Mercurial > repos > jjohnson > query_tabular
annotate query_tabular.xml @ 13:49ca06d66762 draft
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author | jjohnson |
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date | Fri, 12 May 2017 10:21:05 -0400 |
parents | fd16243931d6 |
children | 3003fe70f297 |
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11 | 1 <tool id="query_tabular" name="Query Tabular" version="3.0.0"> |
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2 <description>using sqlite sql</description> |
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3 |
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4 <requirements> |
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5 </requirements> |
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6 <stdio> |
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7 <exit_code range="1:" /> |
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8 </stdio> |
6 | 9 <command><![CDATA[ |
8 | 10 cat $query_file && |
6 | 11 #if $add_to_database.withdb: |
12 #if $save_db: | |
8 | 13 cp "$add_to_database.withdb" "$sqlitedb" && |
6 | 14 #else: |
15 cp "$add_to_database.withdb" "$workdb" && | |
16 #end if | |
17 #end if | |
18 python $__tool_directory__/query_tabular.py | |
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19 #if $save_db |
8 | 20 -s "$sqlitedb" |
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21 #else |
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22 -s $workdb |
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23 #end if |
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24 -j $table_json |
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25 #if $sqlquery: |
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26 -Q "$query_file" |
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27 $no_header |
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28 -o $output |
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29 #end if |
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30 ]]></command> |
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31 <configfiles> |
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32 <configfile name="query_file"> |
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33 $sqlquery |
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34 </configfile> |
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35 <configfile name="table_json"> |
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36 #import json |
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37 #set $jtbldef = dict() |
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38 #set $jtbls = [] |
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39 #set $jtbldef['tables'] = $jtbls |
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40 #for $i,$tbl in enumerate($tables): |
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41 #set $jtbl = dict() |
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42 #set $jtbl['file_path'] = str($tbl.table) |
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43 #if $tbl.tbl_opts.table_name: |
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44 #set $tname = str($tbl.tbl_opts.table_name) |
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45 #else |
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46 #set $tname = 't' + str($i + 1) |
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47 #end if |
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48 #set $jtbl['table_name'] = $tname |
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49 ## #if $tbl.tbl_opts.sel_cols: |
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50 ## #set $jtbl['sel_cols'] = $tbl.tbl_opts.sel_cols el_cols |
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51 ## #end if |
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52 #if $tbl.tbl_opts.pkey_autoincr: |
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53 #set $jtbl['pkey_autoincr'] = str($tbl.tbl_opts.pkey_autoincr) |
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54 #end if |
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55 #if $tbl.tbl_opts.col_names: |
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56 #set $col_names = str($tbl.tbl_opts.col_names) |
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57 #if $tbl.tbl_opts.load_named_columns: |
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58 #set $jtbl['load_named_columns'] = True |
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59 #end if |
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60 #else |
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61 #set $col_names = '' |
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62 #end if |
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63 #set $jtbl['column_names'] = $col_names |
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64 #set $idx_unique = [] |
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65 #set $idx_non = [] |
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66 #for $idx in $tbl.tbl_opts.indexes: |
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67 #if $idx.unique: |
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68 #silent $idx_unique.append(str($idx.index_columns)) |
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69 #else: |
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70 #silent $idx_non.append(str($idx.index_columns)) |
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71 #end if |
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72 #end for |
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73 #if len($idx_unique) > 0: |
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74 #set $jtbl['unique'] = $idx_unique |
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75 #end if |
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76 #if len($idx_non) > 0: |
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77 #set $jtbl['index'] = $idx_non |
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78 #end if |
6 | 79 #set $input_filters = [] |
80 #for $fi in $tbl.input_opts.linefilters: | |
81 #if $fi.filter.filter_type == 'skip': | |
11 | 82 #set $skip_lines = None |
8 | 83 #if str($fi.filter.skip_lines) != '': |
11 | 84 #set $skip_lines = int($fi.filter.skip_lines) |
6 | 85 #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0: |
11 | 86 #set $skip_lines = int($tbl.table.metadata.comment_lines) |
87 #end if | |
88 #if $skip_lines is not None: | |
89 #set $filter_dict = dict() | |
90 #set $filter_dict['filter'] = str($fi.filter.filter_type) | |
91 #set $filter_dict['count'] = $skip_lines | |
92 #silent $input_filters.append($filter_dict) | |
6 | 93 #end if |
