Mercurial > repos > gkumar09 > trinityrnaseq_protocol

changeset 12:895cbd4424a5 draft

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Uploaded
author gkumar09
date Wed, 23 Sep 2015 15:23:49 -0400
parents cad1457c50d2
children 8bf618c08b4d
files EdgeR_differentialExpression.xml
diffstat 1 files changed, 38 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/EdgeR_differentialExpression.xml	Wed Sep 23 15:23:49 2015 -0400
@@ -0,0 +1,38 @@
+<tool id="EdgeR_differentialExpression" name="EdgeR_differentialExpression" version="0.0.1">
+
+    <description>Identify Differentially Expressed Transcripts Using EdgeR</description>
+    <requirements>
+        <requirement type="package">trinity</requirement>
+    </requirements>
+    <command interpreter="python">
+
+ 		EdgeR_differentialExpression_wrapper.py 
+			$counts_matrix 
+			$dispersion
+			
+    </command>
+    <inputs>
+		
+		<param type="data" format="txt" name="counts_matrix" label="Matrix of RNA-Seq fragment counts for transcripts per condition" />
+		<param type="data" format="fasta" name="transcripts_fasta_file" label="Transcripts fasta file corresponding to matrix" />
+		<param type="float" name="dispersion" value="0.1" min="0" label="dispersion value" help="Dispersion value to be used in the negative binomial" />
+	
+    </inputs>
+    <outputs>
+        
+        <data format="tar.gz" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" />
+			
+	</outputs>
+    <tests>
+
+		<test>
+			<param name="myname" value="This is just a simple test" />
+
+        </test>
+	
+
+    </tests>
+    <help>
+         help info here.
+    </help>
+</tool>