Mercurial > repos > bgruening > sklearn_pca
diff pca.xml @ 1:132805688fa3 draft
"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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--- a/pca.xml Fri Oct 02 08:45:21 2020 +0000 +++ b/pca.xml Tue Apr 13 18:49:35 2021 +0000 @@ -1,11 +1,11 @@ -<tool id="sklearn_pca" name="Principal component analysis" version="@VERSION@+galaxy@GALAXY_VERSION@"> +<tool id="sklearn_pca" name="Principal component analysis" version="@VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>with scikit-learn</description> <macros> <import>main_macros.xml</import> <token name="@GALAXY_VERSION@">0</token> </macros> - <expand macro="python_requirements"/> - <expand macro="macro_stdio"/> + <expand macro="python_requirements" /> + <expand macro="macro_stdio" /> <version_command>echo "@VERSION@"</version_command> <command detect_errors="exit_code"> <![CDATA[ @@ -61,10 +61,10 @@ ]]> </command> <inputs> - <param name="infile" type="data" format="tabular" label="Input file"/> - <param name="header" type="boolean" label="Exclude Header" truevalue="--header" falsevalue="" help="If present, exclude the header row from the dataset"/> + <param name="infile" type="data" format="tabular" label="Input file" /> + <param name="header" type="boolean" label="Exclude Header" truevalue="--header" falsevalue="" help="If present, exclude the header row from the dataset" /> <conditional name="column_selector_options"> - <expand macro="samples_column_selector_options" multiple="true" column_option="selected_column_selector_option" col_name="col1" infile="infile"/> + <expand macro="samples_column_selector_options" multiple="true" column_option="selected_column_selector_option" col_name="col1" infile="infile" /> </conditional> <conditional name="select_pca_type"> <param name="select_pca_opts" type="select" label="Select PCA Type" help="Choose which flavour of PCA to use"> @@ -73,8 +73,8 @@ <option value="kernel">Kernel PCA</option> </param> <when value="classical"> - <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept"/> - <param name="whiten" type="boolean" label="Whiten Components" truevalue="--whiten" falsevalue="" help="Setting this option will reduce the redundancy and correlations between the features"/> + <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept" /> + <param name="whiten" type="boolean" label="Whiten Components" truevalue="--whiten" falsevalue="" help="Setting this option will reduce the redundancy and correlations between the features" /> <conditional name="select_solver_type"> <param name="svd_solver_opts" type="select" label="SVD Solver" help="Method to perform the singular value decomposition"> <option value="auto" selected="true">auto</option> @@ -83,20 +83,20 @@ <option value="randomized">randomized</option> </param> <when value="arpack"> - <param name="tolerance" type="float" value="0.0" label="Tolerance" help="Convergence tolerance for arpack. If 0, optimal value will be chosen by arpack"/> + <param name="tolerance" type="float" value="0.0" label="Tolerance" help="Convergence tolerance for arpack. If 0, optimal value will be chosen by arpack" /> </when> - <when value="auto"/> - <when value="full"/> - <when value="randomized"/> + <when value="auto" /> + <when value="full" /> + <when value="randomized" /> </conditional> </when> <when value="incremental"> - <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept"/> - <param name="whiten" type="boolean" label="Whiten Components" truevalue="--whiten" falsevalue=""/> - <param name="batch_size" type="integer" optional="true" label="Batch Size" help="The number of samples to use for each batch"/> + <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept" /> + <param name="whiten" type="boolean" label="Whiten Components" truevalue="--whiten" falsevalue="" /> + <param name="batch_size" type="integer" optional="true" label="Batch Size" help="The number of samples to use for each batch" /> </when> <when value="kernel"> - <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept"/> + <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept" /> <conditional name="select_kernel_opts"> <param name="kernel_opts" type="select" label="Kernel Type"> <option value="linear" selected="true">linear</option> @@ -107,20 +107,20 @@ <option