Mercurial > repos > iuc > jbrowse
changeset 14:18be2d72fdee draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
| author | iuc |
|---|---|
| date | Thu, 08 Jun 2017 17:31:38 -0400 |
| parents | 69c5e9c0add0 |
| children | 4e11a688a635 |
| files | blastxml_to_gapped_gff3.py gff3_rebase.py jbrowse.py |
| diffstat | 3 files changed, 8 insertions(+), 3 deletions(-) [+] |
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--- a/blastxml_to_gapped_gff3.py Thu Feb 09 12:36:16 2017 -0500 +++ b/blastxml_to_gapped_gff3.py Thu Jun 08 17:31:38 2017 -0400 @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env python import argparse import copy import logging
--- a/gff3_rebase.py Thu Feb 09 12:36:16 2017 -0500 +++ b/gff3_rebase.py Thu Jun 08 17:31:38 2017 -0400 @@ -170,8 +170,8 @@ if __name__ == '__main__': parser = argparse.ArgumentParser(description='rebase gff3 features against parent locations', epilog="") - parser.add_argument('parent', type=file, help='Parent GFF3 annotations') - parser.add_argument('child', help='Child GFF3 annotations to rebase against parent') + parser.add_argument('parent', type=argparse.FileType('r'), help='Parent GFF3 annotations') + parser.add_argument('child', type=argparse.FileType('r'), help='Child GFF3 annotations to rebase against parent') parser.add_argument('--interpro', action='store_true', help='Interpro specific modifications') parser.add_argument('--protein2dna', action='store_true',
--- a/jbrowse.py Thu Feb 09 12:36:16 2017 -0500 +++ b/jbrowse.py Thu Jun 08 17:31:38 2017 -0400 @@ -472,6 +472,11 @@ "storeClass": "JBrowse/Store/SeqFeature/BAM", }) + # Apollo will only switch to the (prettier) 'bam-read' className if it's not set explicitly in the track config + # So remove the default 'feature' value for these bam tracks + if 'className' in trackData['style'] and trackData['style']['className'] == 'feature': + del trackData['style']['className'] + self._add_track_json(trackData) if bamOpts.get('auto_snp', 'false') == 'true':