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comparison sqlite_to_tabular.xml @ 3:f079ea3884b3 draft default tip

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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
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2:bc50a7b7f246 3:f079ea3884b3
2 <tool id="sqlite_to_tabular" name="SQLite to tabular" version="0.0.1"> 2 <tool id="sqlite_to_tabular" name="SQLite to tabular" version="0.0.1">
3 <description>for SQL query</description> 3 <description>for SQL query</description>
4 <stdio> 4 <stdio>
5 <exit_code range="1:" level="fatal" description="Error" /> 5 <exit_code range="1:" level="fatal" description="Error" />
6 </stdio> 6 </stdio>
7 <command interpreter="python"><![CDATA[
8 sqlite_to_tabular.py
9 --sqlitedb="$sqlitedb"
10 --query_file="$query_file"
11 $no_header
12 --output="$query_results"
13 ]]></command>
7 <configfiles> 14 <configfiles>
8 <configfile name="query_file"> 15 <configfile name="query_file">
9 $sqlquery 16 $sqlquery
10 </configfile> 17 </configfile>
11 </configfiles> 18 </configfiles>
12
13 <command interpreter="python">
14 sqlite_to_tabular.py
15 --sqlitedb="$sqlitedb"
16 --query_file="$query_file"
17 $no_header
18 --output="$query_results"
19 </command>
20 <inputs> 19 <inputs>
21 <param name="sqlitedb" type="data" format="sqlite" label="SQLite Database"/> 20 <param name="sqlitedb" type="data" format="sqlite" label="SQLite Database"/>
22 <param name="sqlquery" type="text" area="True" size="120x20" label="SQL query"> 21 <param name="sqlquery" type="text" area="True" size="120x20" label="SQL query">
23 <validator type="regex">^(?im)\s*SELECT\s.*\sFROM\s.*$</validator> 22 <validator type="regex">^(?im)\s*SELECT\s.*\sFROM\s.*$</validator>
24 <sanitizer sanitize="False"/> 23 <sanitizer sanitize="False"/>
38 <not_has_text text="Doe" /> 37 <not_has_text text="Doe" />
39 </assert_contents> 38 </assert_contents>
40 </output> 39 </output>
41 </test> 40 </test>
42 </tests> 41 </tests>
43 <help> 42 <help><![CDATA[
44 Outputs the results of a query on a SQLite Database as a tabular file. 43 Outputs the results of a query on a SQLite_ Database as a tabular file.
45 </help> 44
45 In addition to the standard SQLite_functions_ regular_expression_ functions are included.
46
47 For example, with SQLite table "customers":
48
49 =========== ========== ========== ===================== ========== ============
50 #CustomerID FirstName LastName Email BirthDate Phone
51 =========== ========== ========== ===================== ========== ============
52 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
53 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
54 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
55 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
56 =========== ========== ========== ===================== ========== ============
57
58 ::
59
60 matching: re_match('pattern',column)
61
62 SELECT FirstName, LastName
63 FROM customers
64 WHERE re_match('^.*\.(net|org)$',Email)
65
66 Results:
67
68 =========== ==========
69 #FirstName LastName
70 =========== ==========
71 Steven Goldfish
72 Paula Brown
73 =========== ==========
74
75
76 ::
77
78 searching: re_search('pattern',column)
79 substituting: re_sub('pattern','replacement,column)
80
81 SELECT FirstName, LastName, re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB"
82 FROM customers
83 WHERE re_search('[hp]er',Email)
84
85 Results:
86
87 =========== ========== ==========
88 #FirstName LastName DOB
89 =========== ========== ==========
90 Steven Goldfish 04/04/74
91 Paula Brown 24/05/78
92 James Smith 20/10/80
93 =========== ========== ==========
94
95
96
97 .. _Regular_expression: https://docs.python.org/release/2.7/library/re.html
98 .. _SQLite: http://www.sqlite.org/index.html
99 .. _SQLite_functions: http://www.sqlite.org/docs.html
100
101 ]]></help>
46 </tool> 102 </tool>