Mercurial > repos > iuc > sqlite_to_tabular

annotate macros.xml @ 0:859064f07be4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
author iuc
date Tue, 18 Jul 2017 09:07:26 -0400
parents
children c1b700bc0150
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
1 <macros>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
2 <token name="@LINEFILTERS@">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
3 <![CDATA[
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
4 ## set linefilters to the
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
5 #set $input_filters = []
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
6 #for $fi in $linefilters:
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
7 #if $fi.filter.filter_type == 'skip':
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
8 #set $skip_lines = None
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
9 #if str($fi.filter.skip_lines) != '':
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
10 #set $skip_lines = int($fi.filter.skip_lines)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
11 #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0:
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
12 #set $skip_lines = int($tbl.table.metadata.comment_lines)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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13 #end if
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
14 #if $skip_lines is not None:
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff changeset
15 #set $filter_dict = dict()
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff changeset
16 #set $filter_dict['filter'] = str($fi.filter.filter_type)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
17 #set $filter_dict['count'] = $skip_lines
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
18 #silent $input_filters.append($filter_dict)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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19 #end if
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
20 #elif $fi.filter.filter_type == 'comment':
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
21 #set $filter_dict = dict()
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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22 #set $filter_dict['filter'] = 'regex'
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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23 #set $filter_dict['pattern'] = '^(%s).*$' % '|'.join([chr(int(x)).replace('|','[|]') for x in (str($fi.filter.comment_char)).split(',')])
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
24 #set $filter_dict['action'] = 'exclude_match'
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
25 #silent $input_filters.append($filter_dict)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
26 #elif $fi.filter.filter_type == 'regex':
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
27 #set $filter_dict = dict()
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
28 #set $filter_dict['filter'] = str($fi.filter.filter_type)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
29 #set $filter_dict['pattern'] = str($fi.filter.regex_pattern)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
30 #set $filter_dict['action'] = str($fi.filter.regex_action)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
31 #silent $input_filters.append($filter_dict)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
32 #elif $fi.filter.filter_type == 'select_columns':
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
33 #set $filter_dict = dict()
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
34 #set $filter_dict['filter'] = str($fi.filter.filter_type)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
35 #set $filter_dict['columns'] = [int(str($ci).replace('c','')) for $ci in str($fi.filter.columns).split(',')]
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
36 #silent $input_filters.append($filter_dict)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
37 #elif $fi.filter.filter_type == 'replace':
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
38 #set $filter_dict = dict()
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
39 #set $filter_dict['filter'] = str($fi.filter.filter_type)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
40 #set $filter_dict['column'] = int(str($fi.filter.column).replace('c',''))
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
41 #set $filter_dict['pattern'] = str($fi.filter.regex_pattern)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
42 #set $filter_dict['replace'] = str($fi.filter.regex_replace)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
43 #silent $input_filters.append($filter_dict)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
44 #elif str($fi.filter.filter_type).endswith('pend_line_num'):
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
45 #set $filter_dict = dict()
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
46 #set $filter_dict['filter'] = str($fi.filter.filter_type)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
47 #silent $input_filters.append($filter_dict)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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48 #elif str($fi.filter.filter_type).endswith('pend_text'):
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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49 #set $filter_dict = dict()
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
50 #set $filter_dict['filter'] = str($fi.filter.filter_type)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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51 #set $filter_dict['column_text'] = str($fi.filter.column_text)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
52 #silent $input_filters.append($filter_dict)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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53 #elif $fi.filter.filter_type == 'normalize':
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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54 #set $filter_dict = dict()
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
55 #set $filter_dict['filter'] = str($fi.filter.filter_type)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
56 #set $filter_dict['columns'] = [int(str($ci).replace('c','')) for $ci in str($fi.filter.columns).split(',')]
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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57 #set $filter_dict['separator'] = str($fi.filter.separator)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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58 #silent $input_filters.append($filter_dict)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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59 #end if
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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60 #end for
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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61 ]]>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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62 </token>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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63 <xml name="macro_line_filters">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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64 <repeat name="linefilters" title="Filter Tabular Input Lines">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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65 <conditional name="filter">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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66 <param name="filter_type" type="select" label="Filter By">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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67 <option value="skip">skip leading lines</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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68 <option value="comment">comment char</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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69 <option value="regex">by regex expression matching</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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70 <option value="select_columns">select columns</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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71 <option value="replace">regex replace value in column</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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72 <option value="prepend_line_num">prepend a line number column</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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73 <option value="append_line_num">append a line number column</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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74 <option value="prepend_text">prepend a column with the given text</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
75 <option value="append_text">append a column with the given text</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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76 <option value="normalize">normalize list columns, replicates row for each item in list</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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77 </param>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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78 <when value="skip">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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79 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines"
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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80 help="Leave blank to use the comment lines metadata for this dataset" />
