annotate query_tabular.xml @ 10:e84d1c3bf4fe draft

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author jjohnson
date Thu, 02 Mar 2017 13:43:25 -0500
parents ae27dab228b8
children fd16243931d6
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1 <tool id="query_tabular" name="Query Tabular" version="2.0.0">
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2 <description>using sqlite sql</description>
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3
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4 <requirements>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command><![CDATA[
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10 cat $query_file &&
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11 #if $add_to_database.withdb:
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12 #if $save_db:
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13 cp "$add_to_database.withdb" "$sqlitedb" &&
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14 #else:
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15 cp "$add_to_database.withdb" "$workdb" &&
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16 #end if
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17 #end if
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18 python $__tool_directory__/query_tabular.py
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19 #if $save_db
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20 -s "$sqlitedb"
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21 #else
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22 -s $workdb
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23 #end if
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24 -j $table_json
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25 #if $sqlquery:
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26 -Q "$query_file"
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27 $no_header
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28 -o $output
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29 #end if
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30 ]]></command>
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31 <configfiles>
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32 <configfile name="query_file">
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33 $sqlquery
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34 </configfile>
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35 <configfile name="table_json">
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36 #import json
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37 #set $jtbldef = dict()
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38 #set $jtbls = []
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39 #set $jtbldef['tables'] = $jtbls
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40 #for $i,$tbl in enumerate($tables):
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41 #set $jtbl = dict()
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42 #set $jtbl['file_path'] = str($tbl.table)
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43 #if $tbl.tbl_opts.table_name:
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44 #set $tname = str($tbl.tbl_opts.table_name)
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45 #else
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46 #set $tname = 't' + str($i + 1)
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47 #end if
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48 #set $jtbl['table_name'] = $tname
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49 ## #if $tbl.tbl_opts.sel_cols:
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50 ## #set $jtbl['sel_cols'] = $tbl.tbl_opts.sel_cols el_cols
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51 ## #end if
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52 #if $tbl.tbl_opts.pkey_autoincr:
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53 #set $jtbl['pkey_autoincr'] = str($tbl.tbl_opts.pkey_autoincr)
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54 #end if
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55 #if $tbl.tbl_opts.col_names:
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56 #set $col_names = str($tbl.tbl_opts.col_names)
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57 #if $tbl.tbl_opts.load_named_columns:
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58 #set $jtbl['load_named_columns'] = True
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59 #end if
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60 #else
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61 #set $col_names = ''
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62 #end if
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63 #set $jtbl['column_names'] = $col_names
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64 #set $idx_unique = []
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65 #set $idx_non = []
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66 #for $idx in $tbl.tbl_opts.indexes:
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67 #if $idx.unique:
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68 #silent $idx_unique.append(str($idx.index_columns))
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69 #else:
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70 #silent $idx_non.append(str($idx.index_columns))
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71 #end if
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72 #end for
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73 #if len($idx_unique) > 0:
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74 #set $jtbl['unique'] = $idx_unique
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75 #end if
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76 #if len($idx_non) > 0:
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77 #set $jtbl['index'] = $idx_non
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78 #end if
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79 #set $input_filters = []
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80 #for $fi in $tbl.input_opts.linefilters:
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81 #if $fi.filter.filter_type == 'skip':
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82 #if str($fi.filter.skip_lines) != '':
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83 #set $jtbl['comment_lines'] = int($fi.filter.skip_lines)
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84 #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0:
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85 #set $jtbl['comment_lines'] = int($tbl.table.metadata.comment_lines)
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86 #end if
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87 #elif $fi.filter.filter_type == 'comment':
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88 #set $jtbl['comment_char'] = str($fi.filter.comment_char)
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89 #elif $fi.filter.filter_type == 'regex':
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90 #set $filter_dict = dict()
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91 #set $filter_dict['filter'] = str($fi.filter.filter_type)
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92 #set $filter_dict['pattern'] = str($fi.filter.regex_pattern)
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93 #set $filter_dict['action'] = str($fi.filter.regex_action)
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94 #silent $input_filters.append($filter_dict)
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95 #elif $fi.filter.filter_type == 'replace':
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96 #set $filter_dict = dict()
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97 #set $filter_dict['filter'] = str($fi.filter.filter_type)
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98 #set $filter_dict['column'] = int(str($fi.filter.column))
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99 #set $filter_dict['pattern'] = str($fi.filter.regex_pattern)
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100 #set $filter_dict['replace'] = str($fi.filter.regex_replace)
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101 #silent $input_filters.append($filter_dict)
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102 ## #elif $fi.filter.filter_type == 'normalize':
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103 ## #set $filter_dict = dict()
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104 ## #set $filter_dict['filter'] = str($fi.filter.filter_type)
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105 ## #set $filter_dict['columns'] = [int(str($ci)) for $ci in str($fi.filter.columns).split(',')]
