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comparison query_tabular.xml @ 13:cf34c344508d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
author iuc
date Thu, 19 Aug 2021 19:40:53 +0000
parents 623f3eb7aa48
children 3a6b78c39dca
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12:623f3eb7aa48 13:cf34c344508d
1 <tool id="query_tabular" name="Query Tabular" version="3.2.0"> 1 <tool id="query_tabular" name="Query Tabular" version="3.3.0">
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>
76 #set $jtbl['unique'] = $idx_unique 76 #set $jtbl['unique'] = $idx_unique
77 #end if 77 #end if
78 #if len($idx_non) > 0: 78 #if len($idx_non) > 0:
79 #set $jtbl['index'] = $idx_non 79 #set $jtbl['index'] = $idx_non
80 #end if 80 #end if
81 #set $dataset_name = $tbl.table.element_identifier
81 #set $linefilters = $tbl.input_opts.linefilters 82 #set $linefilters = $tbl.input_opts.linefilters
82 @LINEFILTERS@ 83 @LINEFILTERS@
83 #if $input_filters: 84 #if $input_filters:
84 #set $jtbl['filters'] = $input_filters 85 #set $jtbl['filters'] = $input_filters
85 #end if 86 #end if
188 <data format="tabular" name="output3" label="query 3 results on ${on_string}" from_work_dir="results2.tsv"> 189 <data format="tabular" name="output3" label="query 3 results on ${on_string}" from_work_dir="results2.tsv">
189 <filter>len(addqueries['queries']) > 2</filter> 190 <filter>len(addqueries['queries']) > 2</filter>
190 </data> 191 </data>
191 </outputs> 192 </outputs>
192 <tests> 193 <tests>
194 <!-- Test 1 -->
193 <test> 195 <test>
194 <repeat name="tables"> 196 <repeat name="tables">
195 <param name="table" ftype="tabular" value="customers.tsv"/> 197 <param name="table" ftype="tabular" value="customers.tsv"/>
196 <section name="input_opts"> 198 <section name="input_opts">
197 <repeat name="linefilters"> 199 <repeat name="linefilters">
223 </repeat> 225 </repeat>
224 <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"/> 226 <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"/>
225 <output name="output" file="sales_results.tsv"/> 227 <output name="output" file="sales_results.tsv"/>
226 </test> 228 </test>
227 229
230 <!-- Test 2 -->
228 <test> 231 <test>
229 <repeat name="tables"> 232 <repeat name="tables">
230 <param name="table" ftype="tabular" value="customers.tsv"/> 233 <param name="table" ftype="tabular" value="customers.tsv"/>
231 <section name="input_opts"> 234 <section name="input_opts">
232 <repeat name="linefilters"> 235 <repeat name="linefilters">
253 </repeat> 256 </repeat>
254 <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;"/> 257 <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;"/>
255 <output name="output" file="sales_results.tsv"/> 258 <output name="output" file="sales_results.tsv"/>
256 </test> 259 </test>
257 260
261 <!-- Test 3 -->
258 <test> 262 <test>
259 <repeat name="tables"> 263 <repeat name="tables">
260 <param name="table" ftype="tabular" value="customers.tsv"/> 264 <param name="table" ftype="tabular" value="customers.tsv"/>
261 <section name="input_opts"> 265 <section name="input_opts">
262 <repeat name="linefilters"> 266 <repeat name="linefilters">
272 </repeat> 276 </repeat>
273 <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)"/> 277 <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)"/>
274 <output name="output" file="regex_results.tsv"/> 278 <output name="output" file="regex_results.tsv"/>
275 </test> 279 </test>
276 280
281 <!-- Test 4 -->
277 <test> 282 <test>
278 <repeat name="tables"> 283 <repeat name="tables">
279 <param name="table" ftype="tabular" value="IEDB.tsv"/> 284 <param name="table" ftype="tabular" value="IEDB.tsv"/>
280 <section name="input_opts"> 285 <section name="input_opts">
281 <repeat name="linefilters"> 286 <repeat name="linefilters">
307 </repeat> 312 </repeat>
308 <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"/> 313 <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"/>
309 <output name="output" file="query_results.tsv"/> 314 <output name="output" file="query_results.tsv"/>
310 </test> 315 </test>
311 316
317 <!-- Test 5 -->
312 <test> 318 <test>
313 <section name="add_to_database"> 319 <section name="add_to_database">
314 <param name="withdb" ftype="sqlite" value="testdb.sqlite"/> 320 <param name="withdb" ftype="sqlite" value="testdb.sqlite"/>
315 </section> 321 </section>
316 <repeat name="tables"> 322 <repeat name="tables">
356 </repeat> 362 </repeat>
357 <param name="sqlquery" value="SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name"/> 363 <param name="sqlquery" value="SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name"/>
358 <output name="output" file="add_to_db_results.tsv"/> 364 <output name="output" file="add_to_db_results.tsv"/>
