[2] | 1 | <tool id="kcca1" name="Kernel Canonical Correlation Analysis" version="1.0.0">
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| 2 | <description> </description>
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| 3 | <command interpreter="python">
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| 4 | kcca.py
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| 5 | --input=$input1
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| 6 | --output1=$out_file1
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| 7 | --x_cols=$x_cols
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| 8 | --y_cols=$y_cols
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| 9 | --kernel=$kernelChoice.kernel
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| 10 | --features=$features
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| 11 | #if $kernelChoice.kernel == "rbfdot" or $kernelChoice.kernel == "anovadot":
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| 12 | --sigma=$kernelChoice.sigma
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| 13 | --degree="None"
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| 14 | --scale="None"
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| 15 | --offset="None"
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| 16 | --order="None"
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| 17 | #elif $kernelChoice.kernel == "polydot":
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| 18 | --sigma="None"
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| 19 | --degree=$kernelChoice.degree
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| 20 | --scale=$kernelChoice.scale
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| 21 | --offset=$kernelChoice.offset
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| 22 | --order="None"
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| 23 | #elif $kernelChoice.kernel == "tanhdot":
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| 24 | --sigma="None"
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| 25 | --degree="None"
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| 26 | --scale=$kernelChoice.scale
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| 27 | --offset=$kernelChoice.offset
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| 28 | --order="None"
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| 29 | #elif $kernelChoice.kernel == "besseldot":
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| 30 | --sigma=$kernelChoice.sigma
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| 31 | --degree=$kernelChoice.degree
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| 32 | --scale="None"
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| 33 | --offset="None"
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| 34 | --order=$kernelChoice.order
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| 35 | #elif $kernelChoice.kernel == "anovadot":
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| 36 | --sigma=$kernelChoice.sigma
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| 37 | --degree=$kernelChoice.degree
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| 38 | --scale="None"
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| 39 | --offset="None"
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| 40 | --order="None"
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| 41 | #else:
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| 42 | --sigma="None"
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| 43 | --degree="None"
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| 44 | --scale="None"
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| 45 | --offset="None"
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| 46 | --order="None"
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| 47 | #end if
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| 48 | </command>
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| 49 | <inputs>
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| 50 | <param format="tabular" name="input1" type="data" label="Select data" help="Query missing? See TIP below."/>
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| 51 | <param name="x_cols" label="Select columns containing X variables " type="data_column" data_ref="input1" numerical="True" multiple="true" > |
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| 52 | <validator type="no_options" message="Please select at least one column."/> |
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| 53 | </param>
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| 54 | <param name="y_cols" label="Select columns containing Y variables " type="data_column" data_ref="input1" numerical="True" multiple="true" >
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| 55 | <validator type="no_options" message="Please select at least one column."/>
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| 56 | </param>
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| 57 | <param name="features" size="10" type="integer" value="2" label="Number of canonical components to return" help="Enter an integer value greater than 0"/>
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| 58 | <conditional name="kernelChoice">
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| 59 | <param name="kernel" type="select" label="Kernel function">
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| 60 | <option value="rbfdot" selected="true">Gaussian Radial Basis Function</option>
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| 61 | <option value="polydot">Polynomial</option>
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| 62 | <option value="vanilladot">Linear</option>
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| 63 | <option value="tanhdot">Hyperbolic</option>
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| 64 | <option value="laplacedot">Laplacian</option>
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| 65 | <option value="besseldot">Bessel</option>
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| 66 | <option value="anovadot">ANOVA Radial Basis Function</option>
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| 67 | <option value="splinedot">Spline</option>
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| 68 | </param>
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| 69 | <when value="vanilladot" />
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| 70 | <when value="splinedot" />
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| 71 | <when value="rbfdot">
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| 72 | <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" />
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| 73 | </when>
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| 74 | <when value="laplacedot">
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| 75 | <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" />
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| 76 | </when>
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| 77 | <when value="polydot">
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| 78 | <param name="degree" size="10" type="float" value="1" label="degree" />
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| 79 | <param name="scale" size="10" type="float" value="1" label="scale" />
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| 80 | <param name="offset" size="10" type="float" value="1" label="offset" />
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| 81 | </when>
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| 82 | <when value="tanhdot">
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| 83 | <param name="scale" size="10" type="float" value="1" label="scale" />
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| 84 | <param name="offset" size="10" type="float" value="1" label="offset" />
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| 85 | </when>
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| 86 | <when value="besseldot">
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| 87 | <param name="sigma" size="10" type="float" value="1" label="sigma" />
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| 88 | <param name="order" size="10" type="float" value="1" label="order" />
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| 89 | <param name="degree" size="10" type="float" value="1" label="degree" />
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| 90 | </when>
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| 91 | <when value="anovadot">
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| 92 | <param name="sigma" size="10" type="float" value="1" label="sigma" />
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| 93 | <param name="degree" size="10" type="float" value="1" label="degree" />
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| 94 | </when>
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| 95 | </conditional>
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| 96 | </inputs>
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| 97 | <outputs>
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| 98 | <data format="input" name="out_file1" metadata_source="input1" />
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| 99 | </outputs> |
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| 100 | <requirements> |
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| 101 | <requirement type="python-module">rpy</requirement> |
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| 102 | </requirements>
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| 103 | <tests>
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| 104 | <test>
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| 105 | <param name="input1" value="iris.tabular"/>
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| 106 | <param name="x_cols" value="1,2"/>
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| 107 | <param name="y_cols" value="3,4"/>
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| 108 | <param name="kernel" value="anovadot"/>
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| 109 | <param name="features" value="4"/>
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| 110 | <param name="sigma" value="0.1"/>
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| 111 | <param name="degree" value="2"/>
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| 112 | <output name="out_file1" file="kcca_out1.tabular" compare="re_match"/>
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| 113 | </test>
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| 114 | <test>
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| 115 | <param name="input1" value="iris.tabular"/>
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| 116 | <param name="x_cols" value="3,4"/>
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| 117 | <param name="y_cols" value="1,2"/>
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| 118 | <param name="kernel" value="rbfdot"/>
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| 119 | <param name="features" value="2"/>
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| 120 | <param name="sigma" value="0.5"/>
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| 121 | <output name="out_file1" file="kcca_out2.tabular" compare="re_match"/>
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| 122 | </test>
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| 123 | </tests>
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| 124 | <help>
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| 125 |
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| 126 |
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| 127 | .. class:: infomark
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| 128 |
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| 129 | **TIP:** If your data is not TAB delimited, use *Edit Queries->Convert characters*
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| 130 |
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| 131 | -----
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| 132 |
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| 133 | .. class:: infomark
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| 134 |
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| 135 | **What it does**
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| 136 |
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| 137 | This tool uses functions from 'kernlab' library from R statistical package to perform Kernel Canonical Correlation Analysis (kCCA) on the input data.
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| 138 |
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| 139 | *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/*
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| 140 |
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| 141 | -----
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| 142 |
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| 143 | .. class:: warningmark
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| 144 |
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| 145 | **Note**
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| 146 |
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| 147 | 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.
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| 148 |
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| 149 | </help>
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| 150 | </tool>
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