94 #elif $fi.filter.filter_type == 'comment': | |
11 | 95 #set $filter_dict = dict() |
96 #set $filter_dict['filter'] = 'regex' | |
97 #set $filter_dict['pattern'] = '^' + str($fi.filter.comment_char) | |
98 #set $filter_dict['action'] = 'exclude' | |
99 #silent $input_filters.append($filter_dict) | |
6 | 100 #elif $fi.filter.filter_type == 'regex': |
101 #set $filter_dict = dict() | |
102 #set $filter_dict['filter'] = str($fi.filter.filter_type) | |
103 #set $filter_dict['pattern'] = str($fi.filter.regex_pattern) | |
104 #set $filter_dict['action'] = str($fi.filter.regex_action) | |
105 #silent $input_filters.append($filter_dict) | |
106 #elif $fi.filter.filter_type == 'replace': | |
107 #set $filter_dict = dict() | |
108 #set $filter_dict['filter'] = str($fi.filter.filter_type) | |
109 #set $filter_dict['column'] = int(str($fi.filter.column)) | |
110 #set $filter_dict['pattern'] = str($fi.filter.regex_pattern) | |
111 #set $filter_dict['replace'] = str($fi.filter.regex_replace) | |
112 #silent $input_filters.append($filter_dict) | |
11 | 113 #elif str($fi.filter.filter_type).endswith('pend_line_num'): |
114 #set $filter_dict = dict() | |
115 #set $filter_dict['filter'] = str($fi.filter.filter_type) | |
116 #silent $input_filters.append($filter_dict) | |
117 #elif $fi.filter.filter_type == 'normalize': | |
118 #set $filter_dict = dict() | |
119 #set $filter_dict['filter'] = str($fi.filter.filter_type) | |
120 #set $filter_dict['columns'] = [int(str($ci)) for $ci in str($fi.filter.columns).split(',')] | |
121 #set $filter_dict['separator'] = str($fi.filter.separator) | |
122 #silent $input_filters.append($filter_dict) | |
6 | 123 #end if |
124 #end for | |
125 #if $input_filters: | |
126 #set $jtbl['filters'] = $input_filters | |
127 #end if | |
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128 #set $jtbls += [$jtbl] |
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129 #end for |
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130 #echo $json.dumps($jtbldef) |
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131 </configfile> |
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132 </configfiles> |
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133 <inputs> |
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134 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/> |
6 | 135 <section name="add_to_database" expanded="false" title="Add tables to an existing database"> |
136 <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database" | |
137 help="Make sure your added table names are not already in this database"/> | |
138 </section> | |
8 | 139 <repeat name="tables" title="Database Table" min="0"> |
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140 <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/> |
6 | 141 <section name="input_opts" expanded="false" title="Filter Dataset Input"> |
142 <repeat name="linefilters" title="Filter Tabular Input Lines"> | |
143 <conditional name="filter"> | |
144 <param name="filter_type" type="select" label="Filter By"> | |
145 <option value="skip">skip leading lines</option> | |
146 <option value="comment">comment char</option> | |
147 <option value="regex">by regex expression matching</option> | |
148 <option value="replace">regex replace value in column</option> | |
11 | 149 <option value="prepend_line_num">prepend a line number column</option> |
150 <option value="append_line_num">append a line number column</option> | |
6 | 151 <option value="normalize">normalize list columns, replicates row for each item in list</option> |
152 </param> | |
153 <when value="skip"> | |
8 | 154 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" |
6 | 155 help="Leave blank to use the comment lines metadata for this dataset" /> |
156 </when> | |
157 <when value="comment"> | |
158 <param name="comment_char" type="text" value="#" label="Comment line starting text"> | |
8 | 159 <sanitizer sanitize="False"/> |
6 | 160 </param> |
161 </when> | |
11 | 162 <when value="prepend_line_num"/> |
163 <when value="append_line_num"/> | |
6 | 164 <when value="regex"> |
165 <param name="regex_pattern" type="text" value="" label="regex pattern"> | |
166 <sanitizer sanitize="False"/> | |
167 </param> | |
168 <param name="regex_action" type="select" label="action for regex match"> | |
169 <option value="exclude_match">exclude line on pattern match</option> | |
170 <option value="include_match">include line on pattern match</option> | |
171 <option value="exclude_find">exclude line if pattern found</option> | |
172 <option value="include_find">include line if pattern found</option> | |
173 </param> | |
174 </when> | |
175 <when value="replace"> | |
176 <param name="column" type="data_column" data_ref="table" label="Column to replace text" | |
177 help=""/> | |
178 <param name="regex_pattern" type="text" value="" label="regex pattern"> | |
179 <sanitizer sanitize="False"/> | |
180 </param> | |
181 <param name="regex_replace" type="text" value="" label="replacement expression"> | |
182 <sanitizer sanitize="False"/> | |
183 </param> | |
184 </when> | |
185 <when value="normalize"> | |
186 <param name="columns" type="data_column" data_ref="table" multiple="True" label="Columns to split" | |
11 | 187 help="If multiple columns are selected, they should have the same length and separator on each line"/> |
6 | 188 <param name="separator" type="text" value="," label="List item delimiter in column"> |
189 <sanitizer sanitize="False"/> | |
190 <validator type="regex" message="Anything but TAB or Newline">^[^\t\n\r\f\v]+$</validator> | |
191 </param> | |
192 </when> | |
193 </conditional> | |
194 </repeat> | |
195 </section> | |
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196 <section name="tbl_opts" expanded="false" title="Table Options"> |
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197 <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table"> |
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198 <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help> |
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199 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator> |
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200 </param> |
11 | 201 <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)"> |
202 <help>By default, table columns will be named: c1,c2,c3,...,cn (column names for a table must be unique) | |
203 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. | |
204 </help> | |
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205 <sanitizer sanitize="False"/> |
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206 <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+[^,"]*[]])?)*$</validator> |
