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changeset 12:d49d06d35683 draft

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Uploaded
author fcaramia
date Wed, 21 Aug 2013 22:13:23 -0400
parents e5fcbabbdea7
children 6324eefd9e91
files edgeR.xml
diffstat 1 files changed, 2 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/edgeR.xml	Wed Aug 21 22:13:03 2013 -0400
+++ b/edgeR.xml	Wed Aug 21 22:13:23 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="edgeR" name="edgeR" version="0.0.1">
+<tool id="edgeR" name="edgeR" version="0.0.2">
   <description> - Estimates differential gene expression for short read sequence count using methods appropriate for count data</description>
   <requirements>
         <requirement type="R-module">edgeR</requirement>
@@ -10,8 +10,7 @@
   	#if $analysis_type.analysis == "pw":
    		-r $analysis_type.rowsumfilter
   		#if $analysis_type.tagwise_disp.twd == "TRUE":
-   			-p $analysis_type.tagwise_disp.twd_prop
-  			-u $analysis_type.tagwise_disp.twd_trend
+   			-u $analysis_type.tagwise_disp.twd_trend
   			-t
  		#end if
  	## GLM
@@ -71,7 +70,6 @@
 						<option value="tricube">Tricube</option>
 						<option value="none">None</option>
 					</param>
-					<param name="twd_prop" type="float" value="0.3" label="The proportion of all tags/genes to be used for the locally weighted estimation of the tagwise dispersion, allowing the dispersion estimates to vary with abundance (expression level)"/>
 				</when>
 			</conditional>
 		</when>