view edgeR_DGE.xml @ 2:521bfa975110 draft

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<?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>