# HG changeset patch
# User nicolas
# Date 1477520734 14400
# Node ID ecff96cf595872f9d3e05e8599f7c893c08a492d
# Parent  613c81a4f7c0fa74dbcd720767a12aff2960adb1
Uploaded

diff -r 613c81a4f7c0 -r ecff96cf5958 aggregation.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aggregation.xml	Wed Oct 26 18:25:34 2016 -0400
@@ -0,0 +1,78 @@
+<tool id="aggreg" name="aggregation" version="1.0.0">
+  <description>predict phenotype by combining multiple classifiers</description>
+  <command interpreter="Rscript">
+	  aggregation.R $config &gt; ${output1}
+  </command>
+  
+  <inputs>
+	<param name="lassoPred" type="data" optional="true"
+		label="lasso prediction" help="path to rds containing LASSO prediction" 
+	/>
+	
+	<param name="rfPred" type="data" optional="true"
+		label="rf prediction" help="path to rds containing Random Forest prediction" 
+		/>
+		
+	<param name="rrBLUPPred" type="data" optional="true"
+		label="rrBLUP prediction" help="path to rds containing rrBLUP prediction" 
+		/>
+		
+	<param name="svmPred" type="data" optional="true"
+		label="SVM prediction" help="path to rds containing SVM prediction" 
+		/>
+		  
+	<param name="phenotype" type="data"
+			label="phenotype data" help=" a tabular datatype containing the phenotypes " 
+			/>
+	
+	<param name="eval" type="integer" value="0"
+			label="do evaluation" help=" whether to produce a model or to use folds to evaluate the tool. 1 means the tool will be evaluate (and a folds argument is required) any other value produces a model " 
+			/>
+			
+	<param name="folds" type="data" optional="true"
+			label="folds" help=" OPTIONAL ARGUMENT path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. " 
+			/>
+			
+	<param name="model" type="data" optional="true"
+			label="model" help= " a path to a file where the results (depending on the chosen mode) will be writen" 
+			/>
+	<param name="out" type="text"
+			label="output path" help= " a path to a rds file" 
+			/>
+	<param name="method" type="text" value="svm"
+			label="aggregation method" help= "choose among geneticMean, rrBLUP, lasso, rf or svm" 
+			/>
+	<param name="kernel" type="text" value="linear"
+			label="kernel for SVM" help= "choose among linear, polynomial, radial, sigmoid" 
+			/>		
+	
+  </inputs>
+  
+  <configfiles>
+    <configfile name="config">
+## Desc: this file is sourced in encode wrapper script
+##  as means to pass all galaxy params to R
+"${lassoPred}" -> lassoPred
+"${rfPred}" -> rfPred
+"${rrBLUPPred}" -> rrBLUPPred
+"${svmPred}" -> svmPred
+"${phenotype}" -> phenotype
+"${model}" -> model
+"${out}" -> out
+"${eval}" -> evaluation
+"${folds}" -> folds
+"${method}" -> method
+"${kernel}" -> kernel
+"${eval}" -> doEvaluation
+
+    </configfile>
+</configfiles>
+  
+<outputs>
+	<data format="tabular" name = "output1" label="aggregation output" />
+</outputs>
+  
+  <help>
+	  
+  </help>
+  </tool>
\ No newline at end of file