# HG changeset patch
# User mvdbeek
# Date 1499086288 14400
# Node ID a4877f60773a1ad7127d9c44293734b96f6296cc
# Parent  f44435b6ad19b8f4795e1b72188630218b0d8255
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty

diff -r f44435b6ad19 -r a4877f60773a igv_make_screenshots.xml
--- a/igv_make_screenshots.xml	Mon Jul 03 08:46:22 2017 -0400
+++ b/igv_make_screenshots.xml	Mon Jul 03 08:51:28 2017 -0400
@@ -5,8 +5,7 @@
     <command detect_errors="exit_code"><![CDATA[
         #for $inputsection in $inputfiles
             #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
-            #set $abspath=os.path.abspath($path)
-            sed -i.bak -e 's|$path|$abspath|g' '$igv_session' &&
+            sed -i.bak -e 's|$path|$PWD/$path|g' '$igv_session' &&
             ln -fs $inputsection.input $path &&
             #if $inputsection.input.is_of_type('bam')
                 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&