annotate query_tabular.xml @ 22:bed5018e7ae3 draft

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author jjohnson
date Mon, 17 Jul 2017 15:22:04 -0400
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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
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11 <command detect_errors="exit_code"><![CDATA[
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12 cat '$query_file' &&
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13 #if $add_to_database.withdb:
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14 #if $save_db:
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15 cp '$add_to_database.withdb' '$sqlitedb' &&
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16 #else:
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17 cp '$add_to_database.withdb' '$workdb' &&
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18 #end if
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19 #end if
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20 python '$__tool_directory__/query_tabular.py'
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21 #if $save_db
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22 -s '$sqlitedb'
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23 #else
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24 -s '$workdb'
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25 #end if
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26 -j '$table_json'
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27 #if $sqlquery:
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28 -Q '$query_file'
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29 $no_header
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30 -o '$output'
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31 #end if
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32 ]]></command>
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33 <configfiles>
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34 <configfile name="query_file">
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35 $sqlquery
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36 </configfile>
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37 <configfile name="table_json">
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38 #import json
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39 #set $jtbldef = dict()
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40 #set $jtbls = []
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41 #set $jtbldef['tables'] = $jtbls
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42 #for $i,$tbl in enumerate($tables):
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43 #set $jtbl = dict()
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44 #set $jtbl['file_path'] = str($tbl.table)
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45 #if $tbl.tbl_opts.table_name:
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46 #set $tname = str($tbl.tbl_opts.table_name)
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47 #else
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48 #set $tname = 't' + str($i + 1)
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49 #end if
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50 #set $jtbl['table_name'] = $tname
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51 ## #if $tbl.tbl_opts.sel_cols:
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52 ## #set $jtbl['sel_cols'] = $tbl.tbl_opts.sel_cols el_cols
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53 ## #end if
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54 #if $tbl.tbl_opts.pkey_autoincr:
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55 #set $jtbl['pkey_autoincr'] = str($tbl.tbl_opts.pkey_autoincr)
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56 #end if
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57 #if $tbl.tbl_opts.col_names:
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58 #set $col_names = str($tbl.tbl_opts.col_names)
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59 #if $tbl.tbl_opts.load_named_columns:
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60 #set $jtbl['load_named_columns'] = True
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61 #end if
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62 #else
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63 #set $col_names = ''
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64 #end if
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65 #set $jtbl['column_names'] = $col_names
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66 #set $idx_unique = []
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67 #set $idx_non = []
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68 #for $idx in $tbl.tbl_opts.indexes:
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69 #if $idx.unique:
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70 #silent $idx_unique.append(str($idx.index_columns))
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71 #else:
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72 #silent $idx_non.append(str($idx.index_columns))
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73 #end if
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74 #end for
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75 #if len($idx_unique) > 0:
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76 #set $jtbl['unique'] = $idx_unique
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77 #end if
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78 #if len($idx_non) > 0:
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79 #set $jtbl['index'] = $idx_non
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80 #end if
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81 #set $linefilters = $tbl.input_opts.linefilters
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82 @LINEFILTERS@
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83 #if $input_filters:
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84 #set $jtbl['filters'] = $input_filters
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85 #end if
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86 #set $jtbls += [$jtbl]
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87 #end for
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88 #echo $json.dumps($jtbldef)
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89 </configfile>
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90 </configfiles>
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91 <inputs>
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92 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
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93 <section name="add_to_database" expanded="false" title="Add tables to an existing database">
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94 <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database"
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95 help="Make sure your added table names are not already in this database"/>
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96 </section>
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97 <repeat name="tables" title="Database Table" min="0">
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98 <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/>
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99 <section name="input_opts" expanded="false" title="Filter Dataset Input">
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100 <expand macro="macro_line_filters" />
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101 </section>
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102 <section name="tbl_opts" expanded="false" title="Table Options">
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103 <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table">
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104 <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help>
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105 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
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106 </param>
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107 <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)">
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108 <help>By default, table columns will be named: c1,c2,c3,...,cn (column names for a table must be unique)
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109 You can override the default names by entering a comma -separated list of names, e.g. ',name1,,,name2' would rename the second and fifth columns.
