Mercurial > repos > brinkmanlab > microbedb

diff all_fasta.xml @ 10:2f6ef3a184df draft default tip

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 12aaf041d3d5a052c6a3f3aa7f3177591e3b19bf"
author brinkmanlab
date Sat, 16 Jan 2021 03:05:14 +0000
parents b08b09342b92
children
line wrap: on
line diff
--- a/all_fasta.xml	Fri Dec 04 20:07:41 2020 +0000
+++ b/all_fasta.xml	Sat Jan 16 03:05:14 2021 +0000
@@ -26,11 +26,11 @@
             )) FROM (
              SELECT (r.rep_accnum || '.' || r.rep_version) AS unique_build_id,
                     (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
+                    (REPLACE(REPLACE(r.definition, ', complete sequence.', ''), ', complete genome.', '') || ' [' || r.rep_accnum || '.' || r.rep_version || ']') AS label,
+                    ('${os.path.dirname(str($db))}/' || genomeproject.gpv_directory || '/' || r.file_name || '.fna') AS file_path
              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%'
+             WHERE r.file_types IS NOT NULL
+               AND r.file_types LIKE '%.fna%'
                AND r.rep_type = 'chromosome'
             )
         ]]></configfile>