# HG changeset patch
# User alenail
# Date 1459796742 14400
# Node ID a92644537c7d53247a5253bc2372a1b39d81bb3c
# Parent  1c6c8591f76011c38bed7e4018ef1b4c9baece29
Uploaded

diff -r 1c6c8591f760 -r a92644537c7d chipsequtil/._map_to_known_genes.py
Binary file chipsequtil/._map_to_known_genes.py has changed
diff -r 1c6c8591f760 -r a92644537c7d chipsequtil/._map_to_known_genes.xml
Binary file chipsequtil/._map_to_known_genes.xml has changed
diff -r 1c6c8591f760 -r a92644537c7d chipsequtil/map_to_known_genes.xml
--- a/chipsequtil/map_to_known_genes.xml	Mon Apr 04 15:02:08 2016 -0400
+++ b/chipsequtil/map_to_known_genes.xml	Mon Apr 04 15:05:42 2016 -0400
@@ -10,10 +10,10 @@
   <command interpreter="python">
     map_to_known_genes.py
       $tss
+      --peaks-format=$peaks_fmt
       --upstream-window=$upst_win
       --downstream-window=$dnst_win
-      --map-output=$peaksOutput
-      --peaks-format=$peaks_fmt
+      --map-output="$peaksOutput"
       $detail
       $intergenic
       $knownGeneFile $knownGeneRef $macsPeaksFile
@@ -38,7 +38,7 @@
     <param name="intergenic" checked="false" label="Write intergenic peaks to the gene file as well with None as gene ID" type="boolean" truevalue="--intergenic" falsevalue="" help="" />
   </inputs>
   <outputs>
-    <data format="txt" hidden="false" name="peaksOutput"/>
+    <data name="peaksOutput" format="txt" hidden="false" />
   </outputs>
   <help></help>
 </tool>