# HG changeset patch
# User mvdbeek
# Date 1483637276 18000
# Node ID cea423bd0cd24ed6d0f324b2b9462507dca1ac20
# Parent  a5ef6470e54d881b905a41d16fba7120c1ac03b2
planemo upload for repository https://github.com/ListerLab/TEPID commit 40ee682fc4468bcdcc77f79a3bd098dc7f0019a7-dirty

diff -r a5ef6470e54d -r cea423bd0cd2 tepid-discover.xml
--- a/tepid-discover.xml	Thu Dec 15 08:33:53 2016 -0500
+++ b/tepid-discover.xml	Thu Jan 05 12:27:56 2017 -0500
@@ -8,6 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
     @LINK_CONC@
     tepid-discover
+    -n '$split_bam.element_identifier'
     $deletions
     $insertions
     $strict
@@ -20,8 +21,9 @@
     @PROC@
     @NAME@
     -c conc.bam
-    -s '$split_bam'
+    -s split.bam
     -t '$te_annotation_bed'
+    -k
     $se_mode &&  ## The follwing is terrible, but from_work_dir cannot deal with variables
     mv insertions_'$bowtie2_bam.element_identifier'.bed '$insertions_out' &&
     mv deletions_'$bowtie2_bam.element_identifier'.bed '$deletions_out' &&