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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81 </when>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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82 <when value="comment">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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83 <param name="comment_char" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are skipped">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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84 <option value="62">&gt;</option>
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iuc
parents:
diff changeset
85 <option value="64">@</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
86 <option value="43">+</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
87 <option value="60">&lt;</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
88 <option value="42">*</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
89 <option value="45">-</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
90 <option value="61">=</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
91 <option value="124">|</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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92 <option value="63">?</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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93 <option value="36">$</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
94 <option value="46">.</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
95 <option value="58">:</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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96 <option value="38">&amp;</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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97 <option value="37">%</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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98 <option value="94">^</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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99 <option value="35">&#35;</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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100 <option value="33">!</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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101 </param>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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102 </when>
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iuc
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103 <when value="prepend_line_num"/>
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104 <when value="append_line_num"/>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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105 <when value="prepend_text">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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106 <param name="column_text" type="text" value="" label="text for column">
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107 </param>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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108 </when>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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109 <when value="append_text">
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110 <param name="column_text" type="text" value="" label="text for column">
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111 </param>
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112 </when>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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113 <when value="regex">
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114 <param name="regex_pattern" type="text" value="" label="regex pattern">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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115 <sanitizer sanitize="False"/>
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116 </param>
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117 <param name="regex_action" type="select" label="action for regex match">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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118 <option value="exclude_match">exclude line on pattern match</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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119 <option value="include_match">include line on pattern match</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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120 <option value="exclude_find">exclude line if pattern found</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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121 <option value="include_find">include line if pattern found</option>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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122 </param>
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123 </when>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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124 <when value="select_columns">
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125 <param name="columns" type="text" value="" label="enter column numbers to keep"
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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126 help="example: 1,4,2 or c1,c4,c2(selects the first,fourth, and second columns)">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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127 <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</validator>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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128 </param>
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129 </when>
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130 <when value="replace">
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131 <param name="column" type="text" value="" label="enter column number to replace"
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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132 help="example: 1 or c1 (selects the first column)">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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133 <validator type="regex" message="Column ordinal position separated by commas">^(c?[1-9]\d*)$</validator>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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134 </param>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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135 <param name="regex_pattern" type="text" value="" label="regex pattern">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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136 <sanitizer sanitize="False"/>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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137 </param>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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138 <param name="regex_replace" type="text" value="" label="replacement expression">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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139 <sanitizer sanitize="False"/>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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140 </param>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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141 </when>
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142 <when value="normalize">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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143 <param name="columns" type="text" value="" label="enter column numbers to normalize">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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144 <help><![CDATA[
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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145 example: 2,4 or c2,c4 (selects the second, and fourth columns)
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146 If multiple columns are selected, they should have the same length and separator on each line
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147 ]]></help>
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148 <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</validator>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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149 </param>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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150 <param name="separator" type="text" value="," label="List item delimiter in column">
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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151 <sanitizer sanitize="False"/>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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152 <validator type="regex" message="Anything but TAB or Newline">^[^\t\n\r\f\v]+$</validator>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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153 </param>
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154 </when>
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155 </conditional>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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156 </repeat>
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157 </xml>
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158
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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159 <token name="@LINEFILTERS_HELP@">
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160 <![CDATA[
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161 **Input Line Filters**
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162
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163 As a tabular file is being read, line filters may be applied.
