Mercurial > repos > bgruening > sklearn_pca

annotate pca.xml @ 0:2d7016b3ae92 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
author bgruening
date Fri, 02 Oct 2020 08:45:21 +0000
parents
children 132805688fa3
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0
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
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1 <tool id="sklearn_pca" name="Principal component analysis" version="@VERSION@+galaxy@GALAXY_VERSION@">
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
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2 <description>with scikit-learn</description>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
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3 <macros>
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4 <import>main_macros.xml</import>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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7 <expand macro="python_requirements"/>
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8 <expand macro="macro_stdio"/>
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9 <version_command>echo "@VERSION@"</version_command>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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12 python '$__tool_directory__/pca.py'
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13 -i '$infile'
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14 $header
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15 -c '$column_selector_options.selected_column_selector_option'
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16 #if $column_selector_options.selected_column_selector_option != 'all_columns'
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17 -ci '$column_selector_options.col1'
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18 #end if
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19 #if $select_pca_type.number != ''
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20 -n '$select_pca_type.number'
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21 #end if
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22 -t '$select_pca_type.select_pca_opts'
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23 #if $select_pca_type.select_pca_opts == 'classical'
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24 -s '$select_pca_type.select_solver_type.svd_solver_opts'
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25 #if $select_pca_type.select_solver_type.svd_solver_opts == 'arpack'
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26 -tol $select_pca_type.select_solver_type.tolerance
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27 #end if
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28 $select_pca_type.whiten
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29 #elif $select_pca_type.select_pca_opts == 'incremental'
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30 #if $select_pca_type.batch_size != ''
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
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31 -b '$select_pca_type.batch_size'
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
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32 #end if
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33 $select_pca_type.whiten
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34 #elif $select_pca_type.select_pca_opts == 'kernel'
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35 -k '$select_pca_type.select_kernel_opts.kernel_opts'
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36 #if $select_pca_type.select_kernel_opts.kernel_opts == 'poly'
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37 #if $select_pca_type.select_kernel_opts.gamma != ''
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
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38 -g '$select_pca_type.select_kernel_opts.gamma'
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39 #end if
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40 -d '$select_pca_type.select_kernel_opts.degree'
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41 -cf '$select_pca_type.select_kernel_opts.coef0'
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42 #elif $select_pca_type.select_kernel_opts.kernel_opts == 'rbf'
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43 #if $select_pca_type.select_kernel_opts.gamma != ''
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44 -g '$select_pca_type.select_kernel_opts.gamma'
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45 #end if
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46 #elif $select_pca_type.select_kernel_opts.kernel_opts == 'sigmoid'
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47 #if $select_pca_type.select_kernel_opts.gamma != ''
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48 -g '$select_pca_type.select_kernel_opts.gamma'
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49 #end if
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50 -cf '$select_pca_type.select_kernel_opts.coef0'
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51 #end if
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52 -e '$select_pca_type.select_solver_type.eigen_solver_opts'
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53 #if $select_pca_type.select_solver_type.eigen_solver_opts == 'arpack'
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54 -tol $select_pca_type.select_solver_type.tolerance
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55 #if $select_pca_type.select_solver_type.max_iter != ''
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56 -mi $select_pca_type.select_solver_type.max_iter
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57 #end if
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58 #end if
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59 #end if
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60 -o '$outfile'
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61 ]]>
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62 </command>
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63 <inputs>
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64 <param name="infile" type="data" format="tabular" label="Input file"/>
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65 <param name="header" type="boolean" label="Exclude Header" truevalue="--header" falsevalue="" help="If present, exclude the header row from the dataset"/>
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66 <conditional name="column_selector_options">
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67 <expand macro="samples_column_selector_options" multiple="true" column_option="selected_column_selector_option" col_name="col1" infile="infile"/>
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68 </conditional>
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69 <conditional name="select_pca_type">
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70 <param name="select_pca_opts" type="select" label="Select PCA Type" help="Choose which flavour of PCA to use">
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71 <option value="classical" selected="true">Classical PCA</option>
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72 <option value="incremental">Incremental PCA</option>
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73 <option value="kernel">Kernel PCA</option>
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74 </param>
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75 <when value="classical">
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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"/>
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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"/>
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78 <conditional name="select_solver_type">
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79 <param name="svd_solver_opts" type="select" label="SVD Solver" help="Method to perform the singular value decomposition">
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80 <option value="auto" selected="true">auto</option>
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81 <option value="full">full</option>
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82 <option value="arpack">arpack</option>
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83 <option value="randomized">randomized</option>
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84 </param>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
85 <when value="arpack">
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
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"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
87 </when>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
88 <when value="auto"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
89 <when value="full"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
90 <when value="randomized"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
91 </conditional>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
92 </when>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
93 <when value="incremental">
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
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"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
95 <param name="whiten" type="boolean" label="Whiten Components" truevalue="--whiten" falsevalue=""/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
96 <param name="batch_size" type="integer" optional="true" label="Batch Size" help="The number of samples to use for each batch"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
97 </when>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
98 <when value="kernel">
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
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"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
100 <conditional name="select_kernel_opts">
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
101 <param name="kernel_opts" type="select" label="Kernel Type">
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
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102 <option value="linear" selected="true">linear</option>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
103 <option value="poly">poly</option>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
104 <option value="rbf">rbf</option>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
105 <option value="sigmoid">sigmoid</option>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
106 <option value="cosine">cosine</option>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
107 <option value="precomputed">precomputed</option>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
108 </param>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
109 <when value="poly">
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
