dense">dense</option> 128 <option value="dense">dense</option>
129 <option value="arpack">arpack</option> 129 <option value="arpack">arpack</option>
130 </param> 130 </param>
131 <when value="arpack"> 131 <when value="arpack">
132 <param name="tolerance" type="float" value="0.0" label="Tolerance" help="Convergence tolerance for arpack. If 0, optimal value will be chosen by arpack"/> 132 <param name="tolerance" type="float" value="0.0" label="Tolerance" help="Convergence tolerance for arpack. If 0, optimal value will be chosen by arpack" />
133 <param name="max_iter" type="integer" optional="true" label="Maximum Iterations" help="Maximum number of iterations for arpack"/> 133 <param name="max_iter" type="integer" optional="true" label="Maximum Iterations" help="Maximum number of iterations for arpack" />
134 </when> 134 </when>
135 <when value="auto"/> 135 <when value="auto" />
136 <when value="dense"/> 136 <when value="dense" />
137 </conditional> 137 </conditional>
138 </when> 138 </when>
139 </conditional> 139 </conditional>
140 </inputs> 140 </inputs>
141 <outputs> 141 <outputs>
142 <data format="tabular" name="outfile"/> 142 <data format="tabular" name="outfile" />
143 </outputs> 143 </outputs>
144 <tests> 144 <tests>
145 <test> 145 <test>
146 <param name="infile" value="pca_input.dat" ftype="tabular"/> 146 <param name="infile" value="pca_input.dat" ftype="tabular" />
147 <param name="selected_column_selector_option" value="by_index_number" /> 147 <param name="selected_column_selector_option" value="by_index_number" />
148 <param name="col1" value="1,2,4,6,8,5"/> 148 <param name="col1" value="1,2,4,6,8,5" />
149 <param name="number" value="5"/> 149 <param name="number" value="5" />
150 <param name="select_pca_opts" value="classical"/> 150 <param name="select_pca_opts" value="classical" />
151 <param name="svd_solver_opts" value="arpack"/> 151 <param name="svd_solver_opts" value="arpack" />
152 <param name="tolerance" value="0.4"/> 152 <param name="tolerance" value="0.4" />
153 <output name="outfile" ftype='tabular' file="pca_classical_output.dat"/> 153 <output name="outfile" ftype='tabular' file="pca_classical_output.dat" />
154 </test> 154 </test>
155 <test> 155 <test>
156 <param name="infile" value="pca_input_with_headers.dat" ftype="tabular"/> 156 <param name="infile" value="pca_input_with_headers.dat" ftype="tabular" />
157 <param name="header" value="--header"/> 157 <param name="header" value="--header" />
158 <param name="selected_column_selector_option" value="by_header_name" /> 158 <param name="selected_column_selector_option" value="by_header_name" />
159 <param name="col1" value="col_1,col_2,col_4,col_6,col_8,col_5"/> 159 <param name="col1" value="col_1,col_2,col_4,col_6,col_8,col_5" />
160 <param name="number" value="5"/> 160 <param name="number" value="5" />
161 <param name="select_pca_opts" value="classical"/> 161 <param name="select_pca_opts" value="classical" />
162 <param name="svd_solver_opts" value="arpack"/> 162 <param name="svd_solver_opts" value="arpack" />
163 <param name="tolerance" value="0.4"/> 163 <param name="tolerance" value="0.4" />
164 <output name="outfile" ftype='tabular' file="pca_classical_header_names_output.dat"/> 164 <output name="outfile" ftype='tabular' file="pca_classical_header_names_output.dat" />
165 </test> 165 </test>
166 <test> 166 <test>
167 <param name="infile" value="pca_input.dat" ftype="tabular"/> 167 <param name="infile" value="pca_input.dat" ftype="tabular" />
168 <param name="selected_column_selector_option" value="all_but_by_index_number"/> 168 <param name="selected_column_selector_option" value="all_but_by_index_number" />
169 <param name="col1" value="8,5" /> 169 <param name="col1" value="8,5" />
170 <param name="number" value="7"/> 170 <param name="number" value="7" />
171 <param name="select_pca_opts" value="incremental"/> 171 <param name="select_pca_opts" value="incremental" />
172 <param name="batch_size" value="64"/> 172 <param name="batch_size" value="64" />
173 <output name="outfile" ftype='tabular' file="pca_incremental_output.dat"/> 173 <output name="outfile" ftype='tabular' file="pca_incremental_output.dat" />
174 </test> 174 </test>
175 <test> 175 <test>
