Mercurial > repos > fubar > rgrnastar_203e

changeset 12:f81bf1f1d924 draft

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Uploaded
author fubar
date Mon, 12 Aug 2013 19:56:13 -0400
parents 94c94e25d61c
children 9f65a7b3abeb
files rgrnastar/rg_rnaStar.xml
diffstat 1 files changed, 3 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- 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>