Mercurial > repos > jjohnson > query_tabular

annotate query_tabular.xml @ 4:9d73dca48178 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty
author jjohnson
date Tue, 19 Apr 2016 16:46:18 -0400
parents 3e3b3c883bec
children 19ae309ec53c
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1 <tool id="query_tabular" name="Query Tabular" version="0.1.2">
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 interpreter="python"><![CDATA[
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10 query_tabular.py
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11 #if $save_db
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12 -s $sqlitedb
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13 #else
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14 -s $workdb
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15 #end if
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16 -j $table_json
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17 #if $sqlquery:
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18 -Q "$query_file"
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19 $no_header
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20 -o $output
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21 #end if
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22 ]]></command>
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23 <configfiles>
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24 <configfile name="query_file">
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25 $sqlquery
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26 </configfile>
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27 <configfile name="table_json">
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28 #import json
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29 #set $jtbldef = dict()
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30 #set $jtbls = []
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31 #set $jtbldef['tables'] = $jtbls
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32 #for $i,$tbl in enumerate($tables):
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33 #set $jtbl = dict()
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34 #set $jtbl['file_path'] = str($tbl.table)
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35 #if $tbl.tbl_opts.table_name:
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36 #set $tname = str($tbl.tbl_opts.table_name)
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37 #else
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38 #set $tname = 't' + str($i + 1)
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39 #end if
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40 #set $jtbl['table_name'] = $tname
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41 ## #if $tbl.tbl_opts.sel_cols:
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42 ## #set $jtbl['sel_cols'] = $tbl.tbl_opts.sel_cols el_cols
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43 ## #end if
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44 #if $tbl.tbl_opts.col_names:
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45 #set $col_names = str($tbl.tbl_opts.col_names)
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46 #if $tbl.tbl_opts.load_named_columns:
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47 #set $jtbl['load_named_columns'] = True
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48 #end if
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49 #else
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50 #set $col_names = ''
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51 #end if
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52 #set $jtbl['column_names'] = $col_names
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53 #if str($tbl.tbl_opts.skip_lines) != '':
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54 #set $jtbl['comment_lines'] = int($tbl.tbl_opts.skip_lines)
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55 #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0:
0
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56 #set $jtbl['comment_lines'] = int($tbl.table.metadata.comment_lines)
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57 #end if
4
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58 #set $idx_unique = []
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59 #set $idx_non = []
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60 #for $idx in $tbl.tbl_opts.indexes:
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61 #if $idx.unique:
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62 #silent $idx_unique.append(str($idx.index_columns))
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63 #else:
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64 #silent $idx_non.append(str($idx.index_columns))
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65 #end if
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66 #end for
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67 #if len($idx_unique) > 0:
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68 #set $jtbl['unique'] = $idx_unique
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69 #end if
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70 #if len($idx_non) > 0:
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71 #set $jtbl['index'] = $idx_non
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72 #end if
0
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73 #set $jtbls += [$jtbl]
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74 #end for
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75 #echo $json.dumps($jtbldef)
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76 </configfile>
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77 </configfiles>
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78 <inputs>
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79 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
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80 <repeat name="tables" title="Add tables" min="1">
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81 <param name="table" type="data" format="tabular" label="Dataset"/>
4
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82 <section name="tbl_opts" expanded="false" title="Table Options">
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83 <param name="table_name" type="text" value="" optional="true" label="Table name">
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84 <help>By default, tables will be named: t1,t2,...,tn</help>
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85 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
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86 </param>
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87 <param name="col_names" type="text" value="" optional="true" label="Column names">
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88 <help>By default, table columns will be named: c1,c2,c3,...,cn</help>
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89 <sanitizer sanitize="False"/>
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90 <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator>
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91 </param>
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92 <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load named columns into database"/>
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93 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" help="Leave blank to use the datatype comment lines metadata" />
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94 <repeat name="indexes">
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95 <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>
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96 <param name="index_columns" type="text" value="" label="Index on Columns">
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97 <help>Create an index on the column names: e,g, c1 or c2,c4</help>
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98 <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+[^,"]*[]])?)*$</validator>
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99 </param>
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100 </repeat>
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101 </section>
0
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102 </repeat>
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103 <param name="sqlquery" type="text" area="true" size="10x80" value="" optional="true" label="SQL Query">
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104 <help>By default, tables will be named: t1,t2,...,tn</help>
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105 <sanitizer sanitize="False"/>
4
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106 <validator type="regex" message="">^(?ims)\s*select\s+.*\s+from\s+.*$</validator>
0
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107 </param>
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108 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers"/>
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109
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110 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database"/>
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111 </inputs>
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112 <outputs>
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113 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}">
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114 <filter>save_db or not (sqlquery and len(sqlquery) > 0)</filter>
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115 </data>
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116 <data format="tabular" name="output" label="query results on ${on_string}">
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117 <filter>sqlquery and len(sqlquery) > 0</filter>
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118 </data>
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119 </outputs>
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120 <tests>
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121
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122 <test>
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123 <repeat name="tables">
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124 <param name="table" ftype="tabular" value="customers.tsv"/>
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125 <param name="table_name" value="customers"/>
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126 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/>
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127 </repeat>
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128 <repeat name="tables">
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129 <param name="table" ftype="tabular" value="sales.tsv"/>
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130 <param name="table_name" value="sales"/>
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131 <param name="col_names" value="CustomerID,Date,SaleAmount"/>
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132 </repeat>
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133 <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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134 <output name="output" file="sales_results.tsv"/>
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135 </test>
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136
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137 <test>
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138 <repeat name="tables">
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139 <param name="table" ftype="tabular" value="customers.tsv"/>
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140 <param name="col_names" value=",FirstName,LastName,,DOB,"/>
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141 </repeat>
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142 <repeat name="tables">
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143 <param name="table" ftype="tabular" value="sales.tsv"/>
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144 </repeat>
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145 <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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146 <output name="output" file="sales_results.tsv"/>
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147 </test>
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148
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149 <test>
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150 <repeat name="tables">
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151 <param name="table" ftype="tabular" value="customers.tsv"/>
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152 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/>
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153 </repeat>
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154 <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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155 <output name="output" file="regex_results.tsv"/>
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156 </test>
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157
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158 <test>
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159 <repeat name="tables">
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160 <param name="table" ftype="tabular" value="IEDB.tsv"/>
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161 <param name="table_name" value="iedb"/>
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162 <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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163 </repeat>
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164 <repeat name="tables">
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165 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
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166 <param name="table_name" value="mhc_summary"/>
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167 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/>
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168 </repeat>
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169 <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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170 <output name="output" file="query_results.tsv"/>
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171 </test>
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172
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173 </tests>
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174 <help><![CDATA[
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175 =============
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176 Query Tabular
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177 =============
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178
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179 **Inputs**
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180
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181 Loads tabular datasets into a SQLite_ data base.