359 </test> 365 </test>
360 366
367 <!-- Test 6 -->
361 <test> 368 <test>
362 <repeat name="tables"> 369 <repeat name="tables">
363 <param name="table" ftype="tabular" value="pets.tsv"/> 370 <param name="table" ftype="tabular" value="pets.tsv"/>
364 <section name="input_opts"> 371 <section name="input_opts">
365 <repeat name="linefilters"> 372 <repeat name="linefilters">
436 </repeat> 443 </repeat>
437 <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'"/> 444 <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'"/>
438 <output name="output" file="pet_normalized_query_results.tsv"/> 445 <output name="output" file="pet_normalized_query_results.tsv"/>
439 </test> 446 </test>
440 447
448 <!-- Test 7 -->
441 <test> 449 <test>
442 <repeat name="tables"> 450 <repeat name="tables">
443 <param name="table" ftype="tabular" value="psm_report.tsv"/> 451 <param name="table" ftype="tabular" value="psm_report.tsv"/>
444 <section name="input_opts"> 452 <section name="input_opts">
445 <repeat name="linefilters"> 453 <repeat name="linefilters">
461 <param name="header_prefix" value=""/> 469 <param name="header_prefix" value=""/>
462 </conditional> 470 </conditional>
463 <output name="output" file="psm_report_out1.tsv" compare="re_match"/> 471 <output name="output" file="psm_report_out1.tsv" compare="re_match"/>
464 </test> 472 </test>
465 473
474 <!-- Test 8 column_names_from_first_line -->
466 <test> 475 <test>
467 <repeat name="tables"> 476 <repeat name="tables">
468 <param name="table" ftype="tabular" value="psm_report.tsv"/> 477 <param name="table" ftype="tabular" value="psm_report.tsv"/>
469 <section name="input_opts"> 478 <section name="input_opts">
470 <repeat name="linefilters"> 479 <repeat name="linefilters">
486 <param name="header_prefix" value=""/> 495 <param name="header_prefix" value=""/>
487 </conditional> 496 </conditional>
488 <output name="output" file="psm_report_out2.tsv" compare="re_match"/> 497 <output name="output" file="psm_report_out2.tsv" compare="re_match"/>
489 </test> 498 </test>
490 499
500 <!-- Test 9 modify database -->
491 <test> 501 <test>
492 <repeat name="tables"> 502 <repeat name="tables">
493 <param name="table" ftype="tabular" value="psm_report.tsv"/> 503 <param name="table" ftype="tabular" value="psm_report.tsv"/>
494 <section name="input_opts"> 504 <section name="input_opts">
495 <repeat name="linefilters"> 505 <repeat name="linefilters">
526 </section> 536 </section>
527 <output name="output" file="psm_dbmod_output.tsv" compare="re_match"/> 537 <output name="output" file="psm_dbmod_output.tsv" compare="re_match"/>
528 <output name="output1" file="psm_dbmod_output1.tsv" compare="re_match"/> 538 <output name="output1" file="psm_dbmod_output1.tsv" compare="re_match"/>
529 </test> 539 </test>
530 540
541 <!-- Test 10 column_names_from_first_line -->
531 <test> 542 <test>
532 <repeat name="tables"> 543 <repeat name="tables">
533 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/> 544 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
534 <section name="input_opts"> 545 <section name="input_opts">
535 <repeat name="linefilters"> 546 <repeat name="linefilters">
551 <param name="header_prefix" value=""/> 562 <param name="header_prefix" value=""/>
552 </conditional> 563 </conditional>
553 <output name="output" file="netMHC_summary_out1.tsv" ftype="tabular"/> 564 <output name="output" file="netMHC_summary_out1.tsv" ftype="tabular"/>
554 </test> 565 </test>
555 566
567 <!-- Test 11 -->
556 <test> 568 <test>
557 <repeat name="tables"> 569 <repeat name="tables">
558 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/> 570 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
559 <section name="input_opts"> 571 <section name="input_opts">
560 <repeat name="linefilters"> 572 <repeat name="linefilters">
577 <param name="header_prefix" value=""/> 589 <param name="header_prefix" value=""/>
578 </conditional> 590 </conditional>
579 <output name="output" file="netMHC_summary_out2.tsv" ftype="tabular"/> 591 <output name="output" file="netMHC_summary_out2.tsv" ftype="tabular"/>
580 </test> 592 </test>
581 593
582 <test> <!-- math functions --> 594 <!-- Test 12 math functions -->
595 <test>
583 <repeat name="tables"> 596 <repeat name="tables">
584 <param name="table" ftype="tabular" value="math_input.tsv"/> 597 <param name="table" ftype="tabular" value="math_input.tsv"/>
585 </repeat> 598 </repeat>
586 <param name="sqlquery" value="SELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1"/> 599 <param name="sqlquery" value="SELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1"/>
587 <output name="output"> 600 <output name="output">