# HG changeset patch
# User geert-vandeweyer
# Date 1406897312 14400
# Node ID 1312bf8f5e172a77bc2acdb7faa7c80820d0fe09
# Parent  e6da12b2440efd35ac807c0fac819b80796f0c48
Uploaded

diff -r e6da12b2440e -r 1312bf8f5e17 cufflinks_wrapper.xml
--- a/cufflinks_wrapper.xml	Fri Aug 01 08:26:48 2014 -0400
+++ b/cufflinks_wrapper.xml	Fri Aug 01 08:48:32 2014 -0400
@@ -8,7 +8,6 @@
     <command interpreter="python">
         cufflinks_wrapper.py 
             --input=$input
-            --library-type=$library_type
             --assembled-isoforms-output=$assembled_isoforms
             --num-threads="\${GALAXY_SLOTS:-4}"
             -I $max_intron_len
@@ -87,7 +86,7 @@
             <when value="No"></when>
             <when value="Use reference annotation">
                 <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/>
-		<param name="compatible_hits_norm" type="select" label="Count hits compatible with reference RNAs only" help="With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped hits used in the FPKM denominator. This option can be combined with -N/--upper-quartile-norm. It is inactive by default, and can only be used in combination with --GTF.">
+		<param name="compatible_hits_norm" type="select" label="Count hits compatible with reference RNAs only" help="With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped hits used in the FPKM denominator. This option can only be used in combination with --GTF.">
 			<option value="" selected="True">No</option>
 			<option value="--compatible-hits-norm">Yes</option>
 		</param>