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110 </help>
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111 <sanitizer sanitize="False"/>
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112 <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator>
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113 </param>
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114 <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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115 <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name"
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116 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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117 <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator>
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118 </param>
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119 <repeat name="indexes" title="Table Index">
4
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120 <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>
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121 <param name="index_columns" type="text" value="" label="Index on Columns">
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122 <help>Create an index on the column names: e,g, c1 or c2,c4</help>
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123 <validator type="regex" message="Column name, separated by commes if more than one">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator>
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124 </param>
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125 </repeat>
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126 </section>
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127 </repeat>
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128 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history"
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129 help="SQLite to tabular tool can run additional queries on this database"/>
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130 <param name="sqlquery" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to generate tabular output">
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131 <help>By default: tables are named: t1,t2,...,tn and columns in each table: c1,c2,...,cn</help>
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132 <sanitizer sanitize="False"/>
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133 <validator type="regex" message="">^(?ims)\s*select\s+.*\s+from\s+.*$</validator>
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134 </param>
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135 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers from tabular output"/>
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136 </inputs>
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137 <outputs>
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138 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}">
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139 <filter>save_db</filter>
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140 </data>
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141 <data format="tabular" name="output" label="query results on ${on_string}">
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142 <filter>not save_db or (sqlquery and len(sqlquery.strip()) > 0)</filter>
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143 </data>
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144 </outputs>
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145 <tests>
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146 <test>
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147 <repeat name="tables">
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148 <param name="table" ftype="tabular" value="customers.tsv"/>
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149 <section name="input_opts">
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150 <repeat name="linefilters">
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151 <conditional name="filter">
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152 <param name="filter_type" value="comment"/>
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153 <param name="comment_char" value="35"/>
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154 </conditional>
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155 </repeat>
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156 </section>
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157 <section name="tbl_opts">
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158 <param name="table_name" value="customers"/>
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159 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/>
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160 </section>
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161 </repeat>
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162 <repeat name="tables">
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163 <param name="table" ftype="tabular" value="sales.tsv"/>
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164 <section name="input_opts">
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165 <repeat name="linefilters">
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166 <conditional name="filter">
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167 <param name="filter_type" value="comment"/>
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168 <param name="comment_char" value="35"/>
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169 </conditional>
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170 </repeat>
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171 </section>
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172 <section name="tbl_opts">
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173 <param name="table_name" value="sales"/>
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174 <param name="col_names" value="CustomerID,Date,SaleAmount"/>
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175 </section>
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176 </repeat>
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177 <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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178 <output name="output" file="sales_results.tsv"/>
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179 </test>
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180
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181 <test>
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182 <repeat name="tables">
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183 <param name="table" ftype="tabular" value="customers.tsv"/>
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184 <section name="input_opts">
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185 <repeat name="linefilters">
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186 <conditional name="filter">
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187 <param name="filter_type" value="comment"/>
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188 <param name="comment_char" value="35"/>
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189 </conditional>
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190 </repeat>
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191 </section>
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192 <section name="tbl_opts">
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193 <param name="col_names" value=",FirstName,LastName,,DOB,"/>
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194 </section>
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195 </repeat>
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196 <repeat name="tables">
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197 <param name="table" ftype="tabular" value="sales.tsv"/>
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198 <section name="input_opts">
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199 <repeat name="linefilters">
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200 <conditional name="filter">
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201 <param name="filter_type" value="skip"/>
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202 <param name="skip_lines" value="1"/>
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203 </conditional>
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204 </repeat>
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205 </section>
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206 </repeat>
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207 <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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208 <output name="output" file="sales_results.tsv"/>
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209 </test>
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210
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211 <test>
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212 <repeat name="tables">
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213 <param name="table" ftype="tabular" value="customers.tsv"/>
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214 <section name="input_opts">
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215 <repeat name="linefilters">
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216 <conditional name="filter">
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217 <param name="filter_type" value="skip"/>
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218 <param name="skip_lines" value="1"/>
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219 </conditional>
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220 </repeat>
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221 </section>
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222 <section name="tbl_opts">
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223 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/>
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224 </section>
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225 </repeat>
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226 <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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227 <output name="output" file="regex_results.tsv"/>
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228 </test>
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229
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230 <test>
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231 <repeat name="tables">
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232 <param name="table" ftype="tabular" value="IEDB.tsv"/>
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233 <section name="input_opts">
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234 <repeat name="linefilters">
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235 <conditional name="filter">
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236 <param name="filter_type" value="comment"/>
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237 <param name="comment_char" value="35"/>
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238 </conditional>
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239 </repeat>
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240 </section>
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241 <section name="tbl_opts">
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242 <param name="table_name" value="iedb"/>
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243 <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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244 </section>
0
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245 </repeat>
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246 <repeat name="tables">
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247 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
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248 <section name="input_opts">
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249 <repeat name="linefilters">
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250 <conditional name="filter">
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251 <param name="filter_type" value="skip"/>
