Mercurial > repos > iuc > query_tabular

comparison query_tabular.xml @ 10:2e8f945f7285 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
author iuc
date Thu, 24 Sep 2020 11:26:46 +0000
parents a3aab6045663
children 83069b38aa85
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9:a3aab6045663 10:2e8f945f7285
1 <tool id="query_tabular" name="Query Tabular" version="3.1.0"> 1 <tool id="query_tabular" name="Query Tabular" version="3.1.1">
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>
526 </section> 526 </section>
527 <output name="output" file="psm_dbmod_output.tsv" compare="re_match"/> 527 <output name="output" file="psm_dbmod_output.tsv" compare="re_match"/>
528 <output name="output1" file="psm_dbmod_output1.tsv" compare="re_match"/> 528 <output name="output1" file="psm_dbmod_output1.tsv" compare="re_match"/>
529 </test> 529 </test>
530 530
531 <test>
532 <repeat name="tables">
533 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
534 <section name="input_opts">
535 <repeat name="linefilters">
536 <conditional name="filter">
537 <param name="filter_type" value="regex"/>
538 <param name="regex_pattern" value="peptide"/>
539 <param name="regex_action" value="include_find"/>
540 </conditional>
541 </repeat>
542 </section>
543 <section name="tbl_opts">
544 <param name="table_name" value="epitope"/>
545 <param name="column_names_from_first_line" value="True"/>
546 </section>
547 </repeat>
548 <param name="sqlquery" value="SELECT * FROM epitope"/>
549 <conditional name="query_result">
550 <param name="header" value="yes"/>
551 <param name="header_prefix" value=""/>
552 </conditional>
553 <output name="output" file="netMHC_summary_out1.tsv" ftype="tabular"/>
554 </test>
555
556 <test>
557 <repeat name="tables">
558 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
559 <section name="input_opts">
560 <repeat name="linefilters">
561 <conditional name="filter">
562 <param name="filter_type" value="regex"/>
563 <param name="regex_pattern" value="NOT TO BE FOUND"/>
564 <param name="regex_action" value="include_find"/>
565 </conditional>
566 </repeat>
567 </section>
568 <section name="tbl_opts">
569 <param name="table_name" value="epitope"/>
570 <param name="column_names_from_first_line" value="False"/>
571 <param name="col_names" value="pos,peptide,logscore,,,,Allele"/>
572 </section>
573 </repeat>
574 <param name="sqlquery" value="SELECT pos,peptide,logscore,Allele FROM epitope"/>
575 <conditional name="query_result">
576 <param name="header" value="yes"/>
577 <param name="header_prefix" value=""/>
578 </conditional>
579 <output name="output" file="netMHC_summary_out2.tsv" ftype="tabular"/>
580 </test>
581
531 </tests> 582 </tests>
532 <help><![CDATA[ 583 <help><![CDATA[
533 ============= 584 =============
534 Query Tabular 585 Query Tabular
535 ============= 586 =============
537 **Inputs** 588 **Inputs**
538 589
539 Loads tabular datasets into a SQLite_ data base. 590 Loads tabular datasets into a SQLite_ data base.
540 591
541 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. 592 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.
593
594 **NOTE:** If there are no data rows in an input tabular dataset, query_tabular will fail unless:
595
596 - There is a row header line in the dataset and **Use first line as column names** is selected
597 - **Specify Column Names** is used to provide column names
598
599 in which case an empty table will be created with those columns
542 600
543 601
544 @LINEFILTERS_HELP@ 602 @LINEFILTERS_HELP@
545 603
546 **Table Options** 604 **Table Options**