# HG changeset patch
# User trinity_ctat
# Date 1530298480 14400
# Node ID b37d57c8ce7e15bf419d76f78d672de0d329505d
# Parent  68c6c52d2ced73adef35cd7efb95f3e83a508d5c
Uploaded

diff -r 68c6c52d2ced -r b37d57c8ce7e ctat_analyze_differential_expression.xml
--- a/ctat_analyze_differential_expression.xml	Thu Jun 28 22:45:26 2018 -0400
+++ b/ctat_analyze_differential_expression.xml	Fri Jun 29 14:54:40 2018 -0400
@@ -14,43 +14,43 @@
     </requirements>
     <command detect_errors="exit_code">
         <![CDATA[
-        python $__tool_directory__/ctat_analyze_differential_expression.py $Counts_matrix $TMM_Matrix_FPKM $Pvalue $Cvalue 
+        python $__tool_directory__/ctat_analyze_differential_expression.py $EdgeRTarGz $Counts_matrix $Pvalue $Cvalue 
         ]]>
     </command>
     <inputs>
           <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="txt"/>
           <param name="Counts_matrix" label="Counts Matrix" type="data" format="tabular" />
-	      <param name="Pvalue" label="P-value" value="0.05" type="float" />
-	      <param name="Cvalue" label="C-value" value="0" type="float" />
+      <param name="Pvalue" label="P-value" value="0.05" type="float" />
+      <param name="Cvalue" label="C-value" value="0" type="float" />
       
     </inputs>
     <outputs>
         <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/>
-	    <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
-	    <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
-	    <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
+    <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
+    <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
+    <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
     </outputs>
     <tests>
-	<test>
-		<param name="EdgeRTarGz" value="Sp.edgeR.tar.gz" ftype="tar" />
-		<param name="TMM_Matrix_FPKM" value="Sp.TMM.EXPR.matrix" />
-		<param name="Pvalue" value="0.05" />
-		<param name="Cvalue" value="0.0" />
+<test>
+<param name="EdgeRTarGz" value="Sp.edgeR.tar.gz" ftype="tar" />
+<param name="TMM_Matrix_FPKM" value="Sp.TMM.EXPR.matrix" />
+<param name="Pvalue" value="0.05" />
+<param name="Cvalue" value="0.0" />
 
-		<output name="diffExpr_matrix" >
+<output name="diffExpr_matrix" >
                     <assert_contents>
                         <has_line_matching expression=".+" />
                         <has_line line="Sp_ds&#009;Sp_hs" />
                         <has_line_matching expression="TRINITY_DN.+" />
                     </assert_contents>
                 </output>
-		<output name="diffExpr_correlation_matrix" file="Sp.diffExpr.matrix.log2.sample_cor.dat" />
-		<output name="diffExpr_correlation_matrix_pdf" >
+<output name="diffExpr_correlation_matrix" file="Sp.diffExpr.matrix.log2.sample_cor.dat" />
+<output name="diffExpr_correlation_matrix_pdf" >
                     <assert_contents>
                         <has_line_matching expression=".+" />
                     </assert_contents>
                 </output>
-		<output name="Heatmap" >
+<output name="Heatmap" >
                     <assert_contents>
                         <has_line_matching expression=".+" />
                     </assert_contents>