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252 <param name="skip_lines" value="1"/>
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253 </conditional>
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254 </repeat>
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255 </section>
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256 <section name="tbl_opts">
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257 <param name="table_name" value="mhc_summary"/>
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258 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/>
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259 </section>
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260 </repeat>
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261 <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,percentile_rank"/>
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262 <output name="output" file="query_results.tsv"/>
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263 </test>
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264
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265 <test>
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266 <section name="add_to_database">
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267 <param name="withdb" ftype="sqlite" value="testdb.sqlite"/>
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268 </section>
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269 <repeat name="tables">
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270 <param name="table" ftype="tabular" value="pets.tsv"/>
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271 <section name="input_opts">
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272 <repeat name="linefilters">
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273 <conditional name="filter">
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274 <param name="filter_type" value="regex"/>
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275 <param name="regex_pattern" value="^\d+"/>
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276 <param name="regex_action" value="include_find"/>
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277 </conditional>
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278 </repeat>
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279 <repeat name="linefilters">
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280 <conditional name="filter">
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281 <param name="filter_type" value="comment"/>
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282 <param name="comment_char" value="35"/>
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283 </conditional>
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284 </repeat>
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285 <repeat name="linefilters">
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286 <conditional name="filter">
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287 <param name="filter_type" value="append_line_num"/>
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288 </conditional>
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289 </repeat>
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290 <repeat name="linefilters">
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291 <conditional name="filter">
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292 <param name="filter_type" value="select_columns"/>
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293 <param name="columns" value="7,2,3,4,1"/>
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294 </conditional>
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295 </repeat>
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296 <repeat name="linefilters">
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297 <conditional name="filter">
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298 <param name="filter_type" value="replace"/>
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299 <param name="column" value="c4"/>
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300 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/>
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301 <param name="regex_replace" value="19\3-\2-\1"/>
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302 </conditional>
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303 </repeat>
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304 </section>
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305 <section name="tbl_opts">
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306 <param name="table_name" value="people"/>
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307 <param name="col_names" value="id,first,last,dob,pets"/>
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308 </section>
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309 </repeat>
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310 <param name="sqlquery" value="SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name"/>
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311 <output name="output" file="add_to_db_results.tsv"/>
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312 </test>
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313
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314 <test>
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315 <repeat name="tables">
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316 <param name="table" ftype="tabular" value="pets.tsv"/>
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317 <section name="input_opts">
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318 <repeat name="linefilters">
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319 <conditional name="filter">
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320 <param name="filter_type" value="regex"/>
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321 <param name="regex_pattern" value="^\d+"/>
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322 <param name="regex_action" value="include_find"/>
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323 </conditional>
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324 </repeat>
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325 <repeat name="linefilters">
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326 <conditional name="filter">
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327 <param name="filter_type" value="comment"/>
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328 <param name="comment_char" value="35"/>
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329 </conditional>
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330 </repeat>
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331 <repeat name="linefilters">
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332 <conditional name="filter">
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333 <param name="filter_type" value="append_line_num"/>
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334 </conditional>
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335 </repeat>
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336 <repeat name="linefilters">
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337 <conditional name="filter">
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338 <param name="filter_type" value="select_columns"/>
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339 <param name="columns" value="7,2,3,4,1"/>
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340 </conditional>
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341 </repeat>
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342 <repeat name="linefilters">
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343 <conditional name="filter">
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344 <param name="filter_type" value="replace"/>
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345 <param name="column" value="c4"/>
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346 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/>
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347 <param name="regex_replace" value="19\3-\2-\1"/>
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348 </conditional>
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349 </repeat>
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350 </section>
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351 <section name="tbl_opts">
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352 <param name="table_name" value="people"/>
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353 <param name="col_names" value="id,first,last,dob,pets"/>
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354 </section>
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355 </repeat>
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356 <repeat name="tables">
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357 <param name="table" ftype="tabular" value="pets.tsv"/>
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358 <section name="input_opts">
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359 <repeat name="linefilters">
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360 <conditional name="filter">
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361 <param name="filter_type" value="regex"/>
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362 <param name="regex_pattern" value="^\d+"/>
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363 <param name="regex_action" value="include_find"/>
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364 </conditional>
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365 </repeat>
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366 <repeat name="linefilters">
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367 <conditional name="filter">
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368 <param name="filter_type" value="append_line_num"/>
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369 </conditional>
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370 </repeat>
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371 <repeat name="linefilters">
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372 <conditional name="filter">
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373 <param name="filter_type" value="select_columns"/>
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374 <param name="columns" value="c7,c5,c6"/>
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375 </conditional>
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376 </repeat>
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377 <repeat name="linefilters">
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378 <conditional name="filter">
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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 </conditional>
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383 </repeat>
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384 </section>
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385 <section name="tbl_opts">
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386 <param name="table_name" value="pet"/>
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387 <param name="col_names" value="id,name,animal"/>
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388 </section>
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389 </repeat>
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390 <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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391 <output name="output" file="pet_normalized_query_results.tsv"/>
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392 </test>
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393
0
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394 </tests>
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395 <help><![CDATA[
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396 =============
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397 Query Tabular
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398 =============
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399
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400 **Inputs**
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401
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402 Loads tabular datasets into a SQLite_ data base.
