Mercurial > repos > devteam > kernel_principal_component_analysis
annotate kpca.xml @ 1:9246ab62f58f draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:23:23 -0400 |
| parents | 5642f7ee948b |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="kpca1" name="Kernel Principal Component Analysis" version="1.0.0"> |
| 2 <description> </description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0.3">rpy</requirement> | |
| 5 <requirement type="package" version="2.11.0">R</requirement> | |
| 6 <requirement type="package" version="0.1-4">kernlab</requirement> | |
| 7 <requirement type="package" version="1.7.1">numpy</requirement> | |
| 8 <requirement type="package" version="0.7.1">bx-python</requirement> | |
| 9 </requirements> | |
| 10 <command interpreter="python"> | |
| 11 kpca.py | |
| 12 --input=$input1 | |
| 13 --output1=$out_file1 | |
| 14 --output2=$out_file2 | |
| 15 --var_cols=$var_cols | |
| 16 --kernel=$kernelChoice.kernel | |
| 17 --features=$features | |
| 18 #if $kernelChoice.kernel == "rbfdot" or $kernelChoice.kernel == "anovadot": | |
| 19 --sigma=$kernelChoice.sigma | |
| 20 --degree="None" | |
| 21 --scale="None" | |
| 22 --offset="None" | |
| 23 --order="None" | |
| 24 #elif $kernelChoice.kernel == "polydot": | |
| 25 --sigma="None" | |
| 26 --degree=$kernelChoice.degree | |
| 27 --scale=$kernelChoice.scale | |
| 28 --offset=$kernelChoice.offset | |
| 29 --order="None" | |
| 30 #elif $kernelChoice.kernel == "tanhdot": | |
| 31 --sigma="None" | |
| 32 --degree="None" | |
| 33 --scale=$kernelChoice.scale | |
| 34 --offset=$kernelChoice.offset | |
| 35 --order="None" | |
| 36 #elif $kernelChoice.kernel == "besseldot": | |
| 37 --sigma=$kernelChoice.sigma | |
| 38 --degree=$kernelChoice.degree | |
| 39 --scale="None" | |
| 40 --offset="None" | |
| 41 --order=$kernelChoice.order | |
| 42 #elif $kernelChoice.kernel == "anovadot": | |
| 43 --sigma=$kernelChoice.sigma | |
| 44 --degree=$kernelChoice.degree | |
| 45 --scale="None" | |
| 46 --offset="None" | |
| 47 --order="None" | |
| 48 #else: | |
| 49 --sigma="None" | |
| 50 --degree="None" | |
| 51 --scale="None" | |
| 52 --offset="None" | |
| 53 --order="None" | |
| 54 #end if | |
| 55 </command> | |
| 56 <inputs> | |
| 57 <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> | |
| 58 <param name="var_cols" label="Select columns containing input variables " type="data_column" data_ref="input1" numerical="True" multiple="true" > | |
| 59 <validator type="no_options" message="Please select at least one column."/> | |
| 60 </param> | |
|
1
9246ab62f58f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
61 <param name="features" type="integer" value="2" label="Number of principal components to return" help="To return all, enter 0"/> |
| 0 | 62 <conditional name="kernelChoice"> |
| 63 <param name="kernel" type="select" label="Kernel function"> | |
| 64 <option value="rbfdot" selected="true">Gaussian Radial Basis Function</option> | |
| 65 <option value="polydot">Polynomial</option> | |
| 66 <option value="vanilladot">Linear</option> | |
| 67 <option value="tanhdot">Hyperbolic</option> | |
| 68 <option value="laplacedot">Laplacian</option> | |
| 69 <option value="besseldot">Bessel</option> | |
| 70 <option value="anovadot">ANOVA Radial Basis Function</option> | |
| 71 <option value="splinedot">Spline</option> | |
| 72 </param> | |
| 73 <when value="vanilladot" /> | |
| 74 <when value="splinedot" /> | |
| 75 <when value="rbfdot"> | |
|
1
9246ab62f58f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
76 <param name="sigma" type="float" value="1" label="sigma (inverse kernel width)" /> |
| 0 | 77 </when> |
| 78 <when value="laplacedot"> | |
|
1
9246ab62f58f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
79 <param name="sigma" type="float" value="1" label="sigma (inverse kernel width)" /> |
| 0 | 80 </when> |
| 81 <when value="polydot"> | |
|
1
9246ab62f58f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
82 <param name="degree" type="integer" value="1" label="degree" /> |
|
9246ab62f58f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
83 <param name="scale" type="integer" value="1" label="scale" /> |
|
9246ab62f58f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
84 <param name="offset" type="integer" value="1" label="offset" /> |
| 0 | 85 </when> |
| 86 <when value="tanhdot"> | |
|
1
9246ab62f58f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
87 <param name="scale" type="integer" value="1" label="scale" /> |
|
9246ab62f58f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
88 <param name="offset" type="integer" value="1" label="offset" /> |
| 0 | 89 </when> |
| 90 <when value="besseldot"> | |
|
1
9246ab62f58f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
91 <param name="sigma" type="integer" value="1" label="sigma" /> |
|
9246ab62f58f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
92 <param name="order" type="integer" value="1" label="order" /> |
|
9246ab62f58f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
93 <param name="degree" type="integer" value="1" label="degree" /> |
| 0 | 94 </when> |
| 95 <when value="anovadot"> | |
|
1
9246ab62f58f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
96 <param name="sigma" type="integer" value="1" label="sigma" /> |
|
9246ab62f58f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
97 <param name="degree" type="integer" value="1" label="degree" /> |
| 0 | 98 </when> |
| 99 </conditional> | |
| 100 </inputs> | |
| 101 <outputs> | |
| 102 <data format="input" name="out_file1" metadata_source="input1" /> | |
| 103 <data format="pdf" name="out_file2" /> | |
| 104 </outputs> | |
| 105 <tests> | |
| 106 <test> | |
| 107 <param name="input1" value="iris.tabular"/> | |
| 108 <param name="var_cols" value="1,2,3,4"/> | |
| 109 <param name="kernel" value="polydot"/> | |
| 110 <param name="features" value="2"/> | |
| 111 <param name="offset" value="0"/> | |
| 112 <param name="scale" value="1"/> | |
| 113 <param name="degree" value="2"/> | |
| 114 <output name="out_file1" file="kpca_out1.tabular"/> | |
| 115 <output name="out_file2" file="kpca_out2.pdf"/> | |
| 116 </test> | |
| 117 </tests> | |
| 118 <help> | |
| 119 | |
| 120 | |
| 121 .. class:: infomark | |
| 122 | |
| 123 **TIP:** If your data is not TAB delimited, use *Edit Datasets->Convert characters* | |
| 124 | |
| 125 ----- | |
| 126 | |
| 127 .. class:: infomark | |
| 128 | |
| 129 **What it does** | |
| 130 | |
| 131 This tool uses functions from 'kernlab' library from R statistical package to perform Kernel Principal Component Analysis (kPCA) on the input data. It outputs two files, one containing the summary statistics of the performed kPCA, and the other containing a scatterplot matrix of rotated values reported by kPCA. | |
| 132 | |
| 133 *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/* | |
| 134 | |
| 135 ----- | |
| 136 | |
| 137 .. class:: warningmark | |
| 138 | |
| 139 **Note** | |
| 140 | |
| 141 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. | |
| 142 | |
| 143 </help> | |
| 144 </tool> |