annotate sqlite_to_tabular.xml @ 2:123b9ca5e26a draft default tip

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit ae4f3ee9048be3ebc9fa3bc0783e73ac31082899-dirty

<?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">
$sqlquery
        </configfile>
    </configfiles>
    <inputs>
        <param name="sqlitedb" type="data" format="sqlite" label="SQLite Database"/>
        <param name="sqlquery" type="text" area="True" size="120x20" label="SQL query">
            <validator type="regex">(?ims)^\s*SELECT\s.*\sFROM\s.*$</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      [e-mail]  1968-02-04 626 222-2222
    2           Steven     Goldfish   [e-mail] 1974-04-04 323 455-4545
    3           Paula      Brown      [e-mail]   1978-05-24 416 323-3232
    4           James      Smith      [e-mail]    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>