Mercurial > repos > jjohnson > sqlite_to_tabular
annotate 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 |
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date | Thu, 21 Jan 2016 09:35:35 -0500 |
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children | 78e9570fbe08 |
rev | line source |
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0
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
jjohnson
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1 <?xml version="1.0"?> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
jjohnson
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2 <tool id="sqlite_to_tabular" name="SQLite to tabular" version="0.0.1"> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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3 <description>for SQL query</description> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
jjohnson
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4 <stdio> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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5 <exit_code range="1:" level="fatal" description="Error" /> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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6 </stdio> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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7 <command interpreter="python"><![CDATA[ |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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8 sqlite_to_tabular.py |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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9 --sqlitedb="$sqlitedb" |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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10 --query_file="$query_file" |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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11 $no_header |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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12 --output="$query_results" |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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13 ]]></command> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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14 <configfiles> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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15 <configfile name="query_file"> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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16 $sqlquery |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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17 </configfile> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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18 </configfiles> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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19 <inputs> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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20 <param name="sqlitedb" type="data" format="sqlite" label="SQLite Database"/> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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21 <param name="sqlquery" type="text" area="True" size="120x20" label="SQL query"> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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22 <validator type="regex">^(?im)\s*SELECT\s.*\sFROM\s.*$</validator> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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23 <sanitizer sanitize="False"/> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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24 </param> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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25 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers"/> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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26 </inputs> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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27 <outputs> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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28 <data name="query_results" format="tabular" /> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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29 </outputs> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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30 <tests> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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31 <test> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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32 <param name="sqlitedb" ftype="sqlite" value="testdb.sqlite" /> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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33 <param name="sqlquery" value="SELECT first_name, last_name, age FROM contacts WHERE first_name = 'Sam'" /> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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34 <output name="query_results"> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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35 <assert_contents> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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36 <has_text text="Smith" /> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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37 <not_has_text text="Doe" /> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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38 </assert_contents> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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39 </output> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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40 </test> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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41 </tests> |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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42 <help><![CDATA[ |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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43 Outputs the results of a query on a SQLite_ Database as a tabular file. |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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44 |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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45 In addition to the standard SQLite_functions_ regular_expression_ functions are included. |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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46 |
cf32fc695e72
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47 For example, with SQLite table "customers": |
cf32fc695e72
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48 |
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49 =========== ========== ========== ===================== ========== ============ |
cf32fc695e72
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50 #CustomerID FirstName LastName Email BirthDate Phone |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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51 =========== ========== ========== ===================== ========== ============ |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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52 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222 |
cf32fc695e72
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53 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545 |
cf32fc695e72
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54 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232 |
cf32fc695e72
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55 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888 |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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56 =========== ========== ========== ===================== ========== ============ |
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57 |
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58 :: |
cf32fc695e72
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59 |
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60 matching: re_match('pattern',column) |
cf32fc695e72
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
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61 |
cf32fc695e72
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62 SELECT FirstName, LastName |
cf32fc695e72
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63 FROM customers |
cf32fc695e72
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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 |
cf32fc695e72
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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) |
cf32fc695e72
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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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89 =========== ========== ========== |
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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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93 =========== ========== ========== |
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94 |
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95 |
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96 |
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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> |