Mercurial > repos > jjohnson > sqlite_to_tabular

annotate sqlite_to_tabular.xml @ 0:cf32fc695e72 draft

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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 09:35:35 -0500
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children 78e9570fbe08
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cf32fc695e72 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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1 <?xml version="1.0"?>
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2 <tool id="sqlite_to_tabular" name="SQLite to tabular" version="0.0.1">
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3 <description>for SQL query</description>
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4 <stdio>
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5 <exit_code range="1:" level="fatal" description="Error" />
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6 </stdio>
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7 <command interpreter="python"><![CDATA[
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8 sqlite_to_tabular.py
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9 --sqlitedb="$sqlitedb"
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10 --query_file="$query_file"
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11 $no_header
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12 --output="$query_results"
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13 ]]></command>
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14 <configfiles>
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15 <configfile name="query_file">
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16 $sqlquery
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17 </configfile>
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18 </configfiles>
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19 <inputs>
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20 <param name="sqlitedb" type="data" format="sqlite" label="SQLite Database"/>
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21 <param name="sqlquery" type="text" area="True" size="120x20" label="SQL query">
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22 <validator type="regex">^(?im)\s*SELECT\s.*\sFROM\s.*$</validator>
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23 <sanitizer sanitize="False"/>
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24 </param>
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25 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers"/>
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26 </inputs>
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27 <outputs>
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28 <data name="query_results" format="tabular" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="sqlitedb" ftype="sqlite" value="testdb.sqlite" />
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33 <param name="sqlquery" value="SELECT first_name, last_name, age FROM contacts WHERE first_name = 'Sam'" />
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34 <output name="query_results">
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35 <assert_contents>
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36 <has_text text="Smith" />
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37 <not_has_text text="Doe" />
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38 </assert_contents>
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39 </output>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 Outputs the results of a query on a SQLite_ Database as a tabular file.
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44
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45 In addition to the standard SQLite_functions_ regular_expression_ functions are included.
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46
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47 For example, with SQLite table "customers":
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48
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49 =========== ========== ========== ===================== ========== ============
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50 #CustomerID FirstName LastName Email BirthDate Phone
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51 =========== ========== ========== ===================== ========== ============
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52 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
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53 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
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54 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
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55 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
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56 =========== ========== ========== ===================== ========== ============
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57
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58 ::
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59
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60 matching: re_match('pattern',column)
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61
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62 SELECT FirstName, LastName
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63 FROM customers
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64 WHERE re_match('^.*\.(net|org)$',Email)
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65
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66 Results:
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67
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68 =========== ==========
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69 #FirstName LastName
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70 =========== ==========
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71 Steven Goldfish
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72 Paula Brown
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73 =========== ==========
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74
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75
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76 ::
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77
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78 searching: re_search('pattern',column)
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79 substituting: re_sub('pattern','replacement,column)
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80
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81 SELECT FirstName, LastName, re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB"
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82 FROM customers
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83 WHERE re_search('[hp]er',Email)
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84
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85 Results:
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86
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87 =========== ========== ==========
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88 #FirstName LastName DOB
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90 Steven Goldfish 04/04/74
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91 Paula Brown 24/05/78
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92 James Smith 20/10/80
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97 .. _Regular_expression: https://docs.python.org/release/2.7/library/re.html
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98 .. _SQLite: http://www.sqlite.org/index.html
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99 .. _SQLite_functions: http://www.sqlite.org/docs.html
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100
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101 ]]></help>
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102 </tool>