Mercurial > repos > brinkmanlab > microbedb

comparison all_fasta.xml @ 8:7c2f036e13a7 draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 93c3e4d7bc06fd1595bc005081e89248561de56a"
author brinkmanlab
date Tue, 10 Nov 2020 00:15:03 +0000
parents 6ad04790da12
children b08b09342b92
comparison
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7:6ad04790da12 8:7c2f036e13a7
16 sqlite3 -readonly '$db' < '$sql' > '$output' 16 sqlite3 -readonly '$db' < '$sql' > '$output'
17 ]]></command> 17 ]]></command>
18 <configfiles> 18 <configfiles>
19 <configfile name="sql"><![CDATA[ 19 <configfile name="sql"><![CDATA[
20 #import os.path 20 #import os.path
21 SELECT json_object('data_tables', 21 SELECT json_object('data_tables', json_object(
22 json_object('all_fasta', json_group_array(json_object('value', unique_build_id, 'dbkey', dbkey, 'name', label, 'path', file_path))), 22 'all_fasta', json_group_array(json_object('value', unique_build_id, 'dbkey', dbkey, 'name', label, 'path', file_path))
23 #if $builds 23 #if $builds
24 json_object('__dbkeys__', json_group_array(json_object('value', dbkey, 'name', label, 'len_path', ''))), 24 ,'__dbkeys__', json_group_array(json_object('value', dbkey, 'name', label, 'len_path', ''))
25 #end if 25 #end if
26 ) FROM ( 26 )) FROM (
27 SELECT (r.rep_accnum || '.' || r.rep_version) AS unique_build_id, 27 SELECT (r.rep_accnum || '.' || r.rep_version) AS unique_build_id,
28 (r.rep_accnum || '_' || r.rep_version) AS dbkey, 28 (r.rep_accnum || '_' || r.rep_version) AS dbkey,
29 (REPLACE(r.definition, ', complete genome.', '') || ' [' || r.rep_accnum || '.' || r.rep_version || ']') AS label, 29 (REPLACE(r.definition, ', complete genome.', '') || ' [' || r.rep_accnum || '.' || r.rep_version || ']') AS label,
30 ('${os.path.dirname(str($db))}/' || genomeproject.gpv_directory || '/' || genomeproject.filename || '_genomic.fna') AS file_path 30 ('${os.path.dirname(str($db))}/' || genomeproject.gpv_directory || '/' || genomeproject.filename || '_genomic.fna') AS file_path
31 FROM genomeproject 31 FROM genomeproject