Mercurial > repos > jjohnson > query_tabular

annotate query_tabular.xml @ 20:ab27c4bd14b9 draft

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author jjohnson
date Fri, 14 Jul 2017 11:39:27 -0400
parents b9f797bf4f38
children 357fe86f245d
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1 <tool id="query_tabular" name="Query Tabular" version="5.0.0">
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2 <description>using sqlite sql</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <requirements>
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1:" />
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12 </stdio>
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13 <command><![CDATA[
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14 cat $query_file &&
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15 #if $add_to_database.withdb:
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16 #if $save_db:
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17 cp "$add_to_database.withdb" "$sqlitedb" &&
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18 #else:
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19 cp "$add_to_database.withdb" "$workdb" &&
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20 #end if
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21 #end if
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22 python $__tool_directory__/query_tabular.py
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23 #if $save_db
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24 -s "$sqlitedb"
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25 #else
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26 -s $workdb
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27 #end if
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28 -j $table_json
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29 #if $sqlquery:
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30 -Q "$query_file"
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31 $no_header
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32 -o $output
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33 #end if
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34 ]]></command>
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35 <configfiles>
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36 <configfile name="query_file">
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37 $sqlquery
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38 </configfile>
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39 <configfile name="table_json">
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40 #import json
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41 #set $jtbldef = dict()
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42 #set $jtbls = []
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43 #set $jtbldef['tables'] = $jtbls
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44 #for $i,$tbl in enumerate($tables):
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45 #set $jtbl = dict()
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46 #set $jtbl['file_path'] = str($tbl.table)
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47 #if $tbl.tbl_opts.table_name:
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48 #set $tname = str($tbl.tbl_opts.table_name)
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49 #else
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50 #set $tname = 't' + str($i + 1)
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51 #end if
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52 #set $jtbl['table_name'] = $tname
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53 ## #if $tbl.tbl_opts.sel_cols:
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54 ## #set $jtbl['sel_cols'] = $tbl.tbl_opts.sel_cols el_cols
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55 ## #end if
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56 #if $tbl.tbl_opts.pkey_autoincr:
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57 #set $jtbl['pkey_autoincr'] = str($tbl.tbl_opts.pkey_autoincr)
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58 #end if
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59 #if $tbl.tbl_opts.col_names:
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60 #set $col_names = str($tbl.tbl_opts.col_names)
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61 #if $tbl.tbl_opts.load_named_columns:
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62 #set $jtbl['load_named_columns'] = True
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63 #end if
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64 #else
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65 #set $col_names = ''
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66 #end if
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67 #set $jtbl['column_names'] = $col_names
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68 #set $idx_unique = []
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69 #set $idx_non = []
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70 #for $idx in $tbl.tbl_opts.indexes:
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71 #if $idx.unique:
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72 #silent $idx_unique.append(str($idx.index_columns))
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73 #else:
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74 #silent $idx_non.append(str($idx.index_columns))
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75 #end if
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76 #end for
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77 #if len($idx_unique) > 0:
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78 #set $jtbl['unique'] = $idx_unique
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79 #end if
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80 #if len($idx_non) > 0:
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81 #set $jtbl['index'] = $idx_non
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82 #end if
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83 #set $linefilters = $tbl.input_opts.linefilters
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84 @LINEFILTERS@
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85 #if $input_filters:
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86 #set $jtbl['filters'] = $input_filters
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87 #end if
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88 #set $jtbls += [$jtbl]
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89 #end for
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90 #echo $json.dumps($jtbldef)
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91 </configfile>
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92 </configfiles>
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93 <inputs>
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94 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
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95 <section name="add_to_database" expanded="false" title="Add tables to an existing database">
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96 <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database"
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97 help="Make sure your added table names are not already in this database"/>
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98 </section>
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99 <repeat name="tables" title="Database Table" min="0">
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100 <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/>
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101 <section name="input_opts" expanded="false" title="Filter Dataset Input">
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102 <expand macro="macro_line_filters" />
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103 </section>
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104 <section name="tbl_opts" expanded="false" title="Table Options">
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105 <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table">
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106 <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help>
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107 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
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108 </param>
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109 <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)">
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110 <help>By default, table columns will be named: c1,c2,c3,...,cn (column names for a table must be unique)
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111 You can override the default names by entering a comma -separated list of names, e.g. ',name1,,,name2' would rename the second and fifth columns.
