Mercurial > repos > yating-l > jbrowsearchivecreator
changeset 17:315a40b0b694 draft
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 891eca7a697643c9b5365781bbab5b655972ffdc
| author | yating-l |
|---|---|
| date | Mon, 25 Jun 2018 16:05:01 -0400 |
| parents | 8bcec8dbb8be |
| children | 79b23a8afb15 |
| files | jbrowseArchiveCreator.xml tracks/CanvasFeatures.py util/subtools.py |
| diffstat | 3 files changed, 4 insertions(+), 7 deletions(-) [+] |
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--- 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>
--- 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
--- 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)