Mercurial > repos > yhoogstrate > edger_with_design_matrix

diff edgeR_Concatenate_Expression_Matrices.xml @ 94:46745f5666ac draft

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Added test
author yhoogstrate
date Sat, 28 Mar 2015 08:09:03 -0400
parents b2738b4d7c8c
children
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--- a/edgeR_Concatenate_Expression_Matrices.xml	Wed Mar 18 06:40:01 2015 -0400
+++ b/edgeR_Concatenate_Expression_Matrices.xml	Sat Mar 28 08:09:03 2015 -0400
@@ -86,38 +86,79 @@
 	
 	<tests>
 		<test>
-			<param name="add_geneids.choice" value="true" />
-			<param name="choice" value="true" />
-			<param name="add_geneids" value="true" />
+			<conditional name="add_geneids">
+				<param name="choice" value="true" />
+				<param name="sample_geneids" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" />
+				<param name="column_geneids" value="1" />
+			</conditional>
+			
+			<param name="samples_0|sample" value="GSE51403/GSE51403_expression_matrix_Control_1.txt" />
+			<param name="samples_0|column_index" value="2" />
+			
+			<conditional name="add_lengths">
+				<param name="choice" value="false" />
+			</conditional>
+			
+			<param name="remove_comment_lines" value="false" />
 			
+			<output name="expression_matrix" file="GSE51403/GSE51403_expression_matrix_Control_1.txt" />
+		</test>
+		<test>
+			<conditional name="add_geneids">
+				<param name="choice" value="true" />
+				<param name="sample_geneids" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" />
+				<param name="column_geneids" value="1" />
+			</conditional>
+			
+			<!-- <repeat name="samples"> -->
+				<param name="samples_0|sample" value="GSE51403/GSE51403_expression_matrix_Control_1.txt" />
+				<param name="samples_0|column_index" value="2" />
+			<!-- </repeat> -->
+			
+			<!-- <repeat name="samples"> -->
+				<param name="samples_1|sample" value="GSE51403/GSE51403_expression_matrix_Control_2.txt" />
+				<param name="samples_1|column_index" value="2" />
+			<!-- </repeat> -->
 			
-			<!--
-Add a gene-IDs column at the end of the file	true	
-Select Read-count dataset that contains a column for GeneIDs	21: MCF7_featureCounts_E2.txt	
-Select GeneID column	1	
-Read-count dataset that belongs to a pair	14: MCF7_featureCounts_Control_1.txt	
-Select columns that are associated with this factor level	2	
-Read-count dataset that belongs to a pair	15: MCF7_featureCounts_Control_2.txt	
-Select columns that are associated with this factor level	2	
-Read-count dataset that belongs to a pair	16: MCF7_featureCounts_Control_3.txt	
-Select columns that are associated with this factor level	2	
-Read-count dataset that belongs to a pair	17: MCF7_featureCounts_Control_4.txt	
-Select columns that are associated with this factor level	2	
-Read-count dataset that belongs to a pair	18: MCF7_featureCounts_Control_5.txt	
-Select columns that are associated with this factor level	2	
-Read-count dataset that belongs to a pair	22: MCF7_featureCounts_Control_6.txt	
-Select columns that are associated with this factor level	2	
-Read-count dataset that belongs to a pair	20: MCF7_featureCounts_Control_7.txt	
-Select columns that are associated with this factor level	2	
-Read-count dataset that belongs to a pair	21: MCF7_featureCounts_E2.txt	
-Select columns that are associated with this factor level	2 3 4 5 6 7 8	
-Add a gene-lengths column at the end of the file	true	
-Read-count dataset that belongs to a pair	26: MCF7_featureCounts_GeneLengths.txt	
-Select columns that are associated with this factor level	2	
-Automatically remove 'comment' lines starting with a '#'	False
-			-->
+			<!-- <repeat name="samples"> -->
+				<param name="samples_2|sample" value="GSE51403/GSE51403_expression_matrix_Control_3.txt" />
+				<param name="samples_2|column_index" value="2" />
+			<!-- </repeat> -->
+			
+			<!-- <repeat name="samples"> -->
+				<param name="samples_3|sample" value="GSE51403/GSE51403_expression_matrix_Control_4.txt" />
+				<param name="samples_3|column_index" value="2" />
+			<!-- </repeat> -->
+			
+			<!-- <repeat name="samples"> -->
+				<param name="samples_4|sample" value="GSE51403/GSE51403_expression_matrix_Control_5.txt" />
+				<param name="samples_4|column_index" value="2" />
+			<!-- </repeat> -->
+			
+			<!-- <repeat name="samples"> -->
+				<param name="samples_5|sample" value="GSE51403/GSE51403_expression_matrix_Control_6.txt" />
+				<param name="samples_5|column_index" value="2" />
+			<!-- </repeat> -->
 			
-			<output name="expression_matrix" file="MCF7_featureCounts_concatenated.txt" />
+			<!-- <repeat name="samples"> -->
+				<param name="samples_6|sample" value="GSE51403/GSE51403_expression_matrix_Control_7.txt" />
+				<param name="samples_6|column_index" value="2" />
+			<!-- </repeat> -->
+			
+			<!-- <repeat name="samples"> -->
+				<param name="samples_7|sample" value="GSE51403/GSE51403_expression_matrix_E2.txt" />
+				<param name="samples_7|column_index" value="2,3,4,5,6,7,8" />
+			<!-- </repeat> -->
+			
+			<conditional name="add_lengths">
+				<param name="choice" value="true" />
+				<param name="sample_lengths" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" />
+				<param name="column_lengths" value="2" />
+			</conditional>
+			
+			<param name="remove_comment_lines" value="false" />
+			
+			<output name="expression_matrix" file="GSE51403/GSE51403_expression_matrix_full.txt" />
 		</test>
 	</tests>
 	
@@ -157,4 +198,9 @@
 
 http://testtoolshed.g2.bx.psu.edu/
 	</help>
+	
+	<citations>
+		<citation type="doi">10.1093/bioinformatics/btp616</citation>
+		<citation type="doi">10.1093/bioinformatics/btt688</citation>
+	</citations>
 </tool>