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comparison query_tabular.xml @ 21:357fe86f245d draft

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author jjohnson
date Fri, 14 Jul 2017 17:34:22 -0400
parents ab27c4bd14b9
children bed5018e7ae3
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20:ab27c4bd14b9 21:357fe86f245d
1 <tool id="query_tabular" name="Query Tabular" version="5.0.0"> 1 <tool id="query_tabular" name="Query Tabular" version="1.0.0">
2 <description>using sqlite sql</description> 2 <description>using sqlite sql</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 7
8 <requirements> 8 <requirements>
9 </requirements> 9 </requirements>
10 <stdio> 10
11 <exit_code range="1:" /> 11 <command detect_errors="exit_code"><![CDATA[
12 </stdio> 12 cat '$query_file' &&
13 <command><![CDATA[
14 cat $query_file &&
15 #if $add_to_database.withdb: 13 #if $add_to_database.withdb:
16 #if $save_db: 14 #if $save_db:
17 cp "$add_to_database.withdb" "$sqlitedb" && 15 cp '$add_to_database.withdb' '$sqlitedb' &&
18 #else: 16 #else:
19 cp "$add_to_database.withdb" "$workdb" && 17 cp '$add_to_database.withdb' '$workdb' &&
20 #end if 18 #end if
21 #end if 19 #end if
22 python $__tool_directory__/query_tabular.py 20 python '$__tool_directory__/query_tabular.py'
23 #if $save_db 21 #if $save_db
24 -s "$sqlitedb" 22 -s '$sqlitedb'
25 #else 23 #else
26 -s $workdb 24 -s '$workdb'
27 #end if 25 #end if
28 -j $table_json 26 -j '$table_json'
29 #if $sqlquery: 27 #if $sqlquery:
30 -Q "$query_file" 28 -Q '$query_file'
31 $no_header 29 $no_header
32 -o $output 30 -o '$output'
33 #end if 31 #end if
34 ]]></command> 32 ]]></command>
35 <configfiles> 33 <configfiles>
36 <configfile name="query_file"> 34 <configfile name="query_file">
37 $sqlquery 35 $sqlquery
143 <data format="tabular" name="output" label="query results on ${on_string}"> 141 <data format="tabular" name="output" label="query results on ${on_string}">
144 <filter>not save_db or (sqlquery and len(sqlquery.strip()) > 0)</filter> 142 <filter>not save_db or (sqlquery and len(sqlquery.strip()) > 0)</filter>
145 </data> 143 </data>
146 </outputs> 144 </outputs>
147 <tests> 145 <tests>
148
149 <test> 146 <test>
150 <repeat name="tables"> 147 <repeat name="tables">
151 <param name="table" ftype="tabular" value="customers.tsv"/> 148 <param name="table" ftype="tabular" value="customers.tsv"/>
152 <param name="table_name" value="customers"/> 149 <section name="input_opts">
153 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/> 150 <repeat name="linefilters">
151 <conditional name="filter">
152 <param name="filter_type" value="comment"/>
153 <param name="comment_char" value="35"/>
154 </conditional>
155 </repeat>
156 </section>
157 <section name="tbl_opts">
158 <param name="table_name" value="customers"/>
159 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/>
160 </section>
154 </repeat> 161 </repeat>
155 <repeat name="tables"> 162 <repeat name="tables">
156 <param name="table" ftype="tabular" value="sales.tsv"/> 163 <param name="table" ftype="tabular" value="sales.tsv"/>
157 <param name="table_name" value="sales"/> 164 <section name="input_opts">
158 <param name="col_names" value="CustomerID,Date,SaleAmount"/> 165 <repeat name="linefilters">
166 <conditional name="filter">
167 <param name="filter_type" value="comment"/>
168 <param name="comment_char" value="35"/>
169 </conditional>
170 </repeat>
171 </section>
172 <section name="tbl_opts">
173 <param name="table_name" value="sales"/>
174 <param name="col_names" value="CustomerID,Date,SaleAmount"/>
175 </section>
159 </repeat> 176 </repeat>
160 <param name="sqlquery" value="SELECT FirstName,LastName,sum(SaleAmount) as &quot;TotalSales&quot; FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC"/> 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"/>
161 <output name="output" file="sales_results.tsv"/> 178 <output name="output" file="sales_results.tsv"/>
162 </test> 179 </test>
163 180
164 <test> 181 <test>
165 <repeat name="tables"> 182 <repeat name="tables">
166 <param name="table" ftype="tabular" value="customers.tsv"/> 183 <param name="table" ftype="tabular" value="customers.tsv"/>
167 <param name="col_names" value=",FirstName,LastName,,DOB,"/> 184 <section name="input_opts">
185 <repeat name="linefilters">
186 <conditional name="filter">
187 <param name="filter_type" value="comment"/>
188 <param name="comment_char" value="35"/>
189 </conditional>
190 </repeat>
191 </section>
192 <section name="tbl_opts">
193 <param name="col_names" value=",FirstName,LastName,,DOB,"/>
194 </section>
168 </repeat> 195 </repeat>
169 <repeat name="tables"> 196 <repeat name="tables">
170 <param name="table" ftype="tabular" value="sales.tsv"/> 197 <param name="table" ftype="tabular" value="sales.tsv"/>
