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1 <tool id="query_tabular" name="Query Tabular" version="0.1.0">
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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
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10 <command interpreter="python"><![CDATA[
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11 query_tabular.py
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12 #if $save_db
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13 -s $sqlitedb
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14 #else
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15 -s $workdb
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16 #end if
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17 #for $i,$tbl in enumerate($tables):
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18 #if $tbl.table_name
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19 #set $tname = $tbl.table_name
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20 #else
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21 #set $tname = 't' + str($i + 1)
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22 #end if
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23 #if $tbl.col_names:
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24 #set $col_names = ':' + str($tbl.col_names)
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25 #else
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26 #set $col_names = ''
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27 #end if
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28 -t ${tbl.table}=${tname}${$col_names}
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29 #end for
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30 #if $query:
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1
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31 -q "$query"
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32 $no_header
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0
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33 -o $output
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34 #end if
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35 ]]></command>
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36 <inputs>
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37 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
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38 <repeat name="tables" title="Add tables" min="1">
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39 <param name="table" type="data" format="tabular" label="Dataset"/>
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40 <param name="table_name" type="text" value="" optional="true" label="Table name">
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41 <help>By default, tables will be named: t1,t2,...,tn</help>
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42 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
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43 </param>
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44 <!--
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45 <param name="sel_cols" label="Include columns" type="data_column" multiple="true" data_ref="table" />
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46 -->
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47 <param name="col_names" type="text" value="" optional="true" label="Column names">
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48 <help>By default, table columns will be named: c1,c2,c3,...,cn</help>
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49 <validator type="regex" message="A List of separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores">^([A-Za-z]\w*)?(,([A-Za-z]\w*)?)*$</validator>
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50 </param>
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51 </repeat>
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52 <param name="query" type="text" area="true" size="10x80" value="" optional="true" label="SQL Query">
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53 <help>By default, tables will be named: t1,t2,...,tn</help>
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54 <sanitizer sanitize="False"/>
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55 <validator type="regex" message="">^(?i)\s*select\s+.*\s+from\s+.*$</validator>
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56 </param>
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1
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57 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers"/>
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58
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0
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59 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database"/>
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60 </inputs>
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61 <outputs>
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62 <data format="sqlite" name="sqlitedb" label="sqlite">
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63 <filter>save_db or not (query and len(query) > 0)</filter>
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64 </data>
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65 <data format="tabular" name="output" label="query results">
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66 <filter>query and len(query) > 0</filter>
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67 </data>
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68 </outputs>
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69 <tests>
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70
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71 <test>
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72 <repeat name="tables">
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73 <param name="table" ftype="tabular" value="customers.tsv"/>
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74 <param name="table_name" value="customers"/>
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75 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/>
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76 </repeat>
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77 <repeat name="tables">
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78 <param name="table" ftype="tabular" value="sales.tsv"/>
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79 <param name="table_name" value="sales"/>
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80 <param name="col_names" value="CustomerID,Date,SaleAmount"/>
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81 </repeat>
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82 <param name="query" value="SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC"/>
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83 <output name="output" file="sales_results.tsv"/>
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84 </test>
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85
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86 <test>
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87 <repeat name="tables">
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88 <param name="table" ftype="tabular" value="customers.tsv"/>
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89 <param name="col_names" value=",FirstName,LastName,,DOB,"/>
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90 </repeat>
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91 <repeat name="tables">
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92 <param name="table" ftype="tabular" value="sales.tsv"/>
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93 </repeat>
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94 <param name="query" value="SELECT FirstName,LastName,sum(t2.c3) as "TotalSales" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;"/>
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95 <output name="output" file="sales_results.tsv"/>
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96 </test>
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97
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98 <test>
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99 <repeat name="tables">
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100 <param name="table" ftype="tabular" value="IEDB.tsv"/>
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101 <param name="table_name" value="iedb"/>
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102 <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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103 </repeat>
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104 <repeat name="tables">
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105 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
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106 <param name="table_name" value="mhc_summary"/>
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107 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/>
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108 </repeat>
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109 <param name="query" 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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110 <output name="output" file="query_results.tsv"/>
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111 </test>
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112
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113 </tests>
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114 <help><![CDATA[
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115 =============
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116 Query Tabular
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117 =============
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118
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119 **Inputs**
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120
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121 Loads tabular datasets into a SQLite_ data base.
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122
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123 **Outputs**
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124
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125 The results of a SQL query are output to the history as a tabular file.
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126
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127 The SQLite_ data base can also be saved and output as a dataset in the history.
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128
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129
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130 For help in using SQLite_ see: http://www.sqlite.org/docs.html
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131
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132 **NOTE:** input for SQLite dates input field must be in the format: *YYYY-MM-DD* for example: 2015-09-30
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133
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134 See: http://www.sqlite.org/lang_datefunc.html
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135
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136 **Example**
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137
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138 Given 2 tabular datasets: *customers* and *sales*
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139
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140 Dataset *customers*
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141
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142 Table name: "customers"
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143
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144 Column names: "CustomerID,FirstName,LastName,Email,DOB,Phone"
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145
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146 =========== ========== ========== ===================== ========== ============
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147 #CustomerID FirstName LastName Email DOB Phone
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148 =========== ========== ========== ===================== ========== ============
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149 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
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150 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
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151 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
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152 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
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153 =========== ========== ========== ===================== ========== ============
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154
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155 Dataset *sales*
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156
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157 Table name: "sales"
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158
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159 Column names: "CustomerID,Date,SaleAmount"
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160
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161 ============= ============ ============
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162 #CustomerID Date SaleAmount
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163 ============= ============ ============
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164 2 2004-05-06 100.22
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165 1 2004-05-07 99.95
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166 3 2004-05-07 122.95
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167 3 2004-05-13 100.00
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168 4 2004-05-22 555.55
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169 ============= ============ ============
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170
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171 The query
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172
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173 ::
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174
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175 SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales"
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176 FROM customers join sales on customers.CustomerID = sales.CustomerID
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177 GROUP BY customers.CustomerID ORDER BY TotalSales DESC;
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178
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179 Produces this tabular output:
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180
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181 ========== ======== ==========
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182 #FirstName LastName TotalSales
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183 ========== ======== ==========
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184 James Smith 555.55
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185 Paula Brown 222.95
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186 Steven Goldfish 100.22
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187 John Smith 99.95
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188 ========== ======== ==========
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189
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190
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191 If the optional Table name and Column names inputs are not used, the query would be:
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192
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193 ::
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194
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195 SELECT t1.c2 as "FirstName", t1.c3 as "LastName", sum(t2.c3) as "TotalSales"
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196 FROM t1 join t2 on t1.c1 = t2.c1
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197 GROUP BY t1.c1 ORDER BY TotalSales DESC;
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198
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199 You can selectively name columns, e.g. on the customers input you could just name columns 2,3, and 5:
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200
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201 Column names: ,FirstName,LastName,,BirthDate
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202
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203 Results in the following data base table
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204
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205 =========== ========== ========== ===================== ========== ============
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206 #c1 FirstName LastName c4 BithDate c6
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207 =========== ========== ========== ===================== ========== ============
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208 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
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209 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
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210 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
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211 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
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212 =========== ========== ========== ===================== ========== ============
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213
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214 .. _SQLite: http://www.sqlite.org/index.html
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215
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216 ]]></help>
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217 </tool>
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