--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/analyze_diff_exp.xml	Fri Sep 29 14:36:11 2017 -0400
@@ -0,0 +1,69 @@
+<tool id="Analyze_Diff_Exp" name="Analyze_Differential_Expression" version="0.0.1">
+
+    <description>Analyze differential expression</description>
+    <requirements>
+        <requirement type="package" version="2.7">python</requirement>
+        <requirement type="package">trinity</requirement>
+    </requirements>
+    <command>
+        <![CDATA[
+        python $__tool_directory__/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="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" >
+                    <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" >
+                    <assert_contents>
+                        <has_line_matching expression=".+" />
+                    </assert_contents>
+                </output>
+		<output name="Heatmap" >
+                    <assert_contents>
+                        <has_line_matching expression=".+" />
+                    </assert_contents>
+                </output>
+
+        </test>
+    </tests>
+    <help>
+.. class:: infomark 
+
+This tool filters differentially expressed transcripts derived from edgeR using a minimum fold change (C-value) which will be log2 transformed before use and a required significance (P-value) in the pairwise sample comparisons (after false discovery rate correction). 
+
+If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_.
+
+.. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
+.. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
+    </help>
+
+    <citations>
+        <citation type="doi">10.1038/nbt.1883</citation>
+    </citations>
+
+</tool>