diff edgeR_Differential_Gene_Expression.xml @ 94:46745f5666ac draft

Added test

--- a/edgeR_Differential_Gene_Expression.xml	Wed Mar 18 06:40:01 2015 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Sat Mar 28 08:09:03 2015 -0400
@@ -89,6 +89,7 @@
 				> /dev/null
 			#end if
 			
+			<!--
 			2> stderr.txt ; 
 			
 			grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
@@ -103,11 +104,25 @@
 			grep -v 'Setting LC_COLLATE failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
 			
 			cat stderr.txt >&amp;2
+			-->
 	</command>
 	
+	<stdio>
+		<regex match="Calculating library sizes from column" 
+				source="stderr" 
+				level="log" />
+		<regex match="During startup - Warning messages"
+				source="stderr"
+				level="log" />
+		<regex match="Setting LC_[^ ]+ failed"
+				source="stderr"
+				level="warning"
+				description="LOCALE has not been set correctly" />
+	</stdio>
+	
 	<inputs>
 		<param name="expression_matrix" type="data" format="tabular" label="Expression (read count) matrix" />
-		<param name="design_matrix" type="data" format="tabular" label="Design matrix" hepl="Ensure your samplenames are identical to those in the expression matrix. Preferentially, create the contrast matrix using 'edgeR: Design- from Expression matrix'." />
+		<param name="design_matrix" type="data" format="tabular" label="Design matrix" help="Ensure your samplenames are identical to those in the expression matrix. Preferentially, create the contrast matrix using 'edgeR: Design- from Expression 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: http://www.bioconductor.org/packages/release/bioc/html/limma.html and http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf." />
 		
@@ -509,6 +524,21 @@
 		</data>
 	</outputs>
 	
+	<tests>
+		<test>
+			<param name="expression_matrix" value="Differential_Gene_Expression/expression_matrix.tabular.txt" />
+			<param name="design_matrix" value="Differential_Gene_Expression/design_matrix.tabular.txt" />
+			
+			<param name="contrast" value="E-C"/>
+		
+			<param name="fdr" value="0.05" />
+			
+			<param name="output_format_images" value="png" />
+			
+			<output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.tabular.txt" />
+		</test>
+	</tests>
+	
 	<help>
 edgeR: Differential Gene(Expression) Analysis
 #############################################
@@ -635,4 +665,9 @@
 
 I would like to thank Hina Riaz - Naz Khan for her helpful contribution.
 	</help>
+	
+	<citations>
+		<citation type="doi">10.1093/bioinformatics/btp616</citation>
+		<citation type="doi">10.1093/bioinformatics/btt688</citation>
+	</citations>
 </tool>