# HG changeset patch
# User yating-l
# Date 1524974371 14400
# Node ID 627cce51523fc80e34f3cbcc4ee1cad71113dd57
# Parent  b1553f2a4942af3744879e3905be7829555f8288
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 2285eddcfe689d70d89571a045f204b74cc6890c-dirty

diff -r b1553f2a4942 -r 627cce51523f jbrowseArchiveCreator.xml
--- a/jbrowseArchiveCreator.xml	Fri Apr 20 12:29:32 2018 -0400
+++ b/jbrowseArchiveCreator.xml	Sat Apr 28 23:59:31 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.1.1">
+<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.1.2">
     <description>
         This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
     </description>
@@ -7,6 +7,7 @@
     </macros>
     <requirements>
         <requirement type="package" version="1.2">samtools</requirement>
+        <requirement type="package" version="2.6">tabix</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
         <requirement type="package" version="1.68">biopython</requirement>
         <requirement type="package" version="340">ucsc_hac</requirement>
diff -r b1553f2a4942 -r 627cce51523f tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Apr 20 12:29:32 2018 -0400
+++ b/tool_dependencies.xml	Sat Apr 28 23:59:31 2018 -0400
@@ -4,6 +4,10 @@
         <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 
+    <package name="tabix" version="2.6">
+        <repository changeset_revision="54f8b9bf9b6c" name="package_tabix_0_2_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
     <package name="ucsc_hac" version="340">
         <repository changeset_revision="c6311d9e2443" name="package_ucsc_hac_340" owner="yating-l" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
diff -r b1553f2a4942 -r 627cce51523f tracks/CanvasFeatures.py
--- a/tracks/CanvasFeatures.py	Fri Apr 20 12:29:32 2018 -0400
+++ b/tracks/CanvasFeatures.py	Sat Apr 28 23:59:31 2018 -0400
@@ -24,7 +24,10 @@
         track['type'] = 'JBrowse/View/Track/' + self.trackType
         track['storeClass'] = 'JBrowse/Store/SeqFeature/GFF3Tabix'
         if self.dataType == 'gff':
+            # need .gff3.gz extension to index the name of the track with generate-name.pl
             track['urlTemplate'] = os.path.join('tracks', self.trackName + '.gff3.gz')
+            # needed to show match_part in Blat and Blast alignment as subfeatures
+            track['glyph'] = "JBrowse/View/FeatureGlyph/Segments"
         else:
             track['urlTemplate'] = os.path.join('tracks', self.trackName)
         track['label'] = self.trackLabel