# HG changeset patch
# User nicolas
# Date 1477045746 14400
# Node ID 377a34a001b0aa3a7a9bdfa7f83d71dd069ee5aa
# Parent  87f772c49a20fff88dca5e8ade2e388fe2739552
Uploaded

diff -r 87f772c49a20 -r 377a34a001b0 qualityControl.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qualityControl.xml	Fri Oct 21 06:29:06 2016 -0400
@@ -0,0 +1,41 @@
+<tool id="qualityControl" name="qualityControl" version="1.0.0">
+  <description>perform QC on a dataset</description>
+  <command interpreter="Rscript">
+	  qualityControl.R $config &gt; ${reportPath}
+  </command>
+  
+  <inputs>
+	<param name="genotype" type="data"
+		label="genotype data" help="genotype must be a .csv" 
+	/>
+		  
+	<param name="plinkFreq" type="data"
+			  label="plink files with frequencies" help="" 
+	/>
+	
+	<param name="plinkHWE" type="data"
+		label="plink files with HardyWeinberg statistics" help=""  
+	/>
+  </inputs>
+  
+  
+    <configfiles>
+    <configfile name="config">
+## Desc: this file is sourced in encode wrapper script
+##  as means to pass all galaxy params to R
+"${genotype}" -> genotype
+"${plinkFreq}" -> plinkFreq
+"${plinkHWE}" -> plinkHWE
+"${reportPath}" -> out
+
+    </configfile>
+</configfiles>
+  
+<outputs>
+	<data format="plain text" name="reportPath" label="QC report" />
+</outputs>
+  
+  <help>
+	  make a report with dimension of the dataset, MAF, Hardy-Weinberg test
+  </help>
+  </tool>
\ No newline at end of file