Mercurial > repos > mvdbeek > igv_take_screenshots

diff igv_make_screenshots.xml @ 11:64eb1ffd7872 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
author mvdbeek
date Mon, 03 Jul 2017 12:10:06 -0400
parents afb3f4c224d4
children 9dca6aa224a2
line wrap: on
line diff
--- a/igv_make_screenshots.xml	Mon Jul 03 11:42:19 2017 -0400
+++ b/igv_make_screenshots.xml	Mon Jul 03 12:10:06 2017 -0400
@@ -17,7 +17,7 @@
         cat load_session.txt '$script_file' '$exit_session' > igv_script.txt &&
         ## gives the cluster a bit of time to actually create the symlinks ... ughs
         sleep 10s &&
-        python $__tool_directory__/xvfb_igv.py igv_script.txt $width,$height &&
+        python $__tool_directory__/xvfb_igv.py igv_script.txt '$igv_preferences' $width,$height &&
         cp '$igv_session' '$igv_session_out' &&
         zip screenshots.zip *.png &&
         cp screenshots.zip '$screenshots_out'
@@ -67,11 +67,13 @@
         ]]></configfile>
         <configfile name="load_session">
 load igv_session.xml
-preference SAM.SHOW_SOFT_CLIPPED str($show_softclippped)
         </configfile>
         <configfile name="exit_session">
 exit
         </configfile>
+        <configfile name="igv_preferences">
+SAM.SHOW_SOFT_CLIPPED=str($show_softclippped)
+        </configfile>
     </configfiles>
     <inputs>
         <repeat name="inputfiles" min="1" title="Add tracks">