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207 </param> |
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208 <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load the columns you have named into database"/> |
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209 <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name" |
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210 help="Only creates this additional column when a name is entered. (This can not be the same name as any of the other columns in this table.)"> |
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211 <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator> |
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212 </param> |
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213 <repeat name="indexes" title="Table Index"> |
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214 <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/> |
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215 <param name="index_columns" type="text" value="" label="Index on Columns"> |
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216 <help>Create an index on the column names: e,g, c1 or c2,c4</help> |
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217 <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+[^,"]*[]])?)*$</validator> |
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218 </param> |
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219 </repeat> |
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220 </section> |
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221 </repeat> |
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222 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history"/> |
6 | 223 <param name="sqlquery" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to generate tabular output"> |
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224 <help>By default: tables are named: t1,t2,...,tn and columns in each table: c1,c2,...,cn</help> |
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225 <sanitizer sanitize="False"/> |
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226 <validator type="regex" message="">^(?ims)\s*select\s+.*\s+from\s+.*$</validator> |
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227 </param> |
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228 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers from tabular output"/> |
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229 </inputs> |
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230 <outputs> |
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231 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}"> |
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232 <filter>save_db or not (sqlquery and len(sqlquery) > 0)</filter> |
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233 </data> |
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234 <data format="tabular" name="output" label="query results on ${on_string}"> |
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235 <filter>sqlquery and len(sqlquery) > 0</filter> |
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236 </data> |
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237 </outputs> |
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238 <tests> |
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239 |
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240 <test> |
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241 <repeat name="tables"> |
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242 <param name="table" ftype="tabular" value="customers.tsv"/> |
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243 <param name="table_name" value="customers"/> |
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244 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/> |
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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="sales.tsv"/> |
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248 <param name="table_name" value="sales"/> |
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249 <param name="col_names" value="CustomerID,Date,SaleAmount"/> |
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250 </repeat> |
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251 <param name="sqlquery" value="SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC"/> |
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252 <output name="output" file="sales_results.tsv"/> |
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253 </test> |
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254 |
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255 <test> |
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256 <repeat name="tables"> |
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257 <param name="table" ftype="tabular" value="customers.tsv"/> |
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258 <param name="col_names" value=",FirstName,LastName,,DOB,"/> |
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259 </repeat> |
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260 <repeat name="tables"> |
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261 <param name="table" ftype="tabular" value="sales.tsv"/> |
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262 </repeat> |
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263 <param name="sqlquery" value="SELECT FirstName,LastName,sum(t2.c3) as "TotalSales" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;"/> |
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264 <output name="output" file="sales_results.tsv"/> |
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265 </test> |
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266 |
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267 <test> |
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268 <repeat name="tables"> |
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269 <param name="table" ftype="tabular" value="customers.tsv"/> |
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270 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/> |
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271 </repeat> |
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272 <param name="sqlquery" value="select FirstName,LastName,re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB" from t1 WHERE re_search('[hp]er',c4)"/> |
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273 <output name="output" file="regex_results.tsv"/> |
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274 </test> |
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275 |