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164
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165 ::
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166
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167 - skip leading lines skip the first *number* of lines
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168 - comment char omit any lines that start with the specified comment character
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169 - by regex expression matching *include/exclude* lines the match the regex expression
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170 - select columns choose to include only selected columns in the order specified
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171 - regex replace value in column replace a field in a column using a regex substitution (good for date reformatting)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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172 - prepend a line number column each line has the ordinal value of the line read by this filter as the first column
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173 - append a line number column each line has the ordinal value of the line read by this filter as the last column
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174 - prepend a text column each line has the text string as the first column
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175 - append a text column each line has the text string as the last column
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176 - normalize list columns replicates the line for each item in the specified list *columns*
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177 ]]>
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178 </token>
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179
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180 <token name="@LINEFILTERS_HELP_EXAMPLE@">
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181 <![CDATA[
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182 **Line Filtering Example**
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183 *(Six filters are applied as the following file is read)*
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184
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185 ::
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186
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187 Input Tabular File:
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188
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189 #People with pets
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190 Pets FirstName LastName DOB PetNames PetType
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191 2 Paula Brown 24/05/78 Rex,Fluff dog,cat
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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192 1 Steven Jones 04/04/74 Allie cat
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193 0 Jane Doe 24/05/78
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194 1 James Smith 20/10/80 Spot
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195
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196
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197 Filter 1 - append a line number column:
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198
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199 #People with pets 1
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200 Pets FirstName LastName DOB PetNames PetType 2
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201 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3
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202 1 Steven Jones 04/04/74 Allie cat 4
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203 0 Jane Doe 24/05/78 5
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204 1 James Smith 20/10/80 Spot 6
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205
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206 Filter 2 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
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207
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208 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3
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209 1 Steven Jones 04/04/74 Allie cat 4
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210 0 Jane Doe 24/05/78 5
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211 1 James Smith 20/10/80 Spot 6
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212
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213 Filter 3 - append a line number column:
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214
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215 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3 1
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216 1 Steven Jones 04/04/74 Allie cat 4 2
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217 0 Jane Doe 24/05/78 5 3
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218 1 James Smith 20/10/80 Spot 6 4
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219
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220 Filter 4 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format)
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221
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222 2 Paula Brown 1978-05-24 Rex,Fluff dog,cat 3 1
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223 1 Steven Jones 1974-04-04 Allie cat 4 2
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224 0 Jane Doe 1978-05-24 5 3
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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225 1 James Smith 1980-10-20 Spot 6 4
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226
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227 Filter 5 - normalize list columns[5,6]:
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228
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229 2 Paula Brown 1978-05-24 Rex dog 3 1
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230 2 Paula Brown 1978-05-24 Fluff cat 3 1
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231 1 Steven Jones 1974-04-04 Allie cat 4 2
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232 0 Jane Doe 1978-05-24 5 3
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233 1 James Smith 1980-10-20 Spot 6 4
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234
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235 Filter 6 - append a line number column:
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236
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237 2 Paula Brown 1978-05-24 Rex dog 3 1 1
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238 2 Paula Brown 1978-05-24 Fluff cat 3 1 2
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239 1 Steven Jones 1974-04-04 Allie cat 4 2 3
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240 0 Jane Doe 1978-05-24 5 3 4
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241 1 James Smith 1980-10-20 Spot 6 4 5
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242
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243 ]]>
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244 </token>
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245
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246 <token name="@QUERY_HELP@">
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247 <![CDATA[
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248
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249 For help in using SQLite_ see: http://www.sqlite.org/docs.html
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250
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251 **NOTE:** input for SQLite dates input field must be in the format: *YYYY-MM-DD* for example: 2015-09-30
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252
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253 See: http://www.sqlite.org/lang_datefunc.html
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254
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255 **Example**
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256
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257 Given 2 tabular datasets: *customers* and *sales*
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258
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259 Dataset *customers*
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260
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261 Table name: "customers"
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262
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263 Column names: "CustomerID,FirstName,LastName,Email,DOB,Phone"
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264
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265 =========== ========== ========== ===================== ========== ============
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266 #CustomerID FirstName LastName Email DOB Phone
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267 =========== ========== ========== ===================== ========== ============
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268 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
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269 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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270 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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271 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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272 =========== ========== ========== ===================== ========== ============
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273
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274 Dataset *sales*
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275
