annotate query_tabular.xml @ 18:b9f797bf4f38 draft

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author jjohnson
date Wed, 05 Jul 2017 11:51:15 -0400
parents 5b4f6cf857cf
children ab27c4bd14b9
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1 <tool id="query_tabular" name="Query Tabular" version="4.0.0">
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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 #set $skip_lines = None
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83 #if str($fi.filter.skip_lines) != '':
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84 #set $skip_lines = int($fi.filter.skip_lines)
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85 #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0:
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86 #set $skip_lines = int($tbl.table.metadata.comment_lines)
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87 #end if
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88 #if $skip_lines is not None:
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89 #set $filter_dict = dict()
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90 #set $filter_dict['filter'] = str($fi.filter.filter_type)
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91 #set $filter_dict['count'] = $skip_lines
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92 #silent $input_filters.append($filter_dict)
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93 #end if
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94 #elif $fi.filter.filter_type == 'comment':
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95 #set $filter_dict = dict()
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96 #set $filter_dict['filter'] = 'regex'
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97 #set $filter_dict['pattern'] = '^(%s).*$' % '|'.join([chr(int(x)).replace('|','[|]') for x in (str($fi.filter.comment_char)).split(',')])
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98 #set $filter_dict['action'] = 'exclude_match'
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99 #silent $input_filters.append($filter_dict)
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100 #elif $fi.filter.filter_type == 'regex':
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101 #set $filter_dict = dict()
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102 #set $filter_dict['filter'] = str($fi.filter.filter_type)
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103 #set $filter_dict['pattern'] = str($fi.filter.regex_pattern)
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104 #set $filter_dict['action'] = str($fi.filter.regex_action)
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105 #silent $input_filters.append($filter_dict)
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106 #elif $fi.filter.filter_type == 'select_columns':
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107 #set $filter_dict = dict()
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108 #set $filter_dict['filter'] = str($fi.filter.filter_type)
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109 #set $filter_dict['columns'] = [int(str($ci).replace('c','')) for $ci in str($fi.filter.columns).split(',')]
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110 #silent $input_filters.append($filter_dict)
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111 #elif $fi.filter.filter_type == 'replace':
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112 #set $filter_dict = dict()
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113 #set $filter_dict['filter'] = str($fi.filter.filter_type)
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114 #set $filter_dict['column'] = int(str($fi.filter.column).replace('c',''))
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115 #set $filter_dict['pattern'] = str($fi.filter.regex_pattern)
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116 #set $filter_dict['replace'] = str($fi.filter.regex_replace)
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117 #silent $input_filters.append($filter_dict)
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118 #elif str($fi.filter.filter_type).endswith('pend_line_num'):
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119 #set $filter_dict = dict()
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120 #set $filter_dict['filter'] = str($fi.filter.filter_type)
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121 #silent $input_filters.append($filter_dict)
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122 #elif str($fi.filter.filter_type).endswith('pend_text'):
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123 #set $filter_dict = dict()
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124 #set $filter_dict['filter'] = str($fi.filter.filter_type)
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125 #set $filter_dict['column_text'] = str($fi.filter.column_text)
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126 #silent $input_filters.append($filter_dict)
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127 #elif $fi.filter.filter_type == 'normalize':
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128 #set $filter_dict = dict()
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129 #set $filter_dict['filter'] = str($fi.filter.filter_type)
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130 #set $filter_dict['columns'] = [int(str($ci).replace('c','')) for $ci in str($fi.filter.columns).split(',')]
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131 #set $filter_dict['separator'] = str($fi.filter.separator)
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132 #silent $input_filters.append($filter_dict)
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133 #end if
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134 #end for
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135 #if $input_filters:
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136 #set $jtbl['filters'] = $input_filters
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137 #end if
0
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138 #set $jtbls += [$jtbl]
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139 #end for
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140 #echo $json.dumps($jtbldef)
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141 </configfile>
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142 </configfiles>
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143 <inputs>
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144 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
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145 <section name="add_to_database" expanded="false" title="Add tables to an existing database">
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146 <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database"
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147 help="Make sure your added table names are not already in this database"/>
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148 </section>
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149 <repeat name="tables" title="Database Table" min="0">
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150 <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/>
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151 <section name="input_opts" expanded="false" title="Filter Dataset Input">
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152 <repeat name="linefilters" title="Filter Tabular Input Lines">
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153 <conditional name="filter">
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154 <param name="filter_type" type="select" label="Filter By">
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155 <option value="skip">skip leading lines</option>
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156 <option value="comment">comment char</option>
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157 <option value="regex">by regex expression matching</option>
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158 <option value="select_columns">select columns</option>
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159 <option value="replace">regex replace value in column</option>
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160 <option value="prepend_line_num">prepend a line number column</option>
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161 <option value="append_line_num">append a line number column</option>
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162 <option value="prepend_text">prepend a column with the given text</option>
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163 <option value="append_text">append a column with the given text</option>