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276 <test> |
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277 <repeat name="tables"> |
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278 <param name="table" ftype="tabular" value="IEDB.tsv"/> |
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279 <param name="table_name" value="iedb"/> |
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280 <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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281 </repeat> |
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282 <repeat name="tables"> |
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283 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/> |
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284 <param name="table_name" value="mhc_summary"/> |
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285 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/> |
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286 </repeat> |
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287 <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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288 <output name="output" file="query_results.tsv"/> |
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289 </test> |
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290 |
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291 </tests> |
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292 <help><![CDATA[ |
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293 ============= |
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294 Query Tabular |
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295 ============= |
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296 |
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297 **Inputs** |
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298 |
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299 Loads tabular datasets into a SQLite_ data base. |
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300 |
6 | 301 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. |
302 | |
303 | |
11 | 304 **Input Line Filters** |
305 | |
306 As a tabular file is being read, line filters may be applied. | |
307 | |
308 :: | |
309 | |
310 - skip leading lines skip the first *number* of lines | |
311 - comment char omit any lines that start with the specified comment character | |
312 - by regex expression matching *include/exclude* lines the match the regex expression | |
313 - regex replace value in column replace a field in a column using a regex substitution (good for date reformatting) | |
314 - prepend a line number column each line has the ordinal value of the line read by this filter as the first column | |
315 - append a line number column each line has the ordinal value of the line read by this filter as the last column | |
316 - normalize list columns replicates the line for each item in the specified list *columns* | |
317 | |
318 | |
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319 **Outputs** |
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320 |
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321 The results of a SQL query are output to the history as a tabular file. |
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322 |
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323 The SQLite_ data base can also be saved and output as a dataset in the history. |
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324 |
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325 *(The* **SQLite to tabular** *tool can run additional queries on this database.)* |
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326 |
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327 |
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328 For help in using SQLite_ see: http://www.sqlite.org/docs.html |
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329 |
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330 **NOTE:** input for SQLite dates input field must be in the format: *YYYY-MM-DD* for example: 2015-09-30 |
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331 |
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332 See: http://www.sqlite.org/lang_datefunc.html |
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333 |
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334 **Example** |
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335 |
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336 Given 2 tabular datasets: *customers* and *sales* |
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337 |
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338 Dataset *customers* |
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339 |
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340 Table name: "customers" |
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341 |
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342 Column names: "CustomerID,FirstName,LastName,Email,DOB,Phone" |
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343 |
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344 =========== ========== ========== ===================== ========== ============ |
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345 #CustomerID FirstName LastName Email DOB Phone |
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346 =========== ========== ========== ===================== ========== ============ |
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347 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222 |
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348 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545 |
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349 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232 |
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350 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888 |
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351 =========== ========== ========== ===================== ========== ============ |
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352 |
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353 Dataset *sales* |
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354 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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|
355 Table name: "sales" |
926c62f7fa09
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356 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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357 Column names: "CustomerID,Date,SaleAmount" |
926c62f7fa09
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358 |
