Mercurial > repos > yating-l > jbrowsearchivecreator
changeset 18:79b23a8afb15 draft
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 398c2fd8d1cb38decddf8cd58574cf39b1b52eaa
| author | yating-l |
|---|---|
| date | Fri, 20 Jul 2018 12:25:36 -0400 |
| parents | 315a40b0b694 |
| children | 62dee5369e80 |
| files | TrackHub.py jbrowseArchiveCreator.xml util/subtools.py |
| diffstat | 3 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/TrackHub.py Mon Jun 25 16:05:01 2018 -0400 +++ b/TrackHub.py Fri Jul 20 12:25:36 2018 -0400 @@ -106,9 +106,8 @@ subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath) def _indexName(self): - if self.nameIndexTrackList: - subtools.generate_names(self.mySpecieFolderPath, self.nameIndexTrackList) - print "finished name index \n" + subtools.generate_names(self.mySpecieFolderPath, self.nameIndexTrackList) + print "finished name index \n" def _outHtml(self): mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
--- a/jbrowseArchiveCreator.xml Mon Jun 25 16:05:01 2018 -0400 +++ b/jbrowseArchiveCreator.xml Fri Jul 20 12:25:36 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/util/subtools.py Mon Jun 25 16:05:01 2018 -0400 +++ b/util/subtools.py Fri Jul 20 12:25:36 2018 -0400 @@ -384,8 +384,9 @@ def generate_names(outputFolder, nameIndexTrackList, hashBits=4): array_call = ['generate-names.pl', '--hashBits', str(hashBits), '-v', '--completionLimit', '0', '--out', outputFolder] - array_call.append('--tracks') - array_call.append(','.join(nameIndexTrackList)) + if nameIndexTrackList: + array_call.append('--tracks') + array_call.append(','.join(nameIndexTrackList)) p = _handleExceptionAndCheckCall(array_call) return p