# HG changeset patch
# User yhoogstrate
# Date 1393832859 18000
# Node ID 70292f11ba10d59cd4966fc0ad3993b63fb574f8
# Parent  c55c0c51b63466fc6701f8c25bc3327d48c557d4
Uploaded

diff -r c55c0c51b634 -r 70292f11ba10 featurecounts_valid_gff.xml
--- a/featurecounts_valid_gff.xml	Fri Feb 28 07:26:46 2014 -0500
+++ b/featurecounts_valid_gff.xml	Mon Mar 03 02:47:39 2014 -0500
@@ -50,6 +50,7 @@
 						$extended_parameters.summarization_level
 						$extended_parameters.contribute_to_multiple_features
 						$extended_parameters.protocol
+						$extended_parameters.multimapping_counts
 						-Q $extended_parameters.mapping_quality
 						$extended_parameters.fragment_counting
 						$extended_parameters.check_distance
@@ -164,7 +165,7 @@
 					<option value=" -s 2">Stranded (reverse)</option>
 				</param>
 				
-				<param name="multimaping_counts" type="boolean" truevalue=" -M" falsevalue="" label="Count multi-mapping reads/fragments" help="If specified, multi-mapping reads/fragments will be counted (ie. a multi-mapping read will be counted up to N times if it has N reported mapping locations). The program uses the `NH' tag to find multi-mapping reads." />
+				<param name="multimapping_counts" type="boolean" truevalue=" -M" falsevalue="" label="Count multi-mapping reads/fragments" help="If specified, multi-mapping reads/fragments will be counted (ie. a multi-mapping read will be counted up to N times if it has N reported mapping locations). The program uses the `NH' tag to find multi-mapping reads." />
 				
 				<param name="mapping_quality" type="integer" value="0" label="Minimum read quality" help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default." />