926c62f7fa09
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359 ============= ============ ============ |
926c62f7fa09
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360 #CustomerID Date SaleAmount |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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|
361 ============= ============ ============ |
926c62f7fa09
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362 2 2004-05-06 100.22 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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363 1 2004-05-07 99.95 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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364 3 2004-05-07 122.95 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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365 3 2004-05-13 100.00 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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366 4 2004-05-22 555.55 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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367 ============= ============ ============ |
926c62f7fa09
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368 |
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369 The query |
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370 |
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371 :: |
926c62f7fa09
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372 |
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373 SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales" |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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374 FROM customers join sales on customers.CustomerID = sales.CustomerID |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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375 GROUP BY customers.CustomerID ORDER BY TotalSales DESC; |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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376 |
926c62f7fa09
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377 Produces this tabular output: |
926c62f7fa09
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378 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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379 ========== ======== ========== |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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380 #FirstName LastName TotalSales |
926c62f7fa09
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381 ========== ======== ========== |
926c62f7fa09
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382 James Smith 555.55 |
926c62f7fa09
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383 Paula Brown 222.95 |
926c62f7fa09
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384 Steven Goldfish 100.22 |
926c62f7fa09
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385 John Smith 99.95 |
926c62f7fa09
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386 ========== ======== ========== |
926c62f7fa09
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387 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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388 |
926c62f7fa09
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389 If the optional Table name and Column names inputs are not used, the query would be: |
926c62f7fa09
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390 |
926c62f7fa09
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391 :: |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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392 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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393 SELECT t1.c2 as "FirstName", t1.c3 as "LastName", sum(t2.c3) as "TotalSales" |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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394 FROM t1 join t2 on t1.c1 = t2.c1 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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395 GROUP BY t1.c1 ORDER BY TotalSales DESC; |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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396 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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397 You can selectively name columns, e.g. on the customers input you could just name columns 2,3, and 5: |
926c62f7fa09
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398 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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399 Column names: ,FirstName,LastName,,BirthDate |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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400 |
926c62f7fa09
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401 Results in the following data base table |
926c62f7fa09
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402 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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|
403 =========== ========== ========== ===================== ========== ============ |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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404 #c1 FirstName LastName c4 BirthDate c6 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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405 =========== ========== ========== ===================== ========== ============ |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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406 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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407 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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408 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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409 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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|
410 =========== ========== ========== ===================== ========== ============ |
926c62f7fa09
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411 |
11 | 412 |
0
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413 Regular_expression_ functions are included for: |
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414 |
926c62f7fa09
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415 :: |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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416 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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|
