# HG changeset patch
# User geert-vandeweyer
# Date 1406895885 14400
# Node ID aeef617bb99c582bb0420993878e350709879bff
# Parent  ae8ad9d17e3466e8485b787fce42a4c58956f515
Uploaded

diff -r ae8ad9d17e34 -r aeef617bb99c cufflinks_wrapper.xml
--- a/cufflinks_wrapper.xml	Fri Aug 01 07:45:21 2014 -0400
+++ b/cufflinks_wrapper.xml	Fri Aug 01 08:24:45 2014 -0400
@@ -28,11 +28,6 @@
 			$no_faux_reads
             #end if
 
-            ## Normalization?
-            #if str($do_normalization) == "Yes":
-            -N
-            #end if
-            
             ## Bias correction?
             #if $bias_correction.do_bias_correction == "Yes":
                 -b
@@ -83,10 +78,6 @@
 	<param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help="ignore alignments with gaps longer than this"/>
         <param name="min_isoform_fraction" type="float" value="0.10" min="0" max="1" label="Min Isoform Fraction" help="suppress transcripts below this abundance level"/>
         <param name="pre_mrna_fraction" type="float" value="0.15" min="0" max="1" label="Pre MRNA Fraction" help="suppress intra-intronic transcripts below this level"/>
-<!-- XX-->        <param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts.">
-            <option value="No" selected="true">No</option>
-            <option value="Yes">Yes</option>
-        </param>
         <conditional name="reference_annotation">
             <param name="use_ref" type="select" label="Use Reference Annotation">
                 <option value="No" selected="true">No</option>