176 <param name="infile" value="pca_input_with_headers.dat" ftype="tabular"/> 176 <param name="infile" value="pca_input_with_headers.dat" ftype="tabular" />
177 <param name="header" value="--header"/> 177 <param name="header" value="--header" />
178 <param name="selected_column_selector_option" value="all_but_by_header_name" /> 178 <param name="selected_column_selector_option" value="all_but_by_header_name" />
179 <param name="col1" value="col_8,col_5"/> 179 <param name="col1" value="col_8,col_5" />
180 <param name="number" value="7"/> 180 <param name="number" value="7" />
181 <param name="select_pca_opts" value="incremental"/> 181 <param name="select_pca_opts" value="incremental" />
182 <param name="batch_size" value="64"/> 182 <param name="batch_size" value="64" />
183 <output name="outfile" ftype='tabular' file="pca_incremental_header_names_output.dat"/> 183 <output name="outfile" ftype='tabular' file="pca_incremental_header_names_output.dat" />
184 </test> 184 </test>
185 <test> 185 <test>
186 <param name="infile" value="pca_input.dat" ftype="tabular"/> 186 <param name="infile" value="pca_input.dat" ftype="tabular" />
187 <param name="selected_column_selector_option" value="all_columns" /> 187 <param name="selected_column_selector_option" value="all_columns" />
188 <param name="number" value="8"/> 188 <param name="number" value="8" />
189 <param name="select_pca_opts" value="kernel"/> 189 <param name="select_pca_opts" value="kernel" />
190 <param name="kernel_opts" value="linear"/> 190 <param name="kernel_opts" value="linear" />
191 <param name="eigen_solver_opts" value="arpack"/> 191 <param name="eigen_solver_opts" value="arpack" />
192 <param name="tolerance" value="4.3"/> 192 <param name="tolerance" value="4.3" />
193 <param name="max_iter" value="8"/> 193 <param name="max_iter" value="8" />
194 <output name="outfile" ftype="tabular"> 194 <output name="outfile" ftype="tabular">
195 <assert_contents> 195 <assert_contents>
196 <has_n_lines n="300"/> 196 <has_n_lines n="300" />
197 <has_n_columns n="8"/> 197 <has_n_columns n="8" />
198 </assert_contents> 198 </assert_contents>
199 </output> 199 </output>
200 </test> 200 </test>
201 <test> 201 <test>
202 <param name="infile" value="pca_input.dat" ftype="tabular"/> 202 <param name="infile" value="pca_input.dat" ftype="tabular" />
203 <param name="selected_column_selector_option" value="all_columns" /> 203 <param name="selected_column_selector_option" value="all_columns" />
204 <param name="number" value="8"/> 204 <param name="number" value="8" />
205 <param name="select_pca_opts" value="kernel"/> 205 <param name="select_pca_opts" value="kernel" />
206 <param name="kernel_opts" value="poly"/> 206 <param name="kernel_opts" value="poly" />
207 <param name="gamma" value="0.3"/> 207 <param name="gamma" value="0.3" />
208 <param name="degree" value="4"/> 208 <param name="degree" value="4" />
209 <param name="coef0" value="1.6"/> 209 <param name="coef0" value="1.6" />
210 <param name="eigen_solver_opts" value="auto"/> 210 <param name="eigen_solver_opts" value="auto" />
211 <output name="outfile" ftype="tabular"> 211 <output name="outfile" ftype="tabular">
212 <assert_contents> 212 <assert_contents>
213 <has_n_lines n="300"/> 213 <has_n_lines n="300" />
214 <has_n_columns n="8"/> 214 <has_n_columns n="8" />
215 </assert_contents> 215 </assert_contents>
216 </output> 216 </output>
217 </test> 217 </test>
218 </tests> 218 </tests>
219 <help><![CDATA[ 219 <help><![CDATA[
220 .. class:: infomark 220 .. class:: infomark
221 221
222 **What it does** 222 **What it does**
223 223
224 This tool takes a tabular input file (one data point per row, each column a variable) 224 This tool takes a tabular input file (one data point per row, each column a variable)
225 and performs PCA using Singular Value Decomposition, returning an equally sized tabular 225 and performs principal component analysis (PCA) using Singular Value Decomposition,
226 file with the first PC in the first column, second PC in the second column, etc. 226 returning an equally sized tabular file with the first PC in the first column, second
227 PC in the second column, etc.
227 ]]> 228 ]]>
228 </help> 229 </help>
229 <expand macro="sklearn_citation"/> 230 <expand macro="sklearn_citation" />
230 </tool> 231 </tool>