Mercurial > repos > jjohnson > sqlite_to_tabular
diff sqlite_to_tabular.xml @ 0:cf32fc695e72 draft
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 09:35:35 -0500 |
| parents | |
| children | 78e9570fbe08 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sqlite_to_tabular.xml Thu Jan 21 09:35:35 2016 -0500 @@ -0,0 +1,102 @@ +<?xml version="1.0"?> +<tool id="sqlite_to_tabular" name="SQLite to tabular" version="0.0.1"> + <description>for SQL query</description> + <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"> +$sqlquery + </configfile> + </configfiles> + <inputs> + <param name="sqlitedb" type="data" format="sqlite" label="SQLite Database"/> + <param name="sqlquery" type="text" area="True" size="120x20" label="SQL query"> + <validator type="regex">^(?im)\s*SELECT\s.*\sFROM\s.*$</validator> + <sanitizer sanitize="False"/> + </param> + <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers"/> + </inputs> + <outputs> + <data name="query_results" format="tabular" /> + </outputs> + <tests> + <test> + <param name="sqlitedb" ftype="sqlite" value="testdb.sqlite" /> + <param name="sqlquery" value="SELECT first_name, last_name, age FROM contacts WHERE first_name = 'Sam'" /> + <output name="query_results"> + <assert_contents> + <has_text text="Smith" /> + <not_has_text text="Doe" /> + </assert_contents> + </output> + </test> + </tests> + <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>