# HG changeset patch
# User fubar
# Date 1376351773 14400
# Node ID f81bf1f1d9249a518f5ac5bae1f1bd4ec98916ce
# Parent  94c94e25d61ccf11a81bb9cdf0e7894fa5db920f
Uploaded

diff -r 94c94e25d61c -r f81bf1f1d924 rgrnastar/rg_rnaStar.xml
--- a/rgrnastar/rg_rnaStar.xml	Mon Aug 12 05:18:07 2013 -0400
+++ b/rgrnastar/rg_rnaStar.xml	Mon Aug 12 19:56:13 2013 -0400
@@ -18,18 +18,14 @@
     #if $singlePaired.sPaired == "paired"
             $singlePaired.input2
         #end if
-
         --runThreadN 4
-
-    ## Parameters.
-    --outSAMattributes "$outSAMattributes"
     #if $params.settingsType == "full":
         --chimSegmentMin $params.chim_segment_min
         --chimScoreMin $params.chim_score_min
     #end if
 
     ## may or may not need to generate SAM tags and handle non-canonicals for Cufflinks tools.
-    ${outSAMstrandField} $outFilterIntronMotifs}
+    ${outSAMstrandField} ${outFilterIntronMotifs} ${outSAMattributes}
 
     ;
 
@@ -91,8 +87,8 @@
             </when>
         </conditional>
             <param name="outSAMattributes" type="select" label="Include extra sam attributes for downstream processing">
-              <option value="Standard">Standard - eg for old Samtools downstream</option>
-              <option value="All" selected="true">All modern Samtools attributes - see below</option>
+              <option value="--outSAMattributes Standard">Standard - eg for old Samtools downstream</option>
+              <option value="--outSAMattributes All" selected="true">All modern Samtools attributes - see below</option>
             </param>
             <param name="outSAMstrandField" type="select" label="Include extra sam attributes for downstream processing">
               <option value="--outSAMstrandField intronMotif" selected="true">Add XS for cufflinks</option>