Mercurial > repos > brinkmanlab > microbedb

comparison all_fasta.xml @ 9:b08b09342b92 draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 8cc0daf7f7ce6a49483c9152bccd53d66a00f707"
author brinkmanlab
date Fri, 04 Dec 2020 20:07:41 +0000
parents 7c2f036e13a7
children 2f6ef3a184df
comparison
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8:7c2f036e13a7 9:b08b09342b92
1 <tool id="microbedb_all_fasta" name="MicrobeDB All FASTA" version="1.0" tool_type="manage_data" profile="18.09"> 1 <tool id="microbedb_all_fasta" name="MicrobeDB All FASTA" version="1.1" tool_type="manage_data" profile="18.09">
2 <description>Load all fasta files from MicrobeDB into the all_fasta data table</description> 2 <description>Load all fasta files from MicrobeDB into the all_fasta data table</description>
3 <edam_topics> 3 <edam_topics>
4 <edam_topic>topic_3301</edam_topic> 4 <edam_topic>topic_3301</edam_topic>
5 <edam_topic>topic_0080</edam_topic> 5 <edam_topic>topic_0080</edam_topic>
6 <edam_topic>topic_0091</edam_topic> 6 <edam_topic>topic_0091</edam_topic>
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 JOIN replicon r ON genomeproject.gpv_id = r.gpv_id AND r.rep_type = 'chromosome'
32 JOIN replicon r ON genomeproject.gpv_id = r.gpv_id AND r.rep_type = 'chromosome' 32 WHERE genomeproject.file_types IS NOT NULL
33 WHERE genomeproject.version_id = (SELECT version_id FROM version WHERE is_current == 1)
34 AND genomeproject.file_types IS NOT NULL
35 AND genomeproject.file_types LIKE '%.fna%' 33 AND genomeproject.file_types LIKE '%.fna%'
36 AND r.rep_type = 'chromosome' 34 AND r.rep_type = 'chromosome'
37 ) 35 )
38 ]]></configfile> 36 ]]></configfile>
39 </configfiles> 37 </configfiles>