# HG changeset patch
# User nicolas
# Date 1477658930 14400
# Node ID 2212133e6a36463caeae72979da791cf17825e2e
# Parent  94aa63659613852a7ace07c204a3fcd8e8824e07
Uploaded

diff -r 94aa63659613 -r 2212133e6a36 randomForest.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/randomForest.xml	Fri Oct 28 08:48:50 2016 -0400
@@ -0,0 +1,59 @@
+<tool id="randomForest" name="randomForest" version="1.0.1">
+  <description>predict phenotype using a random forest approach</description>
+  <command interpreter="Rscript">
+	  randomForest.R $config &gt; ${output1}
+  </command>
+  
+  <inputs>
+	<param name="genotype" type="data"
+		label="genotype data" help="a tabular datatype containing the encoded genotypes" 
+	/>
+		  
+	<param name="phenotype" type="data"
+			label="phenotype data" help=" a tabular datatype containing the phenotypes " 
+			/>
+	
+	<param name="eval" type="integer" value="0"
+			label="do evaluation" help=" whether to produce a model or to use folds to evaluate the tool. 1 means the tool will be evaluate (and a folds argument is required) any other value produces a model " 
+	/>
+	
+	<param name="ntree" type="float" value="1000"
+			label="ntree" help="the ntree parameter of Random Forest. Suitable value could be around 1000. " 
+			/>
+			
+	<param name="mtry" type="float" value="-1"
+			label="mtry" help="the mtry parameter of Random Forest (number of node per tree). default value are around nuber_of_variable/3 through optimization is highly desirable. -1 means the parameter must be optimized by the tool" 
+			/>
+	
+	<param name="folds" type="data" optional="true"
+			label="folds" help=" OPTIONAL ARGUMENT path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. " 
+			/>
+		
+	<!-- <param name="model" type="text"
+			label="path to the output folds" help= " a path to a file where the results (depending on the chosen mode) will be writen" 
+	/> -->
+  </inputs>
+  
+  <configfiles>
+    <configfile name="config">
+## Desc: this file is sourced in encode wrapper script
+##  as means to pass all galaxy params to R
+"${genotype}" -> genotype
+"${phenotype}" -> phenotype
+"${eval}" -> doEvaluation
+"${folds}" -> folds
+"${output1}" -> out
+"${mtry}" -> mtry
+"${ntree}" -> ntree
+
+    </configfile>
+</configfiles>
+  
+<outputs>
+	<data format="tabular" name = "output1" label="random forest output" />
+</outputs>
+  
+  <help>
+	  make the classification using the random forest method
+  </help>
+</tool>
\ No newline at end of file