198 <section name="input_opts">
199 <repeat name="linefilters">
200 <conditional name="filter">
201 <param name="filter_type" value="skip"/>
202 <param name="skip_lines" value="1"/>
203 </conditional>
204 </repeat>
205 </section>
171 </repeat> 206 </repeat>
172 <param name="sqlquery" value="SELECT FirstName,LastName,sum(t2.c3) as &quot;TotalSales&quot; FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;"/> 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;"/>
173 <output name="output" file="sales_results.tsv"/> 208 <output name="output" file="sales_results.tsv"/>
174 </test> 209 </test>
175 210
176 <test> 211 <test>
177 <repeat name="tables"> 212 <repeat name="tables">
178 <param name="table" ftype="tabular" value="customers.tsv"/> 213 <param name="table" ftype="tabular" value="customers.tsv"/>
179 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/> 214 <section name="input_opts">
215 <repeat name="linefilters">
216 <conditional name="filter">
217 <param name="filter_type" value="skip"/>
218 <param name="skip_lines" value="1"/>
219 </conditional>
220 </repeat>
221 </section>
222 <section name="tbl_opts">
223 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/>
224 </section>
180 </repeat> 225 </repeat>
181 <param name="sqlquery" value="select FirstName,LastName,re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as &quot;DOB&quot; from t1 WHERE re_search('[hp]er',c4)"/> 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)"/>
182 <output name="output" file="regex_results.tsv"/> 227 <output name="output" file="regex_results.tsv"/>
183 </test> 228 </test>
184 229
185 <test> 230 <test>
186 <repeat name="tables"> 231 <repeat name="tables">
187 <param name="table" ftype="tabular" value="IEDB.tsv"/> 232 <param name="table" ftype="tabular" value="IEDB.tsv"/>
188 <param name="table_name" value="iedb"/> 233 <section name="input_opts">
189 <param name="col_names" value="ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank"/> 234 <repeat name="linefilters">
235 <conditional name="filter">
236 <param name="filter_type" value="comment"/>
237 <param name="comment_char" value="35"/>
238 </conditional>
239 </repeat>
240 </section>
241 <section name="tbl_opts">
242 <param name="table_name" value="iedb"/>
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"/>
244 </section>
190 </repeat> 245 </repeat>
191 <repeat name="tables"> 246 <repeat name="tables">
192 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/> 247 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
193 <param name="table_name" value="mhc_summary"/> 248 <section name="input_opts">
194 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/> 249 <repeat name="linefilters">
195 </repeat> 250 <conditional name="filter">
196 <param name="sqlquery" value="select iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level"/> 251 <param name="filter_type" value="skip"/>
252 <param name="skip_lines" value="1"/>
253 </conditional>
254 </repeat>
255 </section>
256 <section name="tbl_opts">
257 <param name="table_name" value="mhc_summary"/>
258 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/>
259 </section>
260 </repeat>
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"/>
197 <output name="output" file="query_results.tsv"/> 262 <output name="output" file="query_results.tsv"/>
198 </test> 263 </test>
199 264
200 <test> 265 <test>
266 <section name="add_to_database">
267 <param name="withdb" ftype="sqlite" value="testdb.sqlite"/>
268 </section>
201 <repeat name="tables"> 269 <repeat name="tables">
202 <param name="table" ftype="tabular" value="pets.tsv"/> 270 <param name="table" ftype="tabular" value="pets.tsv"/>
203 <repeat name="linefilters"> 271 <section name="input_opts">
204 <param name="filter_type" value="comment"/> 272 <repeat name="linefilters">
205 <param name="comment_char" value="35"/> 273 <conditional name="filter">
206 </repeat> 274 <param name="filter_type" value="regex"/>
207 <repeat name="linefilters"> 275 <param name="regex_pattern" value="^\d+"/>
208 <param name="filter_type" value="append_line_num"/> 276 <param name="regex_action" value="include_find"/>
209 </repeat> 277 </conditional>
210 <repeat name="linefilters"> 278 </repeat>
211 <param name="filter_type" value="select_columns"/> 279 <repeat name="linefilters">
212 <param name="columns" value="7,2,3,4,1"/> 280 <conditional name="filter">
213 </repeat> 281 <param name="filter_type" value="comment"/>
214 <repeat name="linefilters"> 282 <param name="comment_char" value="35"/>
215 <param name="filter_type" value="replace"/> 283 </conditional>
216 <param name="column" value="c4"/> 284 </repeat>
217 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/> 285 <repeat name="linefilters">
