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Changeset 90:634533b40622 (2016-10-28)

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Commit message:
Uploaded

added:
svm.xml

diff -r c2efdf0c23a1 -r 634533b40622 svm.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/svm.xml Fri Oct 28 08:49:58 2016 -0400

@@ -0,0 +1,74 @@
+<tool id="svm" name="svm" version="1.0.0">
+  <description>predict phenotype using a SVM approach</description>
+  <command interpreter="Rscript">
+   svm.R $config > ${output1}
+  </command>
+
+  <inputs>
+ <param name="genotype" type="data"
+ label="genotype data" help="a tabular datatype containing the encoded genotypes"
+ />
+
+ <param name="phenotype" type="data"
+ label="phenotype data" help=" a tabular datatype containing the phenotypes "
+ />
+
+ <param name="kernel" type="text" value="radial"
+ label="name of the kernel" help= " four possibilities : radial, linear, polynomial or sigmoid. Any other value is treated as radial"
+ />
+
+ <param name="cost" type="float" value="-1"
+ label="cost" help="the cost parameter of SVM used by all kernels. Suitable values are between 0.1 and 1000. -1 means the parameter must be optimized by the tool "
+ />
+
+ <param name="gamma" type="float" value="-1"
+ label="gamma" help="the gamma parameter of SVM used by radial, polynomial and sigmoid kernels. Suitable values are between 1e-06 and 1. -1 means the parameter must be optimized by the tool "
+ />
+
+ <param name="coeficient" type="float" value="-1"
+ label="coeficient" help="the coeficient parameter of SVM used by polynomial kernel. Suitable values are between 0 and 4. -1 means the parameter must be optimized by the tool "
+ />
+
+ <param name="degree" type="float" value="-1"
+ label="degree" help="the maximum dgree of the polynomial kernel. Suitable values are between 1 and 3. -1 means the parameter must be optimized by the tool "
+ />
+
+ <param name="eval" type="integer" value="0"
+ label="do evaluation" help=" whether to produce a model or to use folds to evaluate the tool. 1 means the tool will be evaluate (and a folds argument is required) any other value produces a model "
+ />
+
+ <param name="folds" type="data" optional="true"
+ label="folds" help=" OPTIONAL ARGUMENT path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. "
+ />
+
+ 
+  </inputs>
+
+  <configfiles>
+    <configfile name="config">
+## Desc: this file is sourced in encode wrapper script
+##  as means to pass all galaxy params to R
+"${genotype}" -> genotype
+"${phenotype}" -> phenotype
+"${eval}" -> doEvaluation
+"${folds}" -> folds
+"${output1}" -> out
+"${kernel}" -> kernel
+"${gamma}" -> g
+"${cost}" -> c
+"${coeficient}" -> coef
+"${degree}" -> d
+
+    </configfile>
+</configfiles>
+
+<outputs>
+ <data format="tabular" name = "output1" label="SVM output" />
+</outputs>
+
+  <help>
+   make the classification using the SVM method
+  </help>
+</tool>
\ No newline at end of file