# HG changeset patch
# User yating-l
# Date 1529955579 14400
# Node ID 8bcec8dbb8bea076f091f206e0ff99c269fcd2a5
# Parent  6464399df918f1ea533f973b9cc325c6d394e334
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 0648e2769587d7fd544b3c6dacfa2b5c15a4c4a9

diff -r 6464399df918 -r 8bcec8dbb8be jbrowseArchiveCreator.xml
--- a/jbrowseArchiveCreator.xml	Wed Jun 20 17:43:26 2018 -0400
+++ b/jbrowseArchiveCreator.xml	Mon Jun 25 15:39:39 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.1">
+<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.2">
     <description>
         This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
     </description>
diff -r 6464399df918 -r 8bcec8dbb8be tracks/CanvasFeatures.py
--- a/tracks/CanvasFeatures.py	Wed Jun 20 17:43:26 2018 -0400
+++ b/tracks/CanvasFeatures.py	Mon Jun 25 15:39:39 2018 -0400
@@ -30,6 +30,8 @@
             track['urlTemplate'] = os.path.join('tracks', self.trackName)
         if 'glyph' in self.extraSettings:
             track['glyph'] = self.extraSettings['glyph']
+        if 'transcriptType' in self.extraSettings:
+            track['transcriptType'] = self.extraSettings['transcriptType']
         if 'subfeatureClasses' in self.extraSettings:
             track['subfeatureClasses'] = self.extraSettings['subfeatureClasses']
         track['label'] = self.trackLabel
diff -r 6464399df918 -r 8bcec8dbb8be util/subtools.py
--- a/util/subtools.py	Wed Jun 20 17:43:26 2018 -0400
+++ b/util/subtools.py	Mon Jun 25 15:39:39 2018 -0400
@@ -294,10 +294,11 @@
         bedSort(inputFile, sortedFile)
     elif "gff" in dataType:
         fileType = 'gff'
-        filteredFile = tempfile.NamedTemporaryFile(bufsize=0)
-        remove_gene_lines(inputFile, filteredFile.name)
+        #filteredFile = tempfile.NamedTemporaryFile(bufsize=0)
+        #remove_gene_lines(inputFile, filteredFile.name)
         sortedFile = tempfile.NamedTemporaryFile(bufsize=0)
-        gff3sort(filteredFile.name, sortedFile)
+        #gff3sort(filteredFile.name, sortedFile)
+        gff3sort(inputFile, sortedFile)
         # add .gff3.gz extension to Tabix GFF3 files, in order to enable creating name index with generate-names.pl
         trackName = trackName + '.gff3.gz'
     compressedFile = bgzip(sortedFile.name)