# HG changeset patch
# User brinkmanlab
# Date 1604698012 0
# Node ID 258826db829182a52d463efec6da41a4275c114b
# Parent  5e94458c2ddea0331ec157c2d7ea4b950ce2c6ff
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 668759e2fc5d53432092d7c1395b402385733171"

diff -r 5e94458c2dde -r 258826db8291 all_fasta.xml
--- 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>
diff -r 5e94458c2dde -r 258826db8291 builds.sql
--- 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