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106 ## #set $filter_dict['separator'] = str($fi.filter.separator)
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107 ## #silent $input_filters.append($filter_dict)
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108 #end if
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109 #end for
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110 #if $input_filters:
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111 #set $jtbl['filters'] = $input_filters
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112 #end if
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113 #set $jtbls += [$jtbl]
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114 #end for
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115 #echo $json.dumps($jtbldef)
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116 </configfile>
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117 </configfiles>
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118 <inputs>
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119 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
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120 <section name="add_to_database" expanded="false" title="Add tables to an existing database">
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121 <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database"
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122 help="Make sure your added table names are not already in this database"/>
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123 </section>
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124 <repeat name="tables" title="Database Table" min="0">
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125 <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/>
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126 <section name="input_opts" expanded="false" title="Filter Dataset Input">
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127 <repeat name="linefilters" title="Filter Tabular Input Lines">
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128 <conditional name="filter">
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129 <param name="filter_type" type="select" label="Filter By">
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130 <option value="skip">skip leading lines</option>
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131 <option value="comment">comment char</option>
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132 <option value="regex">by regex expression matching</option>
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133 <option value="replace">regex replace value in column</option>
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134 <!--
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135 <option value="normalize">normalize list columns, replicates row for each item in list</option>
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136 -->
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137 </param>
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138 <when value="skip">
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139 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines"
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140 help="Leave blank to use the comment lines metadata for this dataset" />
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141 </when>
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142 <when value="comment">
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143 <param name="comment_char" type="text" value="#" label="Comment line starting text">
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144 <sanitizer sanitize="False"/>
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145 </param>
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146 </when>
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147 <when value="regex">
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148 <param name="regex_pattern" type="text" value="" label="regex pattern">
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149 <sanitizer sanitize="False"/>
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150 </param>
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151 <param name="regex_action" type="select" label="action for regex match">
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152 <option value="exclude_match">exclude line on pattern match</option>
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153 <option value="include_match">include line on pattern match</option>
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154 <option value="exclude_find">exclude line if pattern found</option>
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155 <option value="include_find">include line if pattern found</option>
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156 </param>
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157 </when>
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158 <when value="replace">
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159 <param name="column" type="data_column" data_ref="table" label="Column to replace text"
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160 help=""/>
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161 <param name="regex_pattern" type="text" value="" label="regex pattern">
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162 <sanitizer sanitize="False"/>
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163 </param>
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164 <param name="regex_replace" type="text" value="" label="replacement expression">
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165 <sanitizer sanitize="False"/>
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166 </param>
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167 </when>
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168 <!--
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169 <when value="normalize">
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170 <param name="columns" type="data_column" data_ref="table" multiple="True" label="Columns to split"
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171 help=""/>
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172 <param name="separator" type="text" value="," label="List item delimiter in column">
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173 <sanitizer sanitize="False"/>
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174 <validator type="regex" message="Anything but TAB or Newline">^[^\t\n\r\f\v]+$</validator>
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175 </param>
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176 </when>
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177 -->
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178 </conditional>
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179 </repeat>
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180 </section>
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181 <section name="tbl_opts" expanded="false" title="Table Options">
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182 <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table">
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183 <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help>
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184 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
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185 </param>
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186 <param name="col_names" type="text" value="" optional="true" label="Specify Column Names">
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187 <help>By default, table columns will be named: c1,c2,c3,...,cn (column names for a table must be unique)</help>
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188 <sanitizer sanitize="False"/>
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189 <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator>
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190 </param>
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191 <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load the columns you have named into database"/>
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192 <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name"
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193 help="Only creates this additional column when a name is entered. (This can not be the same name as any of the other columns in this table.)">
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194 <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator>
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195 </param>
