# HG changeset patch
# User yhoogstrate
# Date 1389253466 18000
# Node ID 521bfa975110bbf36c57175cc7d9582a5cbd0ac2
# Parent  d7087cb22de96bf8e9c64c4e2c440ed35e0729ed
Uploaded

diff -r d7087cb22de9 -r 521bfa975110 edgeR_DGE.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/edgeR_DGE.xml	Thu Jan 09 02:44:26 2014 -0500
@@ -0,0 +1,70 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="edger_dge" name="edgeR Differential GeneExpression Analysis">
+	<description>RNA-Seq expression analysis using edgeR (R package)</description>
+	
+	<command>
+		<!--
+			The following script is written in the "Cheetah" language:
+			http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html
+		-->
+		
+		R CMD BATCH --vanilla '--args
+			$design_matrix
+			$contrast
+			
+			$output_count_edgeR 
+			$output_cpm
+			output_FPXM
+			$output_raw_counts
+			
+			$qc
+			$output_MDSplot
+			$output_BCVplot
+			$output_MAplot
+			smearPlot '
+			/home/youri/Desktop/galaxy/tools/TraIT/edgeR/DGE/edgeR_DGE_test.R $output_R
+	</command>
+	
+	<inputs>
+		<param name="design_matrix" type="data" format="tabular" help="Design matrix" />
+		
+		<param name="contrast" type="text" label="Contrast (biological question)" help="e.g. 'tumor-normal' or '(G1+G2)/2-G3' using the factors chosen in the design matrix. Read the 'makeContrasts' manual from Limma package for more info." />
+		
+		<param name="qc" type="select" label="Quality control reports">
+			<option value="true">Yes</option>
+			<option value="false" selected="true">No</option>
+		</param>
+		
+		<param name="debug" type="select" label="R Debug output">
+			<option value="true" selected="true"> Yes</option>
+			<option value="false">No</option>
+		</param>
+	</inputs>
+	
+	<outputs>
+		<data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - table" />
+		<data format="tabular" name="output_cpm" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - CPM" />
+		<data format="tabular" name="output_raw_counts" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - raw counts" />
+		
+		<data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output" >
+			<filter>(debug == "true")</filter>
+		</data>
+		
+		<data format="pdf" name="output_MDSplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot">
+			<filter>(qc == "true")</filter>
+		</data>
+		
+		<data format="pdf" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot">
+			<filter>(qc == "true")</filter>
+		</data>
+		
+		<data format="pdf" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot">
+			<filter>(qc == "true")</filter>
+		</data>
+	</outputs>
+	
+	<help>
+		input: Design matrix using "create Design matrix" tool
+		input: contrast
+	</help>
+</tool>