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164 <option value="normalize">normalize list columns, replicates row for each item in list</option>
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165 </param>
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166 <when value="skip">
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167 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines"
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168 help="Leave blank to use the comment lines metadata for this dataset" />
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169 </when>
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170 <when value="comment">
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171 <param name="comment_char" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are skipped">
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172 <option value="62">&gt;</option>
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173 <option value="64">@</option>
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174 <option value="43">+</option>
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175 <option value="60">&lt;</option>
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176 <option value="42">*</option>
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177 <option value="45">-</option>
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178 <option value="61">=</option>
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179 <option value="124">|</option>
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180 <option value="63">?</option>
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181 <option value="36">$</option>
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182 <option value="46">.</option>
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183 <option value="58">:</option>
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184 <option value="38">&amp;</option>
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185 <option value="37">%</option>
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186 <option value="94">^</option>
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187 <option value="35">&#35;</option>
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188 <option value="33">!</option>
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189 </param>
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190 </when>
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191 <when value="prepend_line_num"/>
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192 <when value="append_line_num"/>
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193 <when value="prepend_text">
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194 <param name="column_text" type="text" value="" label="text for column">
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195 </param>
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196 </when>
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197 <when value="append_text">
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198 <param name="column_text" type="text" value="" label="text for column">
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199 </param>
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200 </when>
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201 <when value="regex">
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202 <param name="regex_pattern" type="text" value="" label="regex pattern">
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203 <sanitizer sanitize="False"/>
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204 </param>
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205 <param name="regex_action" type="select" label="action for regex match">
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206 <option value="exclude_match">exclude line on pattern match</option>
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207 <option value="include_match">include line on pattern match</option>
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208 <option value="exclude_find">exclude line if pattern found</option>
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209 <option value="include_find">include line if pattern found</option>
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210 </param>
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211 </when>
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212 <when value="select_columns">
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213 <param name="columns" type="text" value="" label="enter column numbers to keep"
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214 help="example: 1,4,2 or c1,c4,c2(selects the first,fourth, and second columns)">
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215 <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</validator>
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216 </param>
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217 </when>
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218 <when value="replace">
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219 <param name="column" type="text" value="" label="enter column number to replace"
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220 help="example: 1 or c1 (selects the first column)">
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221 <validator type="regex" message="Column ordinal position separated by commas">^(c?[1-9]\d*)$</validator>
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222 </param>
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223 <param name="regex_pattern" type="text" value="" label="regex pattern">
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224 <sanitizer sanitize="False"/>
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225 </param>
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226 <param name="regex_replace" type="text" value="" label="replacement expression">
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227 <sanitizer sanitize="False"/>
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228 </param>
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229 </when>
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230 <when value="normalize">
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231 <param name="columns" type="text" value="" label="enter column numbers to normalize">
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232 <help><![CDATA[
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233 example: 2,4 or c2,c4 (selects the second, and fourth columns)
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234 If multiple columns are selected, they should have the same length and separator on each line
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235 ]]></help>
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236 <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</validator>
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237 </param>
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238 <param name="separator" type="text" value="," label="List item delimiter in column">
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239 <sanitizer sanitize="False"/>
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240 <validator type="regex" message="Anything but TAB or Newline">^[^\t\n\r\f\v]+$</validator>
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241 </param>
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242 </when>
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243 </conditional>
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244 </repeat>
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245 </section>
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246 <section name="tbl_opts" expanded="false" title="Table Options">
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247 <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table">
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248 <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help>
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249 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
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250 </param>
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251 <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)">
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252 <help>By default, table columns will be named: c1,c2,c3,...,cn (column names for a table must be unique)
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253 You can override the default names by entering a comma -separated list of names, e.g. ',name1,,,name2' would rename the second and fifth columns.
