# HG changeset patch
# User mvdbeek
# Date 1483707976 18000
# Node ID 370c325b5941d6c501e173f551564dad49f01767
# Parent  4a028613cfae52bcaabc24e7e057b516561d52a5
planemo upload for repository https://github.com/ListerLab/TEPID commit 48d24b91382cfbe7749d131657efbad47a28f569-dirty

diff -r 4a028613cfae -r 370c325b5941 tepid-discover.xml
--- a/tepid-discover.xml	Thu Jan 05 12:57:26 2017 -0500
+++ b/tepid-discover.xml	Fri Jan 06 08:06:16 2017 -0500
@@ -25,10 +25,14 @@
     -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 '$deletions_out' &&
-    mv insertion_reads_'$bowtie2_bam.element_identifier'.txt '$insertion_reads_out' &&
-    mv deletion_reads_'$bowtie2_bam.element_identifier'.txt '$deletion_reads_out' &&
+    #if not str($deletions)=="--deletions":
+        mv insertions_'$bowtie2_bam.element_identifier'.bed '$insertions_out' &&
+        mv insertion_reads_'$bowtie2_bam.element_identifier'.txt '$insertion_reads_out' &&
+    #end if
+    #if not str($insertions)=="--insertions":
+        mv deletions_'$bowtie2_bam.element_identifier'.bed '$deletions_out' &&
+        mv deletion_reads_'$bowtie2_bam.element_identifier'.txt '$deletion_reads_out' &&
+    #end if
     cat tepid_discover_log_'$bowtie2_bam.element_identifier'.txt
     ]]></command>
     <inputs>