# HG changeset patch
# User mvdbeek
# Date 1527177087 14400
# Node ID 5b8781514bc1a963c8fd3c8e703825ec034e961a
# Parent  4fdf606153df8c287d962b420f5548059300fb15
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 63220935ba51b0b5480da88017d58616bf671337-dirty

diff -r 4fdf606153df -r 5b8781514bc1 filter_insertions.xml
--- a/filter_insertions.xml	Thu May 24 11:05:38 2018 -0400
+++ b/filter_insertions.xml	Thu May 24 11:51:27 2018 -0400
@@ -7,12 +7,14 @@
     <command detect_errors="aggressive"><![CDATA[
         ln -fs $putative_insertions putative_insertions.gff &&
         ln -fs $all_insertions all_insertions.gff &&
-        ln -fs $all_controls all_controls_path.gff &&
+        #for i, p in enumerate($all_controls)
+            ln -fs '$p' all_controls_${i}.gff &&
+        #end for
         confirm_insertions
         --putative_insertions_path putative_insertions.gff
         --all_treatments_path all_insertions.gff
-        #for p in $all_controls
-            --all_controls_paths '$p'
+        #for i, p in enumerate($all_controls)
+            --all_controls_paths all_controls_${i}.gff
         #end for
         --output_path '$output'
         $output_discard