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254 </help>
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255 <sanitizer sanitize="False"/>
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256 <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+[^,"]*[]])?)*$</validator>
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257 </param>
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258 <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load the columns you have named into database"/>
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259 <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name"
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260 help="Only creates this additional column when a name is entered. (This can not be the same name as any of the other columns in this table.)">
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261 <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator>
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262 </param>
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263 <repeat name="indexes" title="Table Index">
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264 <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>
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265 <param name="index_columns" type="text" value="" label="Index on Columns">
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266 <help>Create an index on the column names: e,g, c1 or c2,c4</help>
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267 <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+[^,"]*[]])?)*$</validator>
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268 </param>
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269 </repeat>
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270 </section>
0
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271 </repeat>
5
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272 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history"/>
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273 <param name="sqlquery" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to generate tabular output">
5
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274 <help>By default: tables are named: t1,t2,...,tn and columns in each table: c1,c2,...,cn</help>
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275 <sanitizer sanitize="False"/>
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276 <validator type="regex" message="">^(?ims)\s*select\s+.*\s+from\s+.*$</validator>
0
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277 </param>
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278 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers from tabular output"/>
0
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279 </inputs>
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280 <outputs>
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281 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}">
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282 <filter>save_db or not (sqlquery and len(sqlquery) > 0)</filter>
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283 </data>
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284 <data format="tabular" name="output" label="query results on ${on_string}">
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285 <filter>sqlquery and len(sqlquery) > 0</filter>
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286 </data>
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287 </outputs>
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288 <tests>
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289
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290 <test>
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291 <repeat name="tables">
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292 <param name="table" ftype="tabular" value="customers.tsv"/>
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293 <param name="table_name" value="customers"/>
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294 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/>
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295 </repeat>
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296 <repeat name="tables">
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297 <param name="table" ftype="tabular" value="sales.tsv"/>
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298 <param name="table_name" value="sales"/>
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299 <param name="col_names" value="CustomerID,Date,SaleAmount"/>
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300 </repeat>
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301 <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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302 <output name="output" file="sales_results.tsv"/>
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303 </test>
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304
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305 <test>
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306 <repeat name="tables">
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307 <param name="table" ftype="tabular" value="customers.tsv"/>
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308 <param name="col_names" value=",FirstName,LastName,,DOB,"/>
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309 </repeat>
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310 <repeat name="tables">
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311 <param name="table" ftype="tabular" value="sales.tsv"/>
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312 </repeat>
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313 <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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314 <output name="output" file="sales_results.tsv"/>
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315 </test>
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316
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317 <test>
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318 <repeat name="tables">
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319 <param name="table" ftype="tabular" value="customers.tsv"/>
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320 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/>
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321 </repeat>
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322 <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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323 <output name="output" file="regex_results.tsv"/>
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324 </test>
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325
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326 <test>
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327 <repeat name="tables">
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328 <param name="table" ftype="tabular" value="IEDB.tsv"/>
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329 <param name="table_name" value="iedb"/>
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330 <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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331 </repeat>
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332 <repeat name="tables">
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333 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
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334 <param name="table_name" value="mhc_summary"/>
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335 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/>
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336 </repeat>
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337 <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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338 <output name="output" file="query_results.tsv"/>
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339 </test>
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340
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341 <test>
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342 <repeat name="tables">
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343 <param name="table" ftype="tabular" value="pets.tsv"/>
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344 <repeat name="linefilters">
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345 <param name="filter_type" value="comment"/>
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346 <param name="comment_char" value="35"/>
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347 </repeat>
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348 <repeat name="linefilters">
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349 <param name="filter_type" value="append_line_num"/>
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350 </repeat>
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351 <repeat name="linefilters">
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352 <param name="filter_type" value="select_columns"/>
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353 <param name="columns" value="7,2,3,4,1"/>
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354 </repeat>
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355 <repeat name="linefilters">
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356 <param name="filter_type" value="replace"/>
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357 <param name="column" value="c4"/>
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358 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/>
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359 <param name="regex_replace" value="19\3-\2-\1"/>
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360 </repeat>
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361 <param name="table_name" value="people"/>
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362 <param name="col_names" value="id,first,last,dob,pets"/>
