# HG changeset patch
# User mvdbeek
# Date 1499096179 14400
# Node ID c357862a2927f3160a7ab0a4311bd0aa827d78f4
# Parent  ff0fb6dde58ee1d7c557d8f92c0144c742e482ee
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty

diff -r ff0fb6dde58e -r c357862a2927 igv_make_screenshots.xml
--- a/igv_make_screenshots.xml	Mon Jul 03 10:58:06 2017 -0400
+++ b/igv_make_screenshots.xml	Mon Jul 03 11:36:19 2017 -0400
@@ -15,6 +15,7 @@
         cat '$load_session' > load_session.txt &&
         echo snapshotDirectory "\$PWD" >> load_session.txt &&
         cat load_session.txt '$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 &&
         cp '$igv_session' '$igv_session_out' &&
@@ -66,6 +67,7 @@
         ]]></configfile>
         <configfile name="load_session">
 load igv_session.xml
+preference SAM.SHOW_SOFT_CLIPPED $show_softclippped
         </configfile>
         <configfile name="exit_session">
 exit
@@ -84,9 +86,10 @@
                 </sanitizer>
             </param>
         </repeat>
+        <param name="show_softclippped" type="boolean" label="Show softclipped bases?" truevalue="true" falsevalue="false" checked="true"/>
         <param name="script_file" type="data" format="txt" label="Select a IGV script with regions for which to take screenshots"/>
-        <param name="width" label="Select the screenshot width" type="integer" min="640" value="1080"/>
-        <param name="height" label="Select the screenshot height" type="integer" min="800" value="1920"/>
+        <param name="width" label="Select the screenshot width" type="integer" min="800" value="1920"/>
+        <param name="height" label="Select the screenshot height" type="integer" min="640" value="1080"/>
     </inputs>
     <outputs>
         <data name="igv_session_out" format="xml"/>