# HG changeset patch
# User m-zytnicki
# Date 1491924413 14400
# Node ID fc9d40c697e8132e6253d1ba3af48b5ef3e72023
# Parent  87c5fa8651c1ddab7b0fc0157ef2581817ac4a2f
Uploaded

diff -r 87c5fa8651c1 -r fc9d40c697e8 mmquant.xml
--- a/mmquant.xml	Wed Feb 15 06:03:00 2017 -0500
+++ b/mmquant.xml	Tue Apr 11 11:26:53 2017 -0400
@@ -6,7 +6,7 @@
         <exit_code range="1:" />
     </stdio>
 	<command><![CDATA[
-        mmquant
+        mmquant_static
 			-a "$annotation"
 			-r
 			#for $r in $reads_info
@@ -20,6 +20,10 @@
 			#for $r in $reads_info
 				${r.strand}
 			#end for
+			-t
+			#for $r in $reads_info
+				${r.sorted}
+			#end for
 			-n
 			#for $r in $reads_info
 				${r.name}
@@ -44,6 +48,10 @@
 				<option value="F">forward (for single-end reads)</option>
 				<option value="R">reverse (for single-end reads)</option>
 			</param>
+			<param name="sorted" type="select" label="Sorted" multiple="false" >
+				<option value="Y" selected="yes">yes</option>
+				<option value="N">no</option>
+			</param>
 		</repeat>
 		<param name="overlap" type="float" value="-1" label="Overlap type" help="&lt;0: read is included, &lt;1: overlap, otherwise: # nt" />
         <param name="gene_name" type="boolean" label="Print gene name instead of IDs" truevalue="-g" falsevalue="" help="use gene name instead of gene ID in the output file" />
@@ -78,16 +86,6 @@
 
 .. _article: http://www.genomebiology.com/2015/16/1/177
 
-**Strands**
-
-Strands can be:
-
-* for paired-end reads: ``U`` (unknown), ``FR`` (forward-reverse), ``RF`` (reverse-forward), ``FF`` (forward-forward);
-
-* for single-end reads: ``U`` (unknown), ``F`` (forward), ``R`` (reverse);
-
-* Default: ``U``.
-
 
 **Annotation file**