417 matching: re_match('pattern',column) |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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418 |
926c62f7fa09
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419 SELECT t1.FirstName, t1.LastName |
926c62f7fa09
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420 FROM t1 |
926c62f7fa09
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421 WHERE re_match('^.*\.(net|org)$',c4) |
926c62f7fa09
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422 |
926c62f7fa09
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423 Results: |
926c62f7fa09
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424 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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425 =========== ========== |
926c62f7fa09
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426 #FirstName LastName |
926c62f7fa09
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427 =========== ========== |
926c62f7fa09
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428 Steven Goldfish |
926c62f7fa09
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429 Paula Brown |
926c62f7fa09
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430 =========== ========== |
926c62f7fa09
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431 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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432 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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433 :: |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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parents:
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|
434 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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|
435 searching: re_search('pattern',column) |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff
changeset
|
436 substituting: re_sub('pattern','replacement,column) |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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parents:
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changeset
|
437 |
926c62f7fa09
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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438 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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439 FROM t1 |
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440 WHERE re_search('[hp]er',c4) |
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441 |
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442 Results: |
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443 |
11 | 444 |
0
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445 =========== ========== ========== |
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446 #FirstName LastName DOB |
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447 =========== ========== ========== |
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448 Steven Goldfish 04/04/74 |
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449 Paula Brown 24/05/78 |
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450 James Smith 20/10/80 |
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451 =========== ========== ========== |
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452 |
11 | 453 |
454 **Line Filtering Example** | |
455 *(Six filters are applied as the following file is read)* | |
456 | |
457 :: | |
458 | |
459 Input Tabular File: | |
460 | |
461 #People with pets | |
462 Pets FirstName LastName DOB PetNames PetType | |
463 2 Paula Brown 24/05/78 Rex,Fluff dog,cat | |
464 1 Steven Jones 04/04/74 Allie cat | |
465 0 Jane Doe 24/05/78 | |
466 1 James Smith 20/10/80 Spot | |
467 | |
468 | |
469 Filter 1 - append a line number column: | |
470 | |
471 #People with pets 1 | |
472 Pets FirstName LastName DOB PetNames PetType 2 | |
473 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3 | |
474 1 Steven Jones 04/04/74 Allie cat 4 | |
475 0 Jane Doe 24/05/78 5 | |
476 1 James Smith 20/10/80 Spot 6 | |
477 | |
478 Filter 2 - by regex expression matching [include]: '^\d+' (include lines that start with a number) | |
479 | |
480 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3 | |
481 1 Steven Jones 04/04/74 Allie cat 4 | |
482 0 Jane Doe 24/05/78 5 | |
483 1 James Smith 20/10/80 Spot 6 | |
484 | |
485 Filter 3 - append a line number column: | |
486 | |
487 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3 1 | |
488 1 Steven Jones 04/04/74 Allie cat 4 2 | |
489 0 Jane Doe 24/05/78 5 3 | |
490 1 James Smith 20/10/80 Spot 6 4 | |
491 | |
492 Filter 4 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format) | |
493 | |
494 2 Paula Brown 1978-05-24 Rex,Fluff dog,cat 3 1 | |
495 1 Steven Jones 1974-04-04 Allie cat 4 2 | |
496 0 Jane Doe 1978-05-24 5 3 | |
497 1 James Smith 1980-10-20 Spot 6 4 | |
498 | |
499 Filter 5 - normalize list columns[5,6]: | |
500 | |
501 2 Paula Brown 1978-05-24 Rex dog 3 1 | |
502 2 Paula Brown 1978-05-24 Fluff cat 3 1 | |
503 1 Steven Jones 1974-04-04 Allie cat 4 2 | |
504 0 Jane Doe 1978-05-24 5 3 | |
505 1 James Smith 1980-10-20 Spot 6 4 | |
506 | |
507 Filter 6 - append a line number column: | |
508 | |
509 2 Paula Brown 1978-05-24 Rex dog 3 1 1 | |
510 2 Paula Brown 1978-05-24 Fluff cat 3 1 2 | |
511 1 Steven Jones 1974-04-04 Allie cat 4 2 3 | |
512 0 Jane Doe 1978-05-24 5 3 4 | |
513 1 James Smith 1980-10-20 Spot 6 4 5 | |
514 | |
515 | |
516 Table name: pets | |
517 | |
518 Table columns: Pets,FirstName,LastName,Birthdate,PetNames,PetType,line_num,entry_num,row_num | |
519 | |
520 Query: SELECT * FROM pets | |
521 | |
522 Result: | |
523 | |
524 ===== ========= ======== ========== ======== ======= ======== ========= ======= | |
525 #Pets FirstName LastName Brithdate PetNames PetType line_num entry_num row_num | |
526 ===== ========= ======== ========== ======== ======= ======== ========= ======= | |
527 2 Paula Brown 1978-05-24 Rex dog 3 1 1 | |
528 2 Paula Brown 1978-05-24 Fluff cat 3 1 2 | |
529 1 Steven Jones 1974-04-04 Allie cat 4 2 3 | |
530 0 Jane Doe 1978-05-24 5 3 4 | |
531 1 James Smith 1980-10-20 Spot 6 4 5 | |
532 ===== ========= ======== ========== ======== ======= ======== ========= ======= | |
533 | |
534 | |
0
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535 .. _Regular_expression: https://docs.python.org/release/2.7/library/re.html |
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536 .. _SQLite: http://www.sqlite.org/index.html |
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537 |
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538 ]]></help> |
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539 </tool> |