Mercurial > repos > iuc > query_tabular

comparison query_tabular.xml @ 8:5c3d86bc259c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 1647065a8e6e8d8c98cd0d2194b695fb9425f541"
author iuc
date Thu, 23 Jan 2020 12:35:14 +0000
parents 5b557716b4b3
children 4903740da8bc
comparison
equal deleted inserted replaced
7:ee31b5f5b5d0 8:5c3d86bc259c
1 <tool id="query_tabular" name="Query Tabular" version="3.0.0"> 1 <tool id="query_tabular" name="Query Tabular" version="3.0.1">
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 <expand macro="requirements"/>
8 <requirements>
9 </requirements>
10
11 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
12 cat '$query_file' && 9 cat '$query_file' &&
13 #if $add_to_database.withdb: 10 #if $add_to_database.withdb:
14 #if $save_db: 11 #if $save_db:
15 cp '$add_to_database.withdb' '$sqlitedb' && 12 cp '$add_to_database.withdb' '$sqlitedb' &&
461 <param name="sqlquery" value="SELECT * from PSMs"/> 458 <param name="sqlquery" value="SELECT * from PSMs"/>
462 <conditional name="query_result"> 459 <conditional name="query_result">
463 <param name="header" value="yes"/> 460 <param name="header" value="yes"/>
464 <param name="header_prefix" value=""/> 461 <param name="header_prefix" value=""/>
465 </conditional> 462 </conditional>
466 <output name="output" file="psm_report_out1.tsv"/> 463 <output name="output" file="psm_report_out1.tsv" compare="re_match"/>
467 </test> 464 </test>
468 465
469 <test> 466 <test>
470 <repeat name="tables"> 467 <repeat name="tables">
471 <param name="table" ftype="tabular" value="psm_report.tsv"/> 468 <param name="table" ftype="tabular" value="psm_report.tsv"/>
486 <param name="sqlquery" value="SELECT Scan,&quot;m/z&quot;, &quot;Precursor m/z Error [ppm]&quot;, Sequence, &quot;Protein(s)&quot; FROM PSMs WHERE NOT re_search(', ',&quot;Protein(s)&quot;)"/> 483 <param name="sqlquery" value="SELECT Scan,&quot;m/z&quot;, &quot;Precursor m/z Error [ppm]&quot;, Sequence, &quot;Protein(s)&quot; FROM PSMs WHERE NOT re_search(', ',&quot;Protein(s)&quot;)"/>
487 <conditional name="query_result"> 484 <conditional name="query_result">
488 <param name="header" value="yes"/> 485 <param name="header" value="yes"/>
489 <param name="header_prefix" value=""/> 486 <param name="header_prefix" value=""/>
490 </conditional> 487 </conditional>
491 <output name="output" file="psm_report_out2.tsv"/> 488 <output name="output" file="psm_report_out2.tsv" compare="re_match"/>
492 </test> 489 </test>
493 490
494 <test> 491 <test>
495 <repeat name="tables"> 492 <repeat name="tables">
496 <param name="table" ftype="tabular" value="psm_report.tsv"/> 493 <param name="table" ftype="tabular" value="psm_report.tsv"/>
525 <param name="header" value="yes"/> 522 <param name="header" value="yes"/>
526 <param name="header_prefix" value=""/> 523 <param name="header_prefix" value=""/>
527 </conditional> 524 </conditional>
528 </repeat> 525 </repeat>
529 </section> 526 </section>
530 <output name="output" file="psm_dbmod_output.tsv"/> 527 <output name="output" file="psm_dbmod_output.tsv" compare="re_match"/>
531 <output name="output1" file="psm_dbmod_output1.tsv"/> 528 <output name="output1" file="psm_dbmod_output1.tsv" compare="re_match"/>
532 </test> 529 </test>
533 530
534 </tests> 531 </tests>
535 <help><![CDATA[ 532 <help><![CDATA[
536 ============= 533 =============