# HG changeset patch
# User iuc
# Date 1496957498 14400
# Node ID 18be2d72fdeee69214bae12b5ed576167e09b4b1
# Parent  69c5e9c0add0e84c00dbc2bf46307b4fc6d769e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975

diff -r 69c5e9c0add0 -r 18be2d72fdee blastxml_to_gapped_gff3.py
--- a/blastxml_to_gapped_gff3.py	Thu Feb 09 12:36:16 2017 -0500
+++ b/blastxml_to_gapped_gff3.py	Thu Jun 08 17:31:38 2017 -0400
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env python
 import argparse
 import copy
 import logging
diff -r 69c5e9c0add0 -r 18be2d72fdee gff3_rebase.py
--- a/gff3_rebase.py	Thu Feb 09 12:36:16 2017 -0500
+++ b/gff3_rebase.py	Thu Jun 08 17:31:38 2017 -0400
@@ -170,8 +170,8 @@
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='rebase gff3 features against parent locations', epilog="")
-    parser.add_argument('parent', type=file, help='Parent GFF3 annotations')
-    parser.add_argument('child', help='Child GFF3 annotations to rebase against parent')
+    parser.add_argument('parent', type=argparse.FileType('r'), help='Parent GFF3 annotations')
+    parser.add_argument('child', type=argparse.FileType('r'), help='Child GFF3 annotations to rebase against parent')
     parser.add_argument('--interpro', action='store_true',
                         help='Interpro specific modifications')
     parser.add_argument('--protein2dna', action='store_true',
diff -r 69c5e9c0add0 -r 18be2d72fdee jbrowse.py
--- a/jbrowse.py	Thu Feb 09 12:36:16 2017 -0500
+++ b/jbrowse.py	Thu Jun 08 17:31:38 2017 -0400
@@ -472,6 +472,11 @@
             "storeClass": "JBrowse/Store/SeqFeature/BAM",
         })
 
+        # Apollo will only switch to the (prettier) 'bam-read' className if it's not set explicitly in the track config
+        # So remove the default 'feature' value for these bam tracks
+        if 'className' in trackData['style'] and trackData['style']['className'] == 'feature':
+            del trackData['style']['className']
+
         self._add_track_json(trackData)
 
         if bamOpts.get('auto_snp', 'false') == 'true':