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182
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183 **Outputs**
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184
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185 The results of a SQL query are output to the history as a tabular file.
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186
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187 The SQLite_ data base can also be saved and output as a dataset in the history.
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188
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189
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190 For help in using SQLite_ see: http://www.sqlite.org/docs.html
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191
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192 **NOTE:** input for SQLite dates input field must be in the format: *YYYY-MM-DD* for example: 2015-09-30
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193
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194 See: http://www.sqlite.org/lang_datefunc.html
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195
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196 **Example**
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197
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198 Given 2 tabular datasets: *customers* and *sales*
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199
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200 Dataset *customers*
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201
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202 Table name: "customers"
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203
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204 Column names: "CustomerID,FirstName,LastName,Email,DOB,Phone"
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205
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206 =========== ========== ========== ===================== ========== ============
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207 #CustomerID FirstName LastName Email DOB Phone
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208 =========== ========== ========== ===================== ========== ============
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209 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
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210 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
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211 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
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212 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
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213 =========== ========== ========== ===================== ========== ============
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214
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215 Dataset *sales*
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216
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217 Table name: "sales"
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218
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219 Column names: "CustomerID,Date,SaleAmount"
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220
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221 ============= ============ ============
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222 #CustomerID Date SaleAmount
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223 ============= ============ ============
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224 2 2004-05-06 100.22
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225 1 2004-05-07 99.95
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226 3 2004-05-07 122.95
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227 3 2004-05-13 100.00
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228 4 2004-05-22 555.55
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229 ============= ============ ============
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230
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231 The query
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232
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233 ::
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234
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235 SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales"
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236 FROM customers join sales on customers.CustomerID = sales.CustomerID
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237 GROUP BY customers.CustomerID ORDER BY TotalSales DESC;
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238
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239 Produces this tabular output:
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240
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241 ========== ======== ==========
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242 #FirstName LastName TotalSales
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243 ========== ======== ==========
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244 James Smith 555.55
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245 Paula Brown 222.95
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246 Steven Goldfish 100.22
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247 John Smith 99.95
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248 ========== ======== ==========
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249
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250
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251 If the optional Table name and Column names inputs are not used, the query would be:
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252
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253 ::
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254
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255 SELECT t1.c2 as "FirstName", t1.c3 as "LastName", sum(t2.c3) as "TotalSales"
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256 FROM t1 join t2 on t1.c1 = t2.c1
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257 GROUP BY t1.c1 ORDER BY TotalSales DESC;
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258
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259 You can selectively name columns, e.g. on the customers input you could just name columns 2,3, and 5:
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260
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261 Column names: ,FirstName,LastName,,BirthDate
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262
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263 Results in the following data base table
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264
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265 =========== ========== ========== ===================== ========== ============
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266 #c1 FirstName LastName c4 BirthDate c6
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267 =========== ========== ========== ===================== ========== ============
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268 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
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269 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
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270 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
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271 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
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272 =========== ========== ========== ===================== ========== ============
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273
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274 Regular_expression_ functions are included for:
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275
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276 ::
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277
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278 matching: re_match('pattern',column)
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279
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280 SELECT t1.FirstName, t1.LastName
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281 FROM t1
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282 WHERE re_match('^.*\.(net|org)$',c4)
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283
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284 Results:
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285
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286 =========== ==========
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287 #FirstName LastName
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288 =========== ==========
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289 Steven Goldfish
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290 Paula Brown
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291 =========== ==========
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292
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293
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294 ::
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295
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296 searching: re_search('pattern',column)
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297 substituting: re_sub('pattern','replacement,column)
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298
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299 SELECT t1.FirstName, t1.LastName, re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB"
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300 FROM t1
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301 WHERE re_search('[hp]er',c4)
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302
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303 Results:
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304
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305 =========== ========== ==========
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306 #FirstName LastName DOB
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307 =========== ========== ==========
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308 Steven Goldfish 04/04/74
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309 Paula Brown 24/05/78
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310 James Smith 20/10/80
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311 =========== ========== ==========
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312
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313 .. _Regular_expression: https://docs.python.org/release/2.7/library/re.html
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314 .. _SQLite: http://www.sqlite.org/index.html
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315
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316 ]]></help>
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317 </tool>