Mercurial > repos > brinkmanlab > microbedb
diff all_fasta.xml @ 9:b08b09342b92 draft
"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 |
line wrap: on
line diff
--- a/all_fasta.xml Tue Nov 10 00:15:03 2020 +0000 +++ b/all_fasta.xml Fri Dec 04 20:07:41 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="microbedb_all_fasta" name="MicrobeDB All FASTA" version="1.0" tool_type="manage_data" profile="18.09"> +<tool id="microbedb_all_fasta" name="MicrobeDB All FASTA" version="1.1" tool_type="manage_data" profile="18.09"> <description>Load all fasta files from MicrobeDB into the all_fasta data table</description> <edam_topics> <edam_topic>topic_3301</edam_topic> @@ -28,10 +28,8 @@ (r.rep_accnum || '_' || r.rep_version) AS dbkey, (REPLACE(r.definition, ', complete genome.', '') || ' [' || r.rep_accnum || '.' || r.rep_version || ']') AS label, ('${os.path.dirname(str($db))}/' || genomeproject.gpv_directory || '/' || genomeproject.filename || '_genomic.fna') AS file_path - FROM genomeproject - JOIN replicon r ON genomeproject.gpv_id = r.gpv_id AND r.rep_type = 'chromosome' - WHERE genomeproject.version_id = (SELECT version_id FROM version WHERE is_current == 1) - AND genomeproject.file_types IS NOT NULL + FROM genomeproject JOIN replicon r ON genomeproject.gpv_id = r.gpv_id AND r.rep_type = 'chromosome' + WHERE genomeproject.file_types IS NOT NULL AND genomeproject.file_types LIKE '%.fna%' AND r.rep_type = 'chromosome' )