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112 </help>
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113 <sanitizer sanitize="False"/>
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114 <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator>
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115 </param>
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116 <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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117 <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name"
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118 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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119 <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator>
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120 </param>
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121 <repeat name="indexes" title="Table Index">
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122 <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>
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123 <param name="index_columns" type="text" value="" label="Index on Columns">
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124 <help>Create an index on the column names: e,g, c1 or c2,c4</help>
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125 <validator type="regex" message="Column name, separated by commes if more than one">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator>
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126 </param>
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127 </repeat>
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128 </section>
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129 </repeat>
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130 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history"
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131 help="SQLite to tabular tool can run additional queries on this database"/>
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132 <param name="sqlquery" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to generate tabular output">
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133 <help>By default: tables are named: t1,t2,...,tn and columns in each table: c1,c2,...,cn</help>
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134 <sanitizer sanitize="False"/>
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135 <validator type="regex" message="">^(?ims)\s*select\s+.*\s+from\s+.*$</validator>
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136 </param>
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137 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers from tabular output"/>
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138 </inputs>
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139 <outputs>
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140 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}">
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141 <filter>save_db</filter>
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142 </data>
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143 <data format="tabular" name="output" label="query results on ${on_string}">
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144 <filter>not save_db or (sqlquery and len(sqlquery.strip()) > 0)</filter>
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145 </data>
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146 </outputs>
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147 <tests>
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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="table_name" value="customers"/>
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153 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/>
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154 </repeat>
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155 <repeat name="tables">
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156 <param name="table" ftype="tabular" value="sales.tsv"/>
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157 <param name="table_name" value="sales"/>
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158 <param name="col_names" value="CustomerID,Date,SaleAmount"/>
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159 </repeat>
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160 <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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161 <output name="output" file="sales_results.tsv"/>
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162 </test>
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163
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164 <test>
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165 <repeat name="tables">
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166 <param name="table" ftype="tabular" value="customers.tsv"/>
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167 <param name="col_names" value=",FirstName,LastName,,DOB,"/>
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168 </repeat>
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169 <repeat name="tables">
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170 <param name="table" ftype="tabular" value="sales.tsv"/>
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171 </repeat>
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172 <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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173 <output name="output" file="sales_results.tsv"/>
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174 </test>
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175
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176 <test>
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177 <repeat name="tables">
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178 <param name="table" ftype="tabular" value="customers.tsv"/>
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179 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/>
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180 </repeat>
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181 <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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182 <output name="output" file="regex_results.tsv"/>
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183 </test>
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184
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185 <test>
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186 <repeat name="tables">
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187 <param name="table" ftype="tabular" value="IEDB.tsv"/>
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188 <param name="table_name" value="iedb"/>
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189 <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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190 </repeat>
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191 <repeat name="tables">
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192 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
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193 <param name="table_name" value="mhc_summary"/>
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194 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/>
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195 </repeat>
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196 <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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197 <output name="output" file="query_results.tsv"/>
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198 </test>
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199
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200 <test>
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201 <repeat name="tables">
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202 <param name="table" ftype="tabular" value="pets.tsv"/>
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203 <repeat name="linefilters">
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204 <param name="filter_type" value="comment"/>
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205 <param name="comment_char" value="35"/>
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206 </repeat>
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207 <repeat name="linefilters">
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208 <param name="filter_type" value="append_line_num"/>
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209 </repeat>
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210 <repeat name="linefilters">
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211 <param name="filter_type" value="select_columns"/>
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212 <param name="columns" value="7,2,3,4,1"/>
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213 </repeat>
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214 <repeat name="linefilters">
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215 <param name="filter_type" value="replace"/>
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216 <param name="column" value="c4"/>
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217 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/>
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218 <param name="regex_replace" value="19\3-\2-\1"/>
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219 </repeat>
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220 <param name="table_name" value="people"/>
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221 <param name="col_names" value="id,first,last,dob,pets"/>
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222
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223 </repeat>
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224 <repeat name="tables">
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225 <param name="table" ftype="tabular" value="pets.tsv"/>
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226 <repeat name="linefilters">
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227 <param name="filter_type" value="comment"/>
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228 <param name="comment_char" value="35"/>
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229 </repeat>
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230 <repeat name="linefilters">
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231 <param name="filter_type" value="append_line_num"/>
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232 </repeat>
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233 <repeat name="linefilters">
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234 <param name="filter_type" value="select_columns"/>
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235 <param name="columns" value="c7,c5,c6"/>
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236 </repeat>
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237 <repeat name="linefilters">
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238 <param name="filter_type" value="normalize"/>
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239 <param name="columns" value="c2,c3"/>
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240 <param name="separator" value=","/>
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241 </repeat>
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242 <param name="table_name" value="pet"/>
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243 <param name="col_names" value="id,name,animal"/>
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244 </repeat>
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245 <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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246 <output name="output" file="pet_normalized_query_results.tsv"/>
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247 </test>
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248
0
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249 </tests>
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250 <help><![CDATA[
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251 =============
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252 Query Tabular
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253 =============
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254
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255 **Inputs**
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256
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257 Loads tabular datasets into a SQLite_ data base.
