# HG changeset patch
# User brinkmanlab
# Date 1604091887 0
# Node ID 40d14d5c8125188c997dc24ce11a1ebac784bb2d
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
diff -r 000000000000 -r 40d14d5c8125 all_fasta.sql
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.sql Fri Oct 30 21:04:47 2020 +0000
@@ -0,0 +1,14 @@
+SELECT json_group_array(json_object('value', unique_build_id, 'dbkey', dbkey, 'name', label, 'path', file_path))
+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,
+ (:basepath || '/' || 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
+ AND genomeproject.file_types LIKE '%.fna%'
+ AND r.rep_type = 'chromosome'
+)
\ No newline at end of file
diff -r 000000000000 -r 40d14d5c8125 all_fasta.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.xml Fri Oct 30 21:04:47 2020 +0000
@@ -0,0 +1,50 @@
+
+ Load all fasta files from MicrobeDB into the all_fasta data table
+
+ topic_3301
+ topic_0080
+ topic_0091
+
+
+ operation_2422
+
+
+ sqlite
+
+ sqlite3 --version
+ '$output';
+ #if $builds
+ sqlite3 -readonly $db < '$builds_sql'
+ #endif
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1093/bioinformatics/bts273
+
+
diff -r 000000000000 -r 40d14d5c8125 builds.sql
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/builds.sql Fri Oct 30 21:04:47 2020 +0000
@@ -0,0 +1,19 @@
+DROP TABLE IF EXISTS builds_temp;
+CREATE TEMP TABLE builds_temp(dbkey unique, label);
+.mode csv
+.separator ' '
+.import $__app__.config.builds_file_path builds_temp
+INSERT OR REPLACE INTO builds_temp (dbkey, label)
+SELECT (r.rep_accnum || '_' || r.rep_version) AS dbkey,
+ (REPLACE(r.definition, ', complete genome.', '') || ' [' || r.rep_accnum || '.' || r.rep_version ||
+ ']') AS label
+FROM genomeproject
+ JOIN replicon r ON genomeproject.gpv_id = r.gpv_id AND r.rep_type = 'chromosome'
+WHERE genomeproject.version_id = (SELECT MAX(version_id) FROM version)
+ AND genomeproject.file_types IS NOT NULL
+ AND genomeproject.file_types LIKE '%.fna%'
+ AND r.rep_type = 'chromosome';
+.mode list
+.separator ' '
+.once $__app__.config.builds_file_path
+SELECT dbkey, label FROM builds_temp ORDER BY dbkey;
\ No newline at end of file
diff -r 000000000000 -r 40d14d5c8125 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Fri Oct 30 21:04:47 2020 +0000
@@ -0,0 +1,16 @@
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 40d14d5c8125 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Oct 30 21:04:47 2020 +0000
@@ -0,0 +1,6 @@
+
+
+ value, dbkey, name, path
+
+
+
\ No newline at end of file