# HG changeset patch
# User nicolas
# Date 1477658998 14400
# Node ID 634533b4062229b3b044839a26ca4043d0ee6c72
# Parent  c2efdf0c23a14df53e26d0b3caf0f585d054facc
Uploaded

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 &gt; ${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. " 
+			/>
+		
+	<!-- <param name="model" type="text"
+			label="path to the output folds" help= " a path to a file where the results (depending on the chosen mode) will be writen" 
+	/> -->
+  </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>
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