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258
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259 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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260
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261
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262 @LINEFILTERS_HELP@
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263
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264
0
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265 **Outputs**
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266
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267 The results of a SQL query are output to the history as a tabular file.
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268
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269 The SQLite_ data base can also be saved and output as a dataset in the history.
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270
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271 *(The* **SQLite to tabular** *tool can run additional queries on this database.)*
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272
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273
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274 @QUERY_HELP@
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275
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276 @LINEFILTERS_HELP_EXAMPLE@
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277
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278
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279 Table name: pets
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280
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281 Table columns: Pets,FirstName,LastName,Birthdate,PetNames,PetType,line_num,entry_num,row_num
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282
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283 Query: SELECT * FROM pets
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284
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285 Result:
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286
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287 ====== ========== ======== ========== ========= ======== ========= ========== ========
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288 #Pets FirstName LastName BirthDate PetNames PetType line_num entry_num row_num
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289 ====== ========== ======== ========== ========= ======== ========= ========== ========
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290 2 Paula Brown 1978-05-24 Rex dog 3 1 1
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291 2 Paula Brown 1978-05-24 Fluff cat 3 1 2
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292 1 Steven Jones 1974-04-04 Allie cat 4 2 3
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293 0 Jane Doe 1978-05-24 5 3 4
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294 1 James Smith 1980-10-20 Spot 6 4 5
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295 ====== ========== ======== ========== ========= ======== ========= ========== ========
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296
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297
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298 **Normalizing by Line Filtering into 2 Tables**
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299
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300 *Relational database opertions work with single-valued column entries.
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301 To apply relational operations to tabular files that contain fields with lists of values,
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302 we need to "normalize" those fields, duplicating lines for each item in the list.
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303 In this example we create 2 tables, one for single-valued fields and a second with list-valued fields normalized.
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304 Becauce we add a line number first for each table, we can join the 2 tables on the line number column.*
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305 https://en.wikipedia.org/wiki/First_normal_form
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306
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307 *People Table*
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308
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309 ::
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310
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311 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
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312 Filter 2 - append a line number column:
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313 Filter 3 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format)
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314 Filter 4 - select columns 7,2,3,4,1
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315
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316 Table: People
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317 Columns: id,FirstName,LastName,DOB,Pets
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318
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319 == ========= ======== ========== ====
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320 id FirstName LastName DOB Pets
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321 == ========= ======== ========== ====
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322 1 Paula Brown 1978-05-24 2
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323 2 Steven Jones 1974-04-04 1
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324 3 Jane Doe 1978-05-24 0
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325 4 James Smith 1980-10-20 1
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326 == ========= ======== ========== ====
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327
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328
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329 *Pet Table*
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330
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331 ::
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332
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333 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
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334 Filter 2 - append a line number column:
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335 Filter 3 - by regex expression matching [exclude]: '^0\t' (exclude lines with no pets)
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336 Filter 4 - normalize list columns[5,6]:
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337 Filter 5 - select columns 7,5,6
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338
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339 Table: Pet
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340 Columns: id,PetName,PetType
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341
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342 == ======== ========
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343 id PetName PetType
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344 == ======== ========
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345 1 Rex dog
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346 1 Fluff cat
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347 2 Allie cat
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348 4 Spot
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349 == ======== ========
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350
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351
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352 Query: SELECT FirstName,LastName,PetName FROM People JOIN Pet ON People.id = Pet.id WHERE PetType = 'cat';
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353
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354 Result:
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355
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356 ========= ======== ========
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357 FirstName LastName PetName
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358 ========= ======== ========
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359 Paula Brown Fluff
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360 Steven Jones Allie
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361 ========= ======== ========
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362
0
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363
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364 ]]></help>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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365 </tool>