# HG changeset patch
# User fubar
# Date 1719125996 0
# Node ID a074cd6b590545d222b0bc6110c11e5ae72e2a9c
# Parent  0082924757b094746b020ca696eedb0e4fd5cf91
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty

diff -r 0082924757b0 -r a074cd6b5905 jbrowse2.py
--- a/jbrowse2.py	Sun Jun 23 02:06:21 2024 +0000
+++ b/jbrowse2.py	Sun Jun 23 06:59:56 2024 +0000
@@ -1352,7 +1352,7 @@
                             % (tId, style_data)
                         )
 
-                    if style_data.get('type',None):
+                    if style_data.get('type',None) == None:
                         style_data["type"] = "LinearBasicDisplay"
                     if "displays" in track_conf:
                         disp = track_conf["displays"][0]["type"]
diff -r 0082924757b0 -r a074cd6b5905 jbrowse2.xml
--- a/jbrowse2.xml	Sun Jun 23 02:06:21 2024 +0000
+++ b/jbrowse2.xml	Sun Jun 23 06:59:56 2024 +0000
@@ -1149,8 +1149,9 @@
 Use and local viewing
 =====================
 
-All tracks have a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks.
-There are 10 Galaxy datatypes that can be turned into a track for display - in all cases, the selected reference genome must have been 
+Browser tracks need a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks.
+
+At present, 10 Galaxy datatypes that can be turned into a track for display - in all cases, the selected reference genome must have been 
 used to generate the data:
 
     bam
@@ -1164,8 +1165,7 @@
     paf
     vcf
 
-cram and bam will be large, so very slow amd are only recommended if you need the cigar annotation. 
-Otherwise conversion to bed is recommended to slim them down. 
+Note that cram and bam will be large, so very slow amd are only recommended if you need the cigar annotation. Otherwise conversion to bed is recommended to slim them down. 
 Unfortunately if you have millions of rows in a bed, it will also be very slow - in which case a bigwig is recommended. 
 
 A JBrowse2 history item can be opened by viewing it (the "eye" icon).