# HG changeset patch
# User gkumar09
# Date 1443036126 14400
# Node ID a17bb21b711fcf0dc7b0c77b3a34dec476cf0e43
# Parent  5fadb4b793782bdd70085fbeeab23c027e2a14a4
Uploaded

diff -r 5fadb4b79378 -r a17bb21b711f analyze_diff_exp.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/analyze_diff_exp.xml	Wed Sep 23 15:22:06 2015 -0400
@@ -0,0 +1,41 @@
+<tool id="Analyze_Diff_Exp" name="Analyze_Differential_Expression" version="0.0.1">
+
+    <description>Analyze differential expression</description>
+    <requirements>
+        <requirement type="package">trinity</requirement>
+    </requirements>
+    <command interpreter="python">
+
+        analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue 
+	
+    </command>
+    <inputs>
+              <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="file"/>
+              <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="file" />
+	      <param name="Pvalue" label="P-value" value="0.05" type="float" />
+	      <param name="Cvalue" label="C-value" value="0" type="float" />
+      
+    </inputs>
+    <outputs>
+        <data format="data" name="diffExpr_matrix" label="${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"/>
+    </outputs>
+    <tests>
+
+
+		<test>
+			<param name="target" value="trinity/Trinity.fasta" />
+			<param name="aligner" value="bowtie" />
+			<param name="paired_or_single" value="single" />
+			<param name="library_type" value="None" />
+			<param name="input" value="trinity/reads.left.fq" />
+        </test>
+	
+
+    </tests>
+    <help>
+        .. _Trinity: http://trinityrnaseq.sourceforge.net
+    </help>
+</tool>