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276 Table name: "sales"
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277
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278 Column names: "CustomerID,Date,SaleAmount"
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279
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280 ============= ============ ============
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281 #CustomerID Date SaleAmount
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282 ============= ============ ============
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283 2 2004-05-06 100.22
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284 1 2004-05-07 99.95
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285 3 2004-05-07 122.95
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286 3 2004-05-13 100.00
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287 4 2004-05-22 555.55
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288 ============= ============ ============
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289
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290 The query
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291
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292 ::
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293
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294 SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales"
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295 FROM customers join sales on customers.CustomerID = sales.CustomerID
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296 GROUP BY customers.CustomerID ORDER BY TotalSales DESC;
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297
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298 Produces this tabular output:
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299
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300 ========== ======== ==========
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301 #FirstName LastName TotalSales
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302 ========== ======== ==========
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303 James Smith 555.55
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304 Paula Brown 222.95
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305 Steven Goldfish 100.22
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306 John Smith 99.95
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307 ========== ======== ==========
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308
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309
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310 If the optional Table name and Column names inputs are not used, the query would be:
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311
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312 ::
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313
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314 SELECT t1.c2 as "FirstName", t1.c3 as "LastName", sum(t2.c3) as "TotalSales"
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315 FROM t1 join t2 on t1.c1 = t2.c1
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316 GROUP BY t1.c1 ORDER BY TotalSales DESC;
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317
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318 You can selectively name columns, e.g. on the customers input you could just name columns 2,3, and 5:
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319
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320 Column names: ,FirstName,LastName,,BirthDate
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321
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322 Results in the following data base table
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323
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324 =========== ========== ========== ===================== ========== ============
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325 #c1 FirstName LastName c4 BirthDate c6
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326 =========== ========== ========== ===================== ========== ============
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327 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
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328 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
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329 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
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330 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
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331 =========== ========== ========== ===================== ========== ============
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332
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333
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334 Regular_expression_ functions are included for:
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335
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336 ::
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337
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338 matching: re_match('pattern',column)
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339
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340 SELECT t1.FirstName, t1.LastName
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341 FROM t1
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342 WHERE re_match('^.*\.(net|org)$',c4)
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343
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344 Results:
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345
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346 =========== ==========
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347 #FirstName LastName
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348 =========== ==========
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349 Steven Goldfish
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350 Paula Brown
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351 =========== ==========
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352
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353
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354 ::
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355
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356 searching: re_search('pattern',column)
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357 substituting: re_sub('pattern','replacement,column)
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358
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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359 SELECT t1.FirstName, t1.LastName, re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB"
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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360 FROM t1
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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361 WHERE re_search('[hp]er',c4)
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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362
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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363 Results:
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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364
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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365
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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366 =========== ========== ==========
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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367 #FirstName LastName DOB
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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368 =========== ========== ==========
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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369 Steven Goldfish 04/04/74
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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370 Paula Brown 24/05/78
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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371 James Smith 20/10/80
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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372 =========== ========== ==========
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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373
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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374 .. _Regular_expression: https://docs.python.org/release/2.7/library/re.html
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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375 .. _SQLite: http://www.sqlite.org/index.html
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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376 .. _SQLite_functions: http://www.sqlite.org/docs.html
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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377
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378
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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379 ]]>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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380 </token>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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381
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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382 </macros>
859064f07be4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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383