Mercurial > repos > brinkmanlab > microbedb
changeset 2:258826db8291 draft
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 668759e2fc5d53432092d7c1395b402385733171"
| author | brinkmanlab |
|---|---|
| date | Fri, 06 Nov 2020 21:26:52 +0000 |
| parents | 5e94458c2dde |
| children | 7b432c6ff465 |
| files | all_fasta.xml builds.sql |
| diffstat | 2 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/all_fasta.xml Fri Nov 06 18:00:31 2020 +0000 +++ b/all_fasta.xml Fri Nov 06 21:26:52 2020 +0000 @@ -14,14 +14,14 @@ <version_command>sqlite3 --version</version_command> <command><![CDATA[ #import os.path - sqlite3 -readonly $db '.param set :basepath ${os.path.dirname($db)}' '.read $__tool_directory__/all_fasta.sql' > '$output'; + sqlite3 -readonly $db '.param set :basepath ${os.path.dirname(str($db))}' '.read $__tool_directory__/all_fasta.sql' > '$output'; #if $builds sqlite3 -readonly $db < '$builds_sql' - #endif + #end if ]]></command> <configfiles> <configfile name="builds_sql"><![CDATA[ - #include $__tool_directory__/builds.sql + #include $__tool_directory__+"/builds.sql" ]]></configfile> </configfiles> <inputs>
--- a/builds.sql Fri Nov 06 18:00:31 2020 +0000 +++ b/builds.sql Fri Nov 06 21:26:52 2020 +0000 @@ -2,7 +2,7 @@ CREATE TEMP TABLE builds_temp(dbkey unique, label); .mode csv .separator ' ' -.import $__app__.config.builds_file_path builds_temp +.import '$__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 || @@ -15,5 +15,5 @@ AND r.rep_type = 'chromosome'; .mode list .separator ' ' -.once $__app__.config.builds_file_path +.once '$__app__.config.builds_file_path' SELECT dbkey, label FROM builds_temp ORDER BY dbkey; \ No newline at end of file