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196 <repeat name="indexes" title="Table Index">
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197 <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>
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198 <param name="index_columns" type="text" value="" label="Index on Columns">
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199 <help>Create an index on the column names: e,g, c1 or c2,c4</help>
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200 <validator type="regex" message="Column name, separated by commes if more than one">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator>
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201 </param>
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202 </repeat>
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203 </section>
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204 </repeat>
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205 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history"/>
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206 <param name="sqlquery" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to generate tabular output">
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207 <help>By default: tables are named: t1,t2,...,tn and columns in each table: c1,c2,...,cn</help>
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208 <sanitizer sanitize="False"/>
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209 <validator type="regex" message="">^(?ims)\s*select\s+.*\s+from\s+.*$</validator>
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210 </param>
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211 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers from tabular output"/>
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212 </inputs>
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213 <outputs>
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214 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}">
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215 <filter>save_db or not (sqlquery and len(sqlquery) > 0)</filter>
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216 </data>
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217 <data format="tabular" name="output" label="query results on ${on_string}">
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218 <filter>sqlquery and len(sqlquery) > 0</filter>
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219 </data>
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220 </outputs>
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221 <tests>
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222
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223 <test>
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224 <repeat name="tables">
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225 <param name="table" ftype="tabular" value="customers.tsv"/>
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226 <param name="table_name" value="customers"/>
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227 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/>
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228 </repeat>
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229 <repeat name="tables">
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230 <param name="table" ftype="tabular" value="sales.tsv"/>
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231 <param name="table_name" value="sales"/>
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232 <param name="col_names" value="CustomerID,Date,SaleAmount"/>
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233 </repeat>
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234 <param name="sqlquery" value="SELECT FirstName,LastName,sum(SaleAmount) as &quot;TotalSales&quot; FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC"/>
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235 <output name="output" file="sales_results.tsv"/>
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236 </test>
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237
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238 <test>
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239 <repeat name="tables">
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240 <param name="table" ftype="tabular" value="customers.tsv"/>
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241 <param name="col_names" value=",FirstName,LastName,,DOB,"/>
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242 </repeat>
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243 <repeat name="tables">
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244 <param name="table" ftype="tabular" value="sales.tsv"/>
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245 </repeat>
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246 <param name="sqlquery" value="SELECT FirstName,LastName,sum(t2.c3) as &quot;TotalSales&quot; FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;"/>
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247 <output name="output" file="sales_results.tsv"/>
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248 </test>
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249
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250 <test>
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251 <repeat name="tables">
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252 <param name="table" ftype="tabular" value="customers.tsv"/>
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253 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/>
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254 </repeat>
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255 <param name="sqlquery" value="select FirstName,LastName,re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as &quot;DOB&quot; from t1 WHERE re_search('[hp]er',c4)"/>
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256 <output name="output" file="regex_results.tsv"/>
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257 </test>
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258
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259 <test>
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260 <repeat name="tables">
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261 <param name="table" ftype="tabular" value="IEDB.tsv"/>
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262 <param name="table_name" value="iedb"/>
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263 <param name="col_names" value="ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank"/>
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264 </repeat>
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265 <repeat name="tables">
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266 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
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267 <param name="table_name" value="mhc_summary"/>
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268 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/>
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269 </repeat>
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270 <param name="sqlquery" value="select iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level"/>
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271 <output name="output" file="query_results.tsv"/>
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272 </test>
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273
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274 </tests>
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275 <help><![CDATA[
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276 =============
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277 Query Tabular
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278 =============
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279
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280 **Inputs**
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281
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282 Loads tabular datasets into a SQLite_ data base.
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283
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284 An existing SQLite_ data base can be used as input, and any selected tabular datasets will be added as new tables in that data base.
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285
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286
0
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287 **Outputs**
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288
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289 The results of a SQL query are output to the history as a tabular file.
