Mercurial > repos > jjohnson > sqlite_to_tabular
diff sqlite_to_tabular.xml @ 3:f079ea3884b3 draft default tip
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
author | jjohnson |
---|---|
date | Thu, 21 Jan 2016 09:34:45 -0500 |
parents | bc50a7b7f246 |
children |
line wrap: on
line diff
--- a/sqlite_to_tabular.xml Sun Oct 04 10:51:12 2015 -0400 +++ b/sqlite_to_tabular.xml Thu Jan 21 09:34:45 2016 -0500 @@ -4,19 +4,18 @@ <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> + <command interpreter="python"><![CDATA[ + sqlite_to_tabular.py + --sqlitedb="$sqlitedb" + --query_file="$query_file" + $no_header + --output="$query_results" + ]]></command> <configfiles> <configfile name="query_file"> $sqlquery </configfile> </configfiles> - - <command interpreter="python"> - sqlite_to_tabular.py - --sqlitedb="$sqlitedb" - --query_file="$query_file" - $no_header - --output="$query_results" - </command> <inputs> <param name="sqlitedb" type="data" format="sqlite" label="SQLite Database"/> <param name="sqlquery" type="text" area="True" size="120x20" label="SQL query"> @@ -40,7 +39,64 @@ </output> </test> </tests> - <help> - Outputs the results of a query on a SQLite Database as a tabular file. - </help> + <help><![CDATA[ +Outputs the results of a query on a SQLite_ Database as a tabular file. + +In addition to the standard SQLite_functions_ regular_expression_ functions are included. + +For example, with SQLite table "customers": + + =========== ========== ========== ===================== ========== ============ + #CustomerID FirstName LastName Email BirthDate Phone + =========== ========== ========== ===================== ========== ============ + 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222 + 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545 + 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232 + 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888 + =========== ========== ========== ===================== ========== ============ + + :: + + matching: re_match('pattern',column) + + SELECT FirstName, LastName + FROM customers + WHERE re_match('^.*\.(net|org)$',Email) + + Results: + + =========== ========== + #FirstName LastName + =========== ========== + Steven Goldfish + Paula Brown + =========== ========== + + + :: + + searching: re_search('pattern',column) + substituting: re_sub('pattern','replacement,column) + + SELECT FirstName, LastName, re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB" + FROM customers + WHERE re_search('[hp]er',Email) + + Results: + + =========== ========== ========== + #FirstName LastName DOB + =========== ========== ========== + Steven Goldfish 04/04/74 + Paula Brown 24/05/78 + James Smith 20/10/80 + =========== ========== ========== + + + +.. _Regular_expression: https://docs.python.org/release/2.7/library/re.html +.. _SQLite: http://www.sqlite.org/index.html +.. _SQLite_functions: http://www.sqlite.org/docs.html + + ]]></help> </tool>