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403
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404 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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405
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406
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407 @LINEFILTERS_HELP@
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408
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409
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410 **Outputs**
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411
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412 The results of a SQL query are output to the history as a tabular file.
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413
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414 The SQLite_ data base can also be saved and output as a dataset in the history.
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415
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416 *(The* **SQLite to tabular** *tool can run additional queries on this database.)*
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417
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418
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419 @QUERY_HELP@
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420
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421 @LINEFILTERS_HELP_EXAMPLE@
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422
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423
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424 Table name: pets
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425
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426 Table columns: Pets,FirstName,LastName,Birthdate,PetNames,PetType,line_num,entry_num,row_num
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427
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428 Query: SELECT * FROM pets
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429
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430 Result:
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431
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432 ====== ========== ======== ========== ========= ======== ========= ========== ========
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433 #Pets FirstName LastName BirthDate PetNames PetType line_num entry_num row_num
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434 ====== ========== ======== ========== ========= ======== ========= ========== ========
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435 2 Paula Brown 1978-05-24 Rex dog 3 1 1
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436 2 Paula Brown 1978-05-24 Fluff cat 3 1 2
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437 1 Steven Jones 1974-04-04 Allie cat 4 2 3
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438 0 Jane Doe 1978-05-24 5 3 4
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439 1 James Smith 1980-10-20 Spot 6 4 5
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440 ====== ========== ======== ========== ========= ======== ========= ========== ========
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441
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442
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443 **Normalizing by Line Filtering into 2 Tables**
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444
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445 *Relational database opertions work with single-valued column entries.
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446 To apply relational operations to tabular files that contain fields with lists of values,
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447 we need to "normalize" those fields, duplicating lines for each item in the list.
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448 In this example we create 2 tables, one for single-valued fields and a second with list-valued fields normalized.
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449 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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450 https://en.wikipedia.org/wiki/First_normal_form
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451
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452 *People Table*
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453
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454 ::
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455
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456 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
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457 Filter 2 - append a line number column:
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458 Filter 3 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format)
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459 Filter 4 - select columns 7,2,3,4,1
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460
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461 Table: People
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462 Columns: id,FirstName,LastName,DOB,Pets
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463
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464 == ========= ======== ========== ====
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465 id FirstName LastName DOB Pets
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466 == ========= ======== ========== ====
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467 1 Paula Brown 1978-05-24 2
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468 2 Steven Jones 1974-04-04 1
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469 3 Jane Doe 1978-05-24 0
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470 4 James Smith 1980-10-20 1
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471 == ========= ======== ========== ====
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472
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473
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474 *Pet Table*
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475
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476 ::
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477
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478 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
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479 Filter 2 - append a line number column:
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480 Filter 3 - by regex expression matching [exclude]: '^0\t' (exclude lines with no pets)
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481 Filter 4 - normalize list columns[5,6]:
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482 Filter 5 - select columns 7,5,6
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483
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484 Table: Pet
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485 Columns: id,PetName,PetType
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486
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487 == ======== ========
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488 id PetName PetType
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489 == ======== ========
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490 1 Rex dog
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491 1 Fluff cat
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492 2 Allie cat
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493 4 Spot
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494 == ======== ========
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495
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496
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497 Query: SELECT FirstName,LastName,PetName FROM People JOIN Pet ON People.id = Pet.id WHERE PetType = 'cat';
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498
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499 Result:
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500
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501 ========= ======== ========
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502 FirstName LastName PetName
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503 ========= ======== ========
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504 Paula Brown Fluff
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505 Steven Jones Allie
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506 ========= ======== ========
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507
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508
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509 ]]></help>
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510 </tool>