# HG changeset patch
# User nicolas
# Date 1477907759 14400
# Node ID 642ffa1b14675f7f4dd7e26d4e046ab1357729e4
# Parent  5c895aa6d820eaa27ea6e6e0ad665ebc746fd5b6
Uploaded

diff -r 5c895aa6d820 -r 642ffa1b1467 evaluate_aggregation.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/evaluate_aggregation.xml	Mon Oct 31 05:55:59 2016 -0400
@@ -0,0 +1,70 @@
+<tool id="aggregEval" name="aggregation_evaluation" version="1.0.0">
+  <description>tool to evaluate aggregation accuracy</description>
+  <command interpreter="Rscript">
+	 evaluate_aggregation.R $config &gt; ${output1}
+  </command>
+  
+  <inputs>
+	 
+	 <param name="genotype" type="data"
+		label="genotype data" help="path to a file containing the encoded genotypes" 
+		/> 
+	 
+	<param name="lasso" type="data" optional="true"
+		label="lasso model" help="path to rds containing LASSO model" 
+	/>
+	
+	<param name="rf" type="data" optional="true"
+		label="rf model" help="path to rds containing Random Forest model" 
+		/>
+		
+	<param name="rrBLUP" type="data" optional="true"
+		label="rrBLUP model" help="path to rds containing rrBLUP model" 
+		/>
+		
+	<param name="svm" type="data" optional="true"
+		label="SVM model" help="path to rds containing SVM model" 
+		/>
+		  
+	<param name="phenotype" type="data"
+			label="phenotype data" help=" a tabular datatype containing the phenotypes " 
+			/>
+			
+	<param name="folds" type="data"
+			label="folds" help=" OPTIONAL ARGUMENT path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. " 
+			/>
+	<param name="method" type="text" value="svm"
+			label="aggregation method" help= "choose among geneticMean, dt, lasso, rf or svm" 
+			/>
+	<param name="kernel" type="text" value="linear"
+			label="kernel for SVM" help= "choose among linear, polynomial, radial, sigmoid" 
+			/>		
+	
+  </inputs>
+  
+  <configfiles>
+    <configfile name="config">
+## Desc: this file is sourced in encode wrapper script
+##  as means to pass all galaxy params to R
+"${genotype}" -> genotype
+"${lasso}" -> lassoModel
+"${rf}" -> rfModel
+"${rrBLUP}" -> rrBLUPModel
+"${svm}" -> svmModel
+"${phenotype}" -> phenotype
+"${output1}" -> out
+"${folds}" -> folds
+"${method}" -> method
+"${kernel}" -> kernel
+
+    </configfile>
+</configfiles>
+  
+<outputs>
+	<data format="tabular" name = "output1" label="aggregation evaluation" />
+</outputs>
+  
+  <help>
+	  
+  </help>
+  </tool>
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