Mercurial > repos > yating-l > jbrowsearchivecreator
changeset 16:8bcec8dbb8be draft
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 0648e2769587d7fd544b3c6dacfa2b5c15a4c4a9
| author | yating-l |
|---|---|
| date | Mon, 25 Jun 2018 15:39:39 -0400 |
| parents | 6464399df918 |
| children | 315a40b0b694 |
| files | jbrowseArchiveCreator.xml tracks/CanvasFeatures.py util/subtools.py |
| diffstat | 3 files changed, 7 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- 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>
--- 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
--- 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)