110 <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
111 <param name="degree" type="integer" value="3" label="Degree of the polynomial" help="Degree for poly kernels. Ignored by other kernels"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
112 <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
113 </when>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
114 <when value="sigmoid">
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
115 <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
116 <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
117 </when>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
118 <when value="rbf">
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
119 <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
120 </when>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
121 <when value="linear"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
122 <when value="cosine"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
123 <when value="precomputed"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
124 </conditional>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
125 <conditional name="select_solver_type">
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
126 <param name="eigen_solver_opts" type="select" label="Eigen Solver">
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
127 <option value="auto" selected="true">auto</option>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
128 <option value="dense">dense</option>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
129 <option value="arpack">arpack</option>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
130 </param>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
131 <when value="arpack">
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
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"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
133 <param name="max_iter" type="integer" optional="true" label="Maximum Iterations" help="Maximum number of iterations for arpack"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
134 </when>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
135 <when value="auto"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
136 <when value="dense"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
137 </conditional>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
138 </when>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
139 </conditional>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
140 </inputs>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
141 <outputs>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
142 <data format="tabular" name="outfile"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
143 </outputs>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
144 <tests>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
145 <test>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
146 <param name="infile" value="pca_input.dat" ftype="tabular"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
147 <param name="selected_column_selector_option" value="by_index_number" />
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
148 <param name="col1" value="1,2,4,6,8,5"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
149 <param name="number" value="5"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
150 <param name="select_pca_opts" value="classical"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
151 <param name="svd_solver_opts" value="arpack"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
152 <param name="tolerance" value="0.4"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
153 <output name="outfile" ftype='tabular' file="pca_classical_output.dat"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
154 </test>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
155 <test>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
156 <param name="infile" value="pca_input_with_headers.dat" ftype="tabular"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
157 <param name="header" value="--header"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
158 <param name="selected_column_selector_option" value="by_header_name" />
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
159 <param name="col1" value="col_1,col_2,col_4,col_6,col_8,col_5"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
160 <param name="number" value="5"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
161 <param name="select_pca_opts" value="classical"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
162 <param name="svd_solver_opts" value="arpack"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
163 <param name="tolerance" value="0.4"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
164 <output name="outfile" ftype='tabular' file="pca_classical_header_names_output.dat"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
165 </test>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
166 <test>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
167 <param name="infile" value="pca_input.dat" ftype="tabular"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
168 <param name="selected_column_selector_option" value="all_but_by_index_number"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
169 <param name="col1" value="8,5" />
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
170 <param name="number" value="7"/>
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
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171 <param name="select_pca_opts" value="incremental"/>
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172 <param name="batch_size" value="64"/>
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173 <output name="outfile" ftype='tabular' file="pca_incremental_output.dat"/>
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174 </test>
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175 <test>
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176 <param name="infile" value="pca_input_with_headers.dat" ftype="tabular"/>
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177 <param name="header" value="--header"/>
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178 <param name="selected_column_selector_option" value="all_but_by_header_name" />
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179 <param name="col1" value="col_8,col_5"/>
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180 <param name="number" value="7"/>
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181 <param name="select_pca_opts" value="incremental"/>
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182 <param name="batch_size" value="64"/>
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183 <output name="outfile" ftype='tabular' file="pca_incremental_header_names_output.dat"/>
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184 </test>
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185 <test>
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186 <param name="infile" value="pca_input.dat" ftype="tabular"/>
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187 <param name="selected_column_selector_option" value="all_columns" />
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188 <param name="number" value="8"/>
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189 <param name="select_pca_opts" value="kernel"/>
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190 <param name="kernel_opts" value="linear"/>
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191 <param name="eigen_solver_opts" value="arpack"/>
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192 <param name="tolerance" value="4.3"/>
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193 <param name="max_iter" value="8"/>
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194 <output name="outfile" ftype="tabular">
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195 <assert_contents>
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196 <has_n_lines n="300"/>
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197 <has_n_columns n="8"/>
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198 </assert_contents>
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199 </output>
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200 </test>
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201 <test>
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202 <param name="infile" value="pca_input.dat" ftype="tabular"/>
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203 <param name="selected_column_selector_option" value="all_columns" />
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204 <param name="number" value="8"/>
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205 <param name="select_pca_opts" value="kernel"/>
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206 <param name="kernel_opts" value="poly"/>
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207 <param name="gamma" value="0.3"/>
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208 <param name="degree" value="4"/>
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209 <param name="coef0" value="1.6"/>
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210 <param name="eigen_solver_opts" value="auto"/>
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211 <output name="outfile" ftype="tabular">
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212 <assert_contents>
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213 <has_n_lines n="300"/>
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214 <has_n_columns n="8"/>
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215 </assert_contents>
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216 </output>
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217 </test>
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218 </tests>
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219 <help><![CDATA[
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220 .. class:: infomark
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221
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222 **What it does**
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223
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224 This tool takes a tabular input file (one data point per row, each column a variable)
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225 and performs PCA using Singular Value Decomposition, returning an equally sized tabular
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226 file with the first PC in the first column, second PC in the second column, etc.
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227 ]]>
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228 </help>
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229 <expand macro="sklearn_citation"/>
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230 </tool>