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363
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364 </repeat>
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365 <repeat name="tables">
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366 <param name="table" ftype="tabular" value="pets.tsv"/>
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367 <repeat name="linefilters">
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368 <param name="filter_type" value="comment"/>
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369 <param name="comment_char" value="35"/>
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370 </repeat>
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371 <repeat name="linefilters">
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372 <param name="filter_type" value="append_line_num"/>
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373 </repeat>
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374 <repeat name="linefilters">
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375 <param name="filter_type" value="select_columns"/>
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376 <param name="columns" value="c7,c5,c6"/>
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377 </repeat>
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378 <repeat name="linefilters">
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379 <param name="filter_type" value="normalize"/>
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380 <param name="columns" value="c2,c3"/>
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381 <param name="separator" value=","/>
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382 </repeat>
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383 <param name="table_name" value="pet"/>
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384 <param name="col_names" value="id,name,animal"/>
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385 </repeat>
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386 <param name="sqlquery" value="SELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'"/>
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387 <output name="output" file="pet_normalized_query_results.tsv"/>
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388 </test>
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389
0
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390 </tests>
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391 <help><![CDATA[
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392 =============
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393 Query Tabular
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394 =============
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395
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396 **Inputs**
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397
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398 Loads tabular datasets into a SQLite_ data base.
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399
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400 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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401
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402
11
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403 **Input Line Filters**
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404
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405 As a tabular file is being read, line filters may be applied.
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406
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407 ::
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408
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409 - skip leading lines skip the first *number* of lines
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410 - comment char omit any lines that start with the specified comment character
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411 - by regex expression matching *include/exclude* lines the match the regex expression
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412 - select columns choose to include only selected columns in the order specified
11
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413 - regex replace value in column replace a field in a column using a regex substitution (good for date reformatting)
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414 - 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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415 - 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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416 - normalize list columns replicates the line for each item in the specified list *columns*
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417
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418
0
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419 **Outputs**
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420
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421 The results of a SQL query are output to the history as a tabular file.
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422
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423 The SQLite_ data base can also be saved and output as a dataset in the history.
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424
5
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425 *(The* **SQLite to tabular** *tool can run additional queries on this database.)*
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426
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427
0
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428 For help in using SQLite_ see: http://www.sqlite.org/docs.html
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429
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430 **NOTE:** input for SQLite dates input field must be in the format: *YYYY-MM-DD* for example: 2015-09-30
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431
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432 See: http://www.sqlite.org/lang_datefunc.html
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433
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434 **Example**
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435
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436 Given 2 tabular datasets: *customers* and *sales*
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437
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438 Dataset *customers*
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439
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440 Table name: "customers"
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441
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442 Column names: "CustomerID,FirstName,LastName,Email,DOB,Phone"
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443
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444 =========== ========== ========== ===================== ========== ============
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445 #CustomerID FirstName LastName Email DOB Phone
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446 =========== ========== ========== ===================== ========== ============
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447 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
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448 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
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449 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
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450 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
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451 =========== ========== ========== ===================== ========== ============
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452
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453 Dataset *sales*
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454
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455 Table name: "sales"
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456
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457 Column names: "CustomerID,Date,SaleAmount"
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458
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459 ============= ============ ============
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460 #CustomerID Date SaleAmount
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461 ============= ============ ============
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462 2 2004-05-06 100.22
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463 1 2004-05-07 99.95
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464 3 2004-05-07 122.95
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465 3 2004-05-13 100.00
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466 4 2004-05-22 555.55
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467 ============= ============ ============
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468
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469 The query
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470
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471 ::
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472
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473 SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales"
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diff changeset
474 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
parents:
diff changeset
475 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
parents:
diff changeset
476
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
477 Produces this tabular output:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
478
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
479 ========== ======== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
480 #FirstName LastName TotalSales
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