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290
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291 The SQLite_ data base can also be saved and output as a dataset in the history.
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292
5
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293 *(The* **SQLite to tabular** *tool can run additional queries on this database.)*
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294
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295
0
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296 For help in using SQLite_ see: http://www.sqlite.org/docs.html
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297
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298 **NOTE:** input for SQLite dates input field must be in the format: *YYYY-MM-DD* for example: 2015-09-30
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299
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300 See: http://www.sqlite.org/lang_datefunc.html
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301
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302 **Example**
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303
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304 Given 2 tabular datasets: *customers* and *sales*
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305
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306 Dataset *customers*
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307
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308 Table name: "customers"
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309
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310 Column names: "CustomerID,FirstName,LastName,Email,DOB,Phone"
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311
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312 =========== ========== ========== ===================== ========== ============
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313 #CustomerID FirstName LastName Email DOB Phone
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314 =========== ========== ========== ===================== ========== ============
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315 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
316 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
317 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
318 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
319 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
320
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
321 Dataset *sales*
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
322
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
323 Table name: "sales"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
324
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
325 Column names: "CustomerID,Date,SaleAmount"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
326
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
327 ============= ============ ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
328 #CustomerID Date SaleAmount
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
329 ============= ============ ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
330 2 2004-05-06 100.22
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
331 1 2004-05-07 99.95
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
332 3 2004-05-07 122.95
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
333 3 2004-05-13 100.00
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
334 4 2004-05-22 555.55
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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335 ============= ============ ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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336
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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337 The query
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
338
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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339 ::
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
340
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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341 SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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342 FROM customers join sales on customers.CustomerID = sales.CustomerID
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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343 GROUP BY customers.CustomerID ORDER BY TotalSales DESC;
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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344
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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345 Produces this tabular output:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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346
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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347 ========== ======== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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348 #FirstName LastName TotalSales
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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349 ========== ======== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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350 James Smith 555.55
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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351 Paula Brown 222.95
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
352 Steven Goldfish 100.22
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
353 John Smith 99.95
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
354 ========== ======== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
355
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
356
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
357 If the optional Table name and Column names inputs are not used, the query would be:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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diff changeset
358
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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359 ::
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
360
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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361 SELECT t1.c2 as "FirstName", t1.c3 as "LastName", sum(t2.c3) as "TotalSales"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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362 FROM t1 join t2 on t1.c1 = t2.c1
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
363 GROUP BY t1.c1 ORDER BY TotalSales DESC;
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
364
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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365 You can selectively name columns, e.g. on the customers input you could just name columns 2,3, and 5:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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366
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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367 Column names: ,FirstName,LastName,,BirthDate
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
368
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
369 Results in the following data base table
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
370
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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371 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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372 #c1 FirstName LastName c4 BirthDate c6
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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373 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
374 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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375 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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376 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
377 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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378 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
379
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
380 Regular_expression_ functions are included for:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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381
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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diff changeset
382 ::
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
383
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
384 matching: re_match('pattern',column)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
385
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
386 SELECT t1.FirstName, t1.LastName
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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387 FROM t1
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
388 WHERE re_match('^.*\.(net|org)$',c4)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
389
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
390 Results:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
391
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
392 =========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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393 #FirstName LastName
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
394 =========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
395 Steven Goldfish
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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diff changeset
396 Paula Brown
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
397 =========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
398
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
399
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
400 ::
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
401
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
402 searching: re_search('pattern',column)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
403 substituting: re_sub('pattern','replacement,column)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
404
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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405 SELECT t1.FirstName, t1.LastName, re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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406 FROM t1
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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407 WHERE re_search('[hp]er',c4)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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408
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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409 Results:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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410
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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411 =========== ========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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412 #FirstName LastName DOB
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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413 =========== ========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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414 Steven Goldfish 04/04/74
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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415 Paula Brown 24/05/78
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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416 James Smith 20/10/80
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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417 =========== ========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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418
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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419 .. _Regular_expression: https://docs.python.org/release/2.7/library/re.html
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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420 .. _SQLite: http://www.sqlite.org/index.html
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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421
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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422 ]]></help>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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423 </tool>