value="precomputed">precomputed</option> </param> <when value="poly"> - <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels"/> - <param name="degree" type="integer" value="3" label="Degree of the polynomial" help="Degree for poly kernels. Ignored by other kernels"/> - <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels"/> + <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels" /> + <param name="degree" type="integer" value="3" label="Degree of the polynomial" help="Degree for poly kernels. Ignored by other kernels" /> + <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels" /> </when> <when value="sigmoid"> - <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels"/> - <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels"/> + <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels" /> + <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels" /> </when> <when value="rbf"> - <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels"/> + <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels" /> </when> - <when value="linear"/> - <when value="cosine"/> - <when value="precomputed"/> + <when value="linear" /> + <when value="cosine" /> + <when value="precomputed" /> </conditional> <conditional name="select_solver_type"> <param name="eigen_solver_opts" type="select" label="Eigen Solver"> @@ -129,89 +129,89 @@ <option value="arpack">arpack</option> </param> <when value="arpack"> - <param name="tolerance" type="float" value="0.0" label="Tolerance" help="Convergence tolerance for arpack. If 0, optimal value will be chosen by arpack"/> - <param name="max_iter" type="integer" optional="true" label="Maximum Iterations" help="Maximum number of iterations for arpack"/> + <param name="tolerance" type="float" value="0.0" label="Tolerance" help="Convergence tolerance for arpack. If 0, optimal value will be chosen by arpack" /> + <param name="max_iter" type="integer" optional="true" label="Maximum Iterations" help="Maximum number of iterations for arpack" /> </when> - <when value="auto"/> - <when value="dense"/> + <when value="auto" /> + <when value="dense" /> </conditional> </when> </conditional> </inputs> <outputs> - <data format="tabular" name="outfile"/> + <data format="tabular" name="outfile" /> </outputs> <tests> <test> - <param name="infile" value="pca_input.dat" ftype="tabular"/> - <param name="selected_column_selector_option" value="by_index_number" /> - <param name="col1" value="1,2,4,6,8,5"/> - <param name="number" value="5"/> - <param name="select_pca_opts" value="classical"/> - <param name="svd_solver_opts" value="arpack"/> - <param name="tolerance" value="0.4"/> - <output name="outfile" ftype='tabular' file="pca_classical_output.dat"/> + <param name="infile" value="pca_input.dat" ftype="tabular" /> + <param name="selected_column_selector_option" value="by_index_number" /> + <param name="col1" value="1,2,4,6,8,5" /> + <param name="number" value="5" /> + <param name="select_pca_opts" value="classical" /> + <param name="svd_solver_opts" value="arpack" /> + <param name="tolerance" value="0.4" /> + <output name="outfile" ftype='tabular' file="pca_classical_output.dat" /> </test> <test> - <param name="infile" value="pca_input_with_headers.dat" ftype="tabular"/> - <param name="header" value="--header"/> - <param name="selected_column_selector_option" value="by_header_name" /> - <param name="col1" value="col_1,col_2,col_4,col_6,col_8,col_5"/> - <param name="number" value="5"/> - <param name="select_pca_opts" value="classical"/> - <param name="svd_solver_opts" value="arpack"/> - <param name="tolerance" value="0.4"/> - <output name="outfile" ftype='tabular' file="pca_classical_header_names_output.dat"/> + <param name="infile" value="pca_input_with_headers.dat" ftype="tabular" /> + <param name="header" value="--header" /> + <param name="selected_column_selector_option" value="by_header_name" /> + <param name="col1" value="col_1,col_2,col_4,col_6,col_8,col_5" /> + <param name="number" value="5" /> + <param name="select_pca_opts" value="classical" /> + <param name="svd_solver_opts" value="arpack" /> + <param name="tolerance" value="0.4" /> + <output name="outfile" ftype='tabular' file="pca_classical_header_names_output.dat" /> </test> <test> - <param name="infile" value="pca_input.dat" ftype="tabular"/> - <param