481 ========== ======== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
482 James Smith 555.55
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
483 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
484 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
485 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
486 ========== ======== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
487
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
488
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
489 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
jjohnson
parents:
diff changeset
490
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
491 ::
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
492
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
493 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
parents:
diff changeset
494 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
495 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
parents:
diff changeset
496
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
497 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
parents:
diff changeset
498
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
499 Column names: ,FirstName,LastName,,BirthDate
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
500
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
501 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
parents:
diff changeset
502
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
503 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
504 #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
parents:
diff changeset
505 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
506 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
507 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
508 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
509 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
510 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
511
11
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
512
0
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
513 Regular_expression_ functions are included for:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
514
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
515 ::
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
516
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
517 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
518
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
519 SELECT t1.FirstName, t1.LastName
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
520 FROM t1
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
521 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
522
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
523 Results:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
524
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
525 =========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
526 #FirstName LastName
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
527 =========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
528 Steven Goldfish
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
529 Paula Brown
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
530 =========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
531
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
532
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
533 ::
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
534
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
535 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
536 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
537
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
538 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:
diff changeset
539 FROM t1
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
540 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
parents:
diff changeset
541
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
542 Results:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
543
11
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
544
0
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
545 =========== ========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
546 #FirstName LastName DOB
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
547 =========== ========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
548 Steven Goldfish 04/04/74
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
549 Paula Brown 24/05/78
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
550 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:
diff changeset
551 =========== ========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
552
11
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
553
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
554 **Line Filtering Example**
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
555 *(Six filters are applied as the following file is read)*
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
556
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
557 ::
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
558
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
559 Input Tabular File:
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
560
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
561 #People with pets
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
562 Pets FirstName LastName DOB PetNames PetType
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
563 2 Paula Brown 24/05/78 Rex,Fluff dog,cat
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
564 1 Steven Jones 04/04/74 Allie cat
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
565 0 Jane Doe 24/05/78
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
566 1 James Smith 20/10/80 Spot
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
567
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
568
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
569 Filter 1 - append a line number column:
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
570
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
571 #People with pets 1
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
572 Pets FirstName LastName DOB PetNames PetType 2
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
573 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
574 1 Steven Jones 04/04/74 Allie cat 4
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
575 0 Jane Doe 24/05/78 5
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
576 1 James Smith 20/10/80 Spot 6
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
577
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
578 Filter 2 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
579
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
580 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
581 1 Steven Jones 04/04/74 Allie cat 4
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
582 0 Jane Doe 24/05/78 5
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
583 1 James Smith 20/10/80 Spot 6
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
584
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
585 Filter 3 - append a line number column:
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
586
fd16243931d6 Uploaded
jjohnson
parents: 8
diff changeset
587 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3 1
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588 1 Steven Jones 04/04/74 Allie cat 4 2
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589 0 Jane Doe 24/05/78 5 3
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590 1 James Smith 20/10/80 Spot 6 4
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591
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592 Filter 4 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format)
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593
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594 2 Paula Brown 1978-05-24 Rex,Fluff dog,cat 3 1
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jjohnson
parents: 8
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595 1 Steven Jones 1974-04-04 Allie cat 4 2
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jjohnson
parents: 8
diff changeset
596 0 Jane Doe 1978-05-24 5 3
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jjohnson
parents: 8
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597 1 James Smith 1980-10-20 Spot 6 4
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598
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599 Filter 5 - normalize list columns[5,6]:
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600
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601 2 Paula Brown 1978-05-24 Rex dog 3 1
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parents: 8
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602 2 Paula Brown 1978-05-24 Fluff cat 3 1
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jjohnson
parents: 8
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603 1 Steven Jones 1974-04-04 Allie cat 4 2
fd16243931d6 Uploaded
jjohnson
parents: 8
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604 0 Jane Doe 1978-05-24 5 3
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jjohnson
parents: 8
diff changeset
605 1 James Smith 1980-10-20 Spot 6 4
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jjohnson
parents: 8
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606
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parents: 8
diff changeset
607 Filter 6 - append a line number column:
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parents: 8
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608
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parents: 8
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609 2 Paula Brown 1978-05-24 Rex dog 3 1 1
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jjohnson
parents: 8
diff changeset
610 2 Paula Brown 1978-05-24 Fluff cat 3 1 2
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jjohnson
parents: 8
