Mercurial > repos > brinkmanlab > microbedb

annotate all_fasta.sql @ 6:b7884a377566 draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 7ea4cbe9a0f7347379e245223cc2c40021c586f9"
author brinkmanlab
date Mon, 09 Nov 2020 18:37:30 +0000
parents 40d14d5c8125
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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6
b7884a377566 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 7ea4cbe9a0f7347379e245223cc2c40021c586f9"
brinkmanlab
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diff changeset
1 SELECT json_object('data_tables', json_object('all_fasta', json_group_array(json_object('value', unique_build_id, 'dbkey', dbkey, 'name', label, 'path', file_path))))
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40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
parents:
diff changeset
2 FROM (
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
parents:
diff changeset
3 SELECT (r.rep_accnum || '.' || r.rep_version) AS unique_build_id,
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
parents:
diff changeset
4 (r.rep_accnum || '_' || r.rep_version) AS dbkey,
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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5 (REPLACE(r.definition, ', complete genome.', '') || ' [' || r.rep_accnum || '.' || r.rep_version ||
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
parents:
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6 ']') AS label,
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
parents:
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7 (:basepath || '/' || genomeproject.gpv_directory || '/' || genomeproject.filename || '_genomic.fna') AS file_path
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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8 FROM genomeproject
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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9 JOIN replicon r ON genomeproject.gpv_id = r.gpv_id AND r.rep_type = 'chromosome'
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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10 WHERE genomeproject.version_id = (SELECT version_id FROM version WHERE is_current == 1)
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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11 AND genomeproject.file_types IS NOT NULL
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
parents:
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12 AND genomeproject.file_types LIKE '%.fna%'
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
parents:
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13 AND r.rep_type = 'chromosome'
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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14 )