218 <param name="regex_replace" value="19\3-\2-\1"/> 286 <conditional name="filter">
219 </repeat> 287 <param name="filter_type" value="append_line_num"/>
220 <param name="table_name" value="people"/> 288 </conditional>
221 <param name="col_names" value="id,first,last,dob,pets"/> 289 </repeat>
222 290 <repeat name="linefilters">
223 </repeat> 291 <conditional name="filter">
292 <param name="filter_type" value="select_columns"/>
293 <param name="columns" value="7,2,3,4,1"/>
294 </conditional>
295 </repeat>
296 <repeat name="linefilters">
297 <conditional name="filter">
298 <param name="filter_type" value="replace"/>
299 <param name="column" value="c4"/>
300 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/>
301 <param name="regex_replace" value="19\3-\2-\1"/>
302 </conditional>
303 </repeat>
304 </section>
305 <section name="tbl_opts">
306 <param name="table_name" value="people"/>
307 <param name="col_names" value="id,first,last,dob,pets"/>
308 </section>
309 </repeat>
310 <param name="sqlquery" value="SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name"/>
311 <output name="output" file="add_to_db_results.tsv"/>
312 </test>
313
314 <test>
224 <repeat name="tables"> 315 <repeat name="tables">
225 <param name="table" ftype="tabular" value="pets.tsv"/> 316 <param name="table" ftype="tabular" value="pets.tsv"/>
226 <repeat name="linefilters"> 317 <section name="input_opts">
227 <param name="filter_type" value="comment"/> 318 <repeat name="linefilters">
228 <param name="comment_char" value="35"/> 319 <conditional name="filter">
229 </repeat> 320 <param name="filter_type" value="regex"/>
230 <repeat name="linefilters"> 321 <param name="regex_pattern" value="^\d+"/>
231 <param name="filter_type" value="append_line_num"/> 322 <param name="regex_action" value="include_find"/>
232 </repeat> 323 </conditional>
233 <repeat name="linefilters"> 324 </repeat>
234 <param name="filter_type" value="select_columns"/> 325 <repeat name="linefilters">
235 <param name="columns" value="c7,c5,c6"/> 326 <conditional name="filter">
236 </repeat> 327 <param name="filter_type" value="comment"/>
237 <repeat name="linefilters"> 328 <param name="comment_char" value="35"/>
238 <param name="filter_type" value="normalize"/> 329 </conditional>
239 <param name="columns" value="c2,c3"/> 330 </repeat>
240 <param name="separator" value=","/> 331 <repeat name="linefilters">
241 </repeat> 332 <conditional name="filter">
242 <param name="table_name" value="pet"/> 333 <param name="filter_type" value="append_line_num"/>
243 <param name="col_names" value="id,name,animal"/> 334 </conditional>
335 </repeat>
336 <repeat name="linefilters">
337 <conditional name="filter">
338 <param name="filter_type" value="select_columns"/>
339 <param name="columns" value="7,2,3,4,1"/>
340 </conditional>
341 </repeat>
342 <repeat name="linefilters">
343 <conditional name="filter">
344 <param name="filter_type" value="replace"/>
345 <param name="column" value="c4"/>
346 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/>
347 <param name="regex_replace" value="19\3-\2-\1"/>
348 </conditional>
349 </repeat>
350 </section>
351 <section name="tbl_opts">
352 <param name="table_name" value="people"/>
353 <param name="col_names" value="id,first,last,dob,pets"/>
354 </section>
355 </repeat>
356 <repeat name="tables">
357 <param name="table" ftype="tabular" value="pets.tsv"/>
358 <section name="input_opts">
359 <repeat name="linefilters">
360 <conditional name="filter">
361 <param name="filter_type" value="regex"/>
362 <param name="regex_pattern" value="^\d+"/>
363 <param name="regex_action" value="include_find"/>
364 </conditional>
365 </repeat>
366 <repeat name="linefilters">
367 <conditional name="filter">
368 <param name="filter_type" value="append_line_num"/>
369 </conditional>
370 </repeat>
371 <repeat name="linefilters">
372 <conditional name="filter">
373 <param name="filter_type" value="select_columns"/>
374 <param name="columns" value="c7,c5,c6"/>
375 </conditional>
376 </repeat>
377 <repeat name="linefilters">
378 <conditional name="filter">
379 <param name="filter_type" value="normalize"/>
380 <param name="columns" value="c2,c3"/>
381 <param name="separator" value=","/>
382 </conditional>
383 </repeat>
384 </section>
385 <section name="tbl_opts">
386 <param name="table_name" value="pet"/>
387 <param name="col_names" value="id,name,animal"/>
388 </section>
244 </repeat> 389 </repeat>
245 <param name="sqlquery" value="SELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'"/> 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'"/>
246 <output name="output" file="pet_normalized_query_results.tsv"/> 391 <output name="output" file="pet_normalized_query_results.tsv"/>
247 </test> 392 </test>
248 393