name="selected_column_selector_option" value="all_but_by_index_number"/> + <param name="infile" value="pca_input.dat" ftype="tabular" /> + <param name="selected_column_selector_option" value="all_but_by_index_number" /> <param name="col1" value="8,5" /> - <param name="number" value="7"/> - <param name="select_pca_opts" value="incremental"/> - <param name="batch_size" value="64"/> - <output name="outfile" ftype='tabular' file="pca_incremental_output.dat"/> + <param name="number" value="7" /> + <param name="select_pca_opts" value="incremental" /> + <param name="batch_size" value="64" /> + <output name="outfile" ftype='tabular' file="pca_incremental_output.dat" /> </test> <test> - <param name="infile" value="pca_input_with_headers.dat" ftype="tabular"/> - <param name="header" value="--header"/> - <param name="selected_column_selector_option" value="all_but_by_header_name" /> - <param name="col1" value="col_8,col_5"/> - <param name="number" value="7"/> - <param name="select_pca_opts" value="incremental"/> - <param name="batch_size" value="64"/> - <output name="outfile" ftype='tabular' file="pca_incremental_header_names_output.dat"/> + <param name="infile" value="pca_input_with_headers.dat" ftype="tabular" /> + <param name="header" value="--header" /> + <param name="selected_column_selector_option" value="all_but_by_header_name" /> + <param name="col1" value="col_8,col_5" /> + <param name="number" value="7" /> + <param name="select_pca_opts" value="incremental" /> + <param name="batch_size" value="64" /> + <output name="outfile" ftype='tabular' file="pca_incremental_header_names_output.dat" /> </test> <test> - <param name="infile" value="pca_input.dat" ftype="tabular"/> - <param name="selected_column_selector_option" value="all_columns" /> - <param name="number" value="8"/> - <param name="select_pca_opts" value="kernel"/> - <param name="kernel_opts" value="linear"/> - <param name="eigen_solver_opts" value="arpack"/> - <param name="tolerance" value="4.3"/> - <param name="max_iter" value="8"/> + <param name="infile" value="pca_input.dat" ftype="tabular" /> + <param name="selected_column_selector_option" value="all_columns" /> + <param name="number" value="8" /> + <param name="select_pca_opts" value="kernel" /> + <param name="kernel_opts" value="linear" /> + <param name="eigen_solver_opts" value="arpack" /> + <param name="tolerance" value="4.3" /> + <param name="max_iter" value="8" /> <output name="outfile" ftype="tabular"> <assert_contents> - <has_n_lines n="300"/> - <has_n_columns n="8"/> + <has_n_lines n="300" /> + <has_n_columns n="8" /> </assert_contents> </output> </test> <test> - <param name="infile" value="pca_input.dat" ftype="tabular"/> - <param name="selected_column_selector_option" value="all_columns" /> - <param name="number" value="8"/> - <param name="select_pca_opts" value="kernel"/> - <param name="kernel_opts" value="poly"/> - <param name="gamma" value="0.3"/> - <param name="degree" value="4"/> - <param name="coef0" value="1.6"/> - <param name="eigen_solver_opts" value="auto"/> + <param name="infile" value="pca_input.dat" ftype="tabular" /> + <param name="selected_column_selector_option" value="all_columns" /> + <param name="number" value="8" /> + <param name="select_pca_opts" value="kernel" /> + <param name="kernel_opts" value="poly" /> + <param name="gamma" value="0.3" /> + <param name="degree" value="4" /> + <param name="coef0" value="1.6" /> + <param name="eigen_solver_opts" value="auto" /> <output name="outfile" ftype="tabular"> <assert_contents> - <has_n_lines n="300"/> - <has_n_columns n="8"/> + <has_n_lines n="300" /> + <has_n_columns n="8" /> </assert_contents> </output> </test> @@ -222,9 +222,10 @@ **What it does** This tool takes a tabular input file (one data point per row, each column a variable) -and performs PCA using Singular Value Decomposition, returning an equally sized tabular -file with the first PC in the first column, second PC in the second column, etc. +and performs principal component analysis (PCA) using Singular Value Decomposition, +returning an equally sized tabular file with the first PC in the first column, second +PC in the second column, etc. ]]> </help> - <expand macro="sklearn_citation"/> + <expand macro="sklearn_citation" /> </tool>