# HG changeset patch
# User yating-l
# Date 1529957101 14400
# Node ID 315a40b0b69436ba17b0f26a592813931595ad84
# Parent  8bcec8dbb8bea076f091f206e0ff99c269fcd2a5
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 891eca7a697643c9b5365781bbab5b655972ffdc

diff -r 8bcec8dbb8be -r 315a40b0b694 jbrowseArchiveCreator.xml
--- a/jbrowseArchiveCreator.xml	Mon Jun 25 15:39:39 2018 -0400
+++ b/jbrowseArchiveCreator.xml	Mon Jun 25 16:05:01 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.2">
+<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.1">
     <description>
         This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
     </description>
diff -r 8bcec8dbb8be -r 315a40b0b694 tracks/CanvasFeatures.py
--- a/tracks/CanvasFeatures.py	Mon Jun 25 15:39:39 2018 -0400
+++ b/tracks/CanvasFeatures.py	Mon Jun 25 16:05:01 2018 -0400
@@ -30,8 +30,6 @@
             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 8bcec8dbb8be -r 315a40b0b694 util/subtools.py
--- a/util/subtools.py	Mon Jun 25 15:39:39 2018 -0400
+++ b/util/subtools.py	Mon Jun 25 16:05:01 2018 -0400
@@ -294,11 +294,10 @@
         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(inputFile, sortedFile)
+        gff3sort(filteredFile.name, 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)