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611 1 Steven Jones 1974-04-04 Allie cat 4 2 3
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jjohnson
parents: 8
diff changeset
612 0 Jane Doe 1978-05-24 5 3 4
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jjohnson
parents: 8
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613 1 James Smith 1980-10-20 Spot 6 4 5
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jjohnson
parents: 8
diff changeset
614
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615
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616 Table name: pets
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617
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618 Table columns: Pets,FirstName,LastName,Birthdate,PetNames,PetType,line_num,entry_num,row_num
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619
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620 Query: SELECT * FROM pets
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621
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622 Result:
11
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623
14
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624 ====== ========== ======== ========== ========= ======== ========= ========== ========
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625 #Pets FirstName LastName BirthDate PetNames PetType line_num entry_num row_num
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parents: 11
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626 ====== ========== ======== ========== ========= ======== ========= ========== ========
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627 2 Paula Brown 1978-05-24 Rex dog 3 1 1
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jjohnson
parents: 11
diff changeset
628 2 Paula Brown 1978-05-24 Fluff cat 3 1 2
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parents: 11
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629 1 Steven Jones 1974-04-04 Allie cat 4 2 3
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jjohnson
parents: 11
diff changeset
630 0 Jane Doe 1978-05-24 5 3 4
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parents: 11
diff changeset
631 1 James Smith 1980-10-20 Spot 6 4 5
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jjohnson
parents: 11
diff changeset
632 ====== ========== ======== ========== ========= ======== ========= ========== ========
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633
11
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parents: 8
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634
14
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635 **Normalizing by Line Filtering into 2 Tables**
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636
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637 *People Table*
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638
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jjohnson
parents: 11
diff changeset
639 ::
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parents: 11
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640
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parents: 11
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641 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
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jjohnson
parents: 11
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642 Filter 2 - append a line number column:
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parents: 11
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643 Filter 3 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format)
16
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diff changeset
644 Filter 4 - select columns 7,2,3,4,1
14
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645
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646 Table: People
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parents: 14
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647 Columns: id,FirstName,LastName,DOB,Pets
11
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648
16
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649 == ========= ======== ========== ====
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650 id FirstName LastName DOB Pets
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651 == ========= ======== ========== ====
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parents: 14
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652 1 Paula Brown 1978-05-24 2
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jjohnson
parents: 14
diff changeset
653 2 Steven Jones 1974-04-04 1
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jjohnson
parents: 14
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654 3 Jane Doe 1978-05-24 0
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jjohnson
parents: 14
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655 4 James Smith 1980-10-20 1
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jjohnson
parents: 14
diff changeset
656 == ========= ======== ========== ====
14
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parents: 11
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657
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parents: 11
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658
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659 *Pet Table*
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parents: 11
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660
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jjohnson
parents: 11
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661 ::
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jjohnson
parents: 11
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662
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663 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
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parents: 11
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664 Filter 2 - append a line number column:
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parents: 11
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665 Filter 3 - by regex expression matching [exclude]: '^0\t' (exclude lines with no pets)
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parents: 11
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666 Filter 4 - normalize list columns[5,6]:
16
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parents: 14
diff changeset
667 Filter 5 - select columns 7,5,6
11
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parents: 8
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668
14
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669 Table: Pet
16
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parents: 14
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670 Columns: id,PetName,PetType
14
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parents: 11
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671
16
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parents: 14
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672 == ======== ========
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673 id PetName PetType
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parents: 14
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674 == ======== ========
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parents: 14
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675 1 Rex dog
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parents: 14
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676 1 Fluff cat
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jjohnson
parents: 14
diff changeset
677 2 Allie cat
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jjohnson
parents: 14
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678 4 Spot
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jjohnson
parents: 14
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679 == ======== ========
14
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parents: 11
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680
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681
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682 Query: SELECT FirstName,LastName,PetName FROM People join Pet on People.id = Pet.id WHERE PetType = 'cat';
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parents: 11
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683
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684 Result:
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parents: 11
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685
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686 ========= ======== ========
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parents: 11
diff changeset
687 FirstName LastName PetName
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parents: 11
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688 ========= ======== ========
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parents: 11
diff changeset
689 Paula Brown Fluff
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parents: 11
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690 Steven Jones Allie
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jjohnson
parents: 11
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691 ========= ======== ========
11
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parents: 8
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692
0
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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693 .. _Regular_expression: https://docs.python.org/release/2.7/library/re.html
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694 .. _SQLite: http://www.sqlite.org/index.html
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695
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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696 ]]></help>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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697 </tool>