Mercurial > repos > gga > jbrowse_to_container

annotate jbrowse_to_container.py @ 0:9956a177595f draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:38:47 -0400
parents
children b6bc8f5e1fdb
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9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
1 #!/usr/bin/env python
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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2 from __future__ import print_function
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
4 import argparse
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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5 import base64
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
8 if __name__ == '__main__':
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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9 parser = argparse.ArgumentParser(description='Generates an iframe to access a jbrowse instance')
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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10 parser.add_argument('external_jbrowse_url', help='Jbrowse full URL')
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
12 args = parser.parse_args()
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
14 # This is base64 encoded to get past the toolshed's filters.
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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15 HTML_TPL = """
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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16 PGh0bWw+PGhlYWQ+PHRpdGxlPkVtYmVkZGVkIEpCcm93c2UgQWNjZXNzPC90aXRsZT48c3R5bGUg
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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17 dHlwZT0idGV4dC9jc3MiPmJvZHkge3ttYXJnaW46IDA7fX0gaWZyYW1lIHt7Ym9yZGVyOiAwO3dp
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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18 ZHRoOiAxMDAlO2hlaWdodDogMTAwJX19PC9zdHlsZT48L2hlYWQ+PGJvZHk+PGlmcmFtZSBzcmM9
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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19 IntiYXNlX3VybH0iPjwvaWZyYW1lPjwvYm9keT48L2h0bWw+DQo=
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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20 """
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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21 HTML_TPL = base64.b64decode(HTML_TPL.replace('\n', ''))
9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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9956a177595f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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23 print(HTML_TPL.format(base_url=args.external_jbrowse_url))