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author | devteam |
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date | Wed, 11 Nov 2015 12:17:43 -0500 |
parents | 7a092113eb8c |
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<tool id="kcca1" name="Kernel Canonical Correlation Analysis" version="1.0.0"> <description> </description> <requirements> <requirement type="package" version="1.0.3">rpy</requirement> <requirement type="package" version="2.11.0">R</requirement> <requirement type="package" version="0.1-4">kernlab</requirement> <requirement type="package" version="1.7.1">numpy</requirement> <requirement type="package" version="0.7.1">bx-python</requirement> </requirements> <command interpreter="python"> kcca.py --input=$input1 --output1=$out_file1 --x_cols=$x_cols --y_cols=$y_cols --kernel=$kernelChoice.kernel --features=$features #if $kernelChoice.kernel == "rbfdot" or $kernelChoice.kernel == "anovadot": --sigma=$kernelChoice.sigma --degree="None" --scale="None" --offset="None" --order="None" #elif $kernelChoice.kernel == "polydot": --sigma="None" --degree=$kernelChoice.degree --scale=$kernelChoice.scale --offset=$kernelChoice.offset --order="None" #elif $kernelChoice.kernel == "tanhdot": --sigma="None" --degree="None" --scale=$kernelChoice.scale --offset=$kernelChoice.offset --order="None" #elif $kernelChoice.kernel == "besseldot": --sigma=$kernelChoice.sigma --degree=$kernelChoice.degree --scale="None" --offset="None" --order=$kernelChoice.order #elif $kernelChoice.kernel == "anovadot": --sigma=$kernelChoice.sigma --degree=$kernelChoice.degree --scale="None" --offset="None" --order="None" #else: --sigma="None" --degree="None" --scale="None" --offset="None" --order="None" #end if </command> <inputs> <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> <param name="x_cols" label="Select columns containing X variables " type="data_column" data_ref="input1" numerical="True" multiple="true" > <validator type="no_options" message="Please select at least one column."/> </param> <param name="y_cols" label="Select columns containing Y variables " type="data_column" data_ref="input1" numerical="True" multiple="true" > <validator type="no_options" message="Please select at least one column."/> </param> <param name="features" type="integer" value="2" label="Number of canonical components to return" help="Enter an integer value greater than 0"/> <conditional name="kernelChoice"> <param name="kernel" type="select" label="Kernel function"> <option value="rbfdot" selected="true">Gaussian Radial Basis Function</option> <option value="polydot">Polynomial</option> <option value="vanilladot">Linear</option> <option value="tanhdot">Hyperbolic</option> <option value="laplacedot">Laplacian</option> <option value="besseldot">Bessel</option> <option value="anovadot">ANOVA Radial Basis Function</option> <option value="splinedot">Spline</option> </param> <when value="vanilladot" /> <when value="splinedot" /> <when value="rbfdot"> <param name="sigma" type="float" value="1" label="sigma (inverse kernel width)" /> </when> <when value="laplacedot"> <param name="sigma" type="float" value="1" label="sigma (inverse kernel width)" /> </when> <when value="polydot"> <param name="degree" type="float" value="1" label="degree" /> <param name="scale" type="float" value="1" label="scale" /> <param name="offset" type="float" value="1" label="offset" /> </when> <when value="tanhdot"> <param name="scale" type="float" value="1" label="scale" /> <param name="offset" type="float" value="1" label="offset" /> </when> <when value="besseldot"> <param name="sigma" type="float" value="1" label="sigma" /> <param name="order" type="float" value="1" label="order" /> <param name="degree" type="float" value="1" label="degree" /> </when> <when value="anovadot"> <param name="sigma" type="float" value="1" label="sigma" /> <param name="degree" type="float" value="1" label="degree" /> </when> </conditional> </inputs> <outputs> <data format="input" name="out_file1" metadata_source="input1" /> </outputs> <tests> <test> <param name="input1" value="iris.tabular"/> <param name="x_cols" value="1,2"/> <param name="y_cols" value="3,4"/> <param name="kernel" value="anovadot"/> <param name="features" value="4"/> <param name="sigma" value="0.1"/> <param name="degree" value="2"/> <output name="out_file1" file="kcca_out1.tabular" compare="re_match"/> </test> <test> <param name="input1" value="iris.tabular"/> <param name="x_cols" value="3,4"/> <param name="y_cols" value="1,2"/> <param name="kernel" value="rbfdot"/> <param name="features" value="2"/> <param name="sigma" value="0.5"/> <output name="out_file1" file="kcca_out2.tabular" compare="re_match"/> </test> </tests> <help> .. class:: infomark **TIP:** If your data is not TAB delimited, use *Edit Datasets->Convert characters* ----- .. class:: infomark **What it does** This tool uses functions from 'kernlab' library from R statistical package to perform Kernel Canonical Correlation Analysis (kCCA) on the input data. *Alexandros Karatzoglou, Alex Smola, Kurt Hornik, Achim Zeileis (2004). kernlab - An S4 Package for Kernel Methods in R. Journal of Statistical Software 11(9), 1-20. URL http://www.jstatsoft.org/v11/i09/* ----- .. class:: warningmark **Note** This tool currently treats all variables as continuous numeric variables. Running the tool on categorical variables might result in incorrect results. Rows containing non-numeric (or missing) data in any of the chosen columns will be skipped from the analysis. </help> </tool>