Mercurial > repos > iuc > rpy_statistics_collection
diff kcca.xml @ 1:2e7bc1bb2dbe draft default tip
Uploaded
| author | iuc |
|---|---|
| date | Fri, 09 Jan 2015 12:56:07 -0500 |
| parents | ffcdde989859 |
| children |
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--- a/kcca.xml Tue Jul 29 06:30:45 2014 -0400 +++ b/kcca.xml Fri Jan 09 12:56:07 2015 -0500 @@ -1,151 +1,155 @@ -<tool id="kcca1" name="Kernel Canonical Correlation Analysis" version="1.1.0"> - <description> </description> - <expand macro="requirements" /> - <macros> - <import>statistic_tools_macros.xml</import> - </macros> - <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" size="10" 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" size="10" type="float" value="1" label="sigma (inverse kernel width)" /> - </when> - <when value="laplacedot"> - <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" /> - </when> - <when value="polydot"> - <param name="degree" size="10" type="float" value="1" label="degree" /> - <param name="scale" size="10" type="float" value="1" label="scale" /> - <param name="offset" size="10" type="float" value="1" label="offset" /> - </when> - <when value="tanhdot"> - <param name="scale" size="10" type="float" value="1" label="scale" /> - <param name="offset" size="10" type="float" value="1" label="offset" /> - </when> - <when value="besseldot"> - <param name="sigma" size="10" type="float" value="1" label="sigma" /> - <param name="order" size="10" type="float" value="1" label="order" /> - <param name="degree" size="10" type="float" value="1" label="degree" /> - </when> - <when value="anovadot"> - <param name="sigma" size="10" type="float" value="1" label="sigma" /> - <param name="degree" size="10" 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> +<tool id="kcca1" name="Kernel Canonical Correlation Analysis" version="1.1.0"> + <description> </description> + <expand macro="requirements" /> + <macros> + <import>statistic_tools_macros.xml</import> + </macros> + <command interpreter="python"> +<![CDATA[ + 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" size="10" 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" size="10" type="float" value="1" label="sigma (inverse kernel width)" /> + </when> + <when value="laplacedot"> + <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" /> + </when> + <when value="polydot"> + <param name="degree" size="10" type="float" value="1" label="degree" /> + <param name="scale" size="10" type="float" value="1" label="scale" /> + <param name="offset" size="10" type="float" value="1" label="offset" /> + </when> + <when value="tanhdot"> + <param name="scale" size="10" type="float" value="1" label="scale" /> + <param name="offset" size="10" type="float" value="1" label="offset" /> + </when> + <when value="besseldot"> + <param name="sigma" size="10" type="float" value="1" label="sigma" /> + <param name="order" size="10" type="float" value="1" label="order" /> + <param name="degree" size="10" type="float" value="1" label="degree" /> + </when> + <when value="anovadot"> + <param name="sigma" size="10" type="float" value="1" label="sigma" /> + <param name="degree" size="10" 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> +<![CDATA[ + + +.. 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>