# HG changeset patch
# User trinity_ctat
# Date 1530897174 14400
# Node ID 690a6696ce1172463175a18ddf76d6733163fe6b
# Parent  3e375492af68511d4e80717aedf6ade56d0c1319
Uploaded

diff -r 3e375492af68 -r 690a6696ce11 ctat_star_fusion.xml
--- a/ctat_star_fusion.xml	Thu Jul 05 11:56:35 2018 -0400
+++ b/ctat_star_fusion.xml	Fri Jul 06 13:12:54 2018 -0400
@@ -20,6 +20,7 @@
         --left_fq  "${left_input}"
         --right_fq "${right_input}"
         --output_dir subdir
+        --STAR_SortedByCoordinate
       ]]>
     </command>
 
@@ -36,8 +37,8 @@
 
     <outputs>
       <data format="txt" name="starfusion_log" label="${tool.name} on ${on_string}: log" from_work_dir="subdir/Log.out"/>
-      <data format="bam" name="aligned_bam" label="${tool.name} on ${on_string}: Aligned Bam" from_work_dir="subdir/std.STAR.bam"/>
-      <data format="tabular" name="candidates" label="${tool.name} on ${on_string}: Fusion candidates" from_work_dir="subdir/star-fusion.fusion_predictions.abridged.tsv"/>
+      <data format="bam" name="aligned_bam" label="${tool.name} on ${on_string}: Aligned Bam" from_work_dir="subdir/Aligned.sortedByCoord.out.bam"/>
+      <data format="tabular" name="candidates" label="${tool.name} on ${on_string}: Fusion candidates" from_work_dir="subdir/star-fusion.fusion_candidates.final.abridged"/>
       <data format="tabular" name="chimeric_junc" label="${tool.name} on ${on_string}: Chimeric.out.junction" from_work_dir="subdir/Chimeric.out.junction"/> 
     </outputs>
     <tests>