Mercurial > repos > mvdbeek > tepid_discover

changeset 1:cea423bd0cd2 draft

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planemo upload for repository https://github.com/ListerLab/TEPID commit 40ee682fc4468bcdcc77f79a3bd098dc7f0019a7-dirty
author mvdbeek
date Thu, 05 Jan 2017 12:27:56 -0500
parents a5ef6470e54d
children 4a028613cfae
files tepid-discover.xml
diffstat 1 files changed, 3 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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' &&