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annotate cummeRbund_options.py @ 6:c3b54a4b7741 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 20:25:47 -0400
parents ac2ebc60ef5d
children
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ac2ebc60ef5d Uploaded corrected dynamic options
devteam
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1 import sqlite3
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587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
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c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 2
diff changeset
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c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 2
diff changeset
4 def get_genes(database_path):
c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 2
diff changeset
5 conn = sqlite3.connect(database_path)
c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 2
diff changeset
6 gene_ids = conn.execute('SELECT gene_short_name, gene_id FROM genes ORDER BY gene_short_name')
c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 2
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7 return [(gene_id[0], gene_id[1], False) for gene_id in gene_ids]
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587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
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c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 2
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c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 2
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10 def get_samples(database_path):
c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 2
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11 conn = sqlite3.connect(database_path)
c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 2
diff changeset
12 samples = conn.execute('SELECT sample_name FROM samples ORDER BY sample_name')
c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 2
diff changeset
13 return [(sample[0], sample[0], False) for sample in samples]