query_tabular: query_tabular.xml annotate

annotate query_tabular.xml @ 9:b7f149b4792f draft

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty

author	jjohnson
date	Fri, 15 Apr 2016 16:48:50 -0400
parents	6d9c91071884
children	98bd1e29d669

rev	line source
8 6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	1 <tool id="query_tabular" name="Query Tabular" version="0.1.2">
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	2 <description>using sqlite sql</description>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	3
763c4f968dc6 Uploaded jjohnson parents: diff changeset	4 <requirements>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	5 </requirements>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	6 <stdio>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	7 <exit_code range="1:" />
763c4f968dc6 Uploaded jjohnson parents: diff changeset	8 </stdio>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	9 <command interpreter="python"><![CDATA[
763c4f968dc6 Uploaded jjohnson parents: diff changeset	10 query_tabular.py
763c4f968dc6 Uploaded jjohnson parents: diff changeset	11 #if $save_db
763c4f968dc6 Uploaded jjohnson parents: diff changeset	12 -s $sqlitedb
763c4f968dc6 Uploaded jjohnson parents: diff changeset	13 #else
763c4f968dc6 Uploaded jjohnson parents: diff changeset	14 -s $workdb
763c4f968dc6 Uploaded jjohnson parents: diff changeset	15 #end if
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	16 -j $table_json
2 ffa5e34a55c1 Uploaded jjohnson parents: 1 diff changeset	17 #if $sqlquery:
ffa5e34a55c1 Uploaded jjohnson parents: 1 diff changeset	18 -Q "$query_file"
1 24f0911f75ee Uploaded jjohnson parents: 0 diff changeset	19 $no_header
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	20 -o $output
763c4f968dc6 Uploaded jjohnson parents: diff changeset	21 #end if
763c4f968dc6 Uploaded jjohnson parents: diff changeset	22 ]]></command>
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	23 <configfiles>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	24 <configfile name="query_file">
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	25 $sqlquery
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	26 </configfile>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	27 <configfile name="table_json">
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	28 #import json
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	29 #set $jtbldef = dict()
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	30 #set $jtbls = []
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	31 #set $jtbldef['tables'] = $jtbls
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	32 #for $i,$tbl in enumerate($tables):
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	33 #set $jtbl = dict()
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	34 #set $jtbl['file_path'] = str($tbl.table)
8 6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	35 #if $tbl.tbl_opts.table_name:
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	36 #set $tname = str($tbl.tbl_opts.table_name)
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	37 #else
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	38 #set $tname = 't' + str($i + 1)
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	39 #end if
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	40 #set $jtbl['table_name'] = $tname
8 6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	41 ## #if $tbl.tbl_opts.sel_cols:
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	42 ## #set $jtbl['sel_cols'] = $tbl.tbl_opts.sel_cols el_cols
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	43 ## #end if
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	44 #if $tbl.tbl_opts.col_names:
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	45 #set $col_names = str($tbl.tbl_opts.col_names)
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	46 #if $tbl.tbl_opts.load_named_columns:
7 aa2409ae9dc0 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 6 diff changeset	47 #set $jtbl['load_named_columns'] = True
aa2409ae9dc0 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 6 diff changeset	48 #end if
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	49 #else
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	50 #set $col_names = ''
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	51 #end if
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	52 #set $jtbl['column_names'] = $col_names
8 6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	53 #if str($tbl.tbl_opts.skip_lines) != '':
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	54 #set $jtbl['comment_lines'] = int($tbl.tbl_opts.skip_lines)
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	55 #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0:
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	56 #set $jtbl['comment_lines'] = int($tbl.table.metadata.comment_lines)
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	57 #end if
8 6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	58 #set $idx_unique = []
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	59 #set $idx_non = []
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	60 #for $idx in $tbl.tbl_opts.indexes:
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	61 #if $idx.unique:
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	62 #silent $idx_unique.append(str($idx.index_columns))
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	63 #else:
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	64 #silent $idx_non.append(str($idx.index_columns))
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	65 #end if
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	66 #end for
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	67 #if len($idx_unique) > 0:
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	68 #set $jtbl['unique'] = $idx_unique
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	69 #end if
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	70 #if len($idx_non) > 0:
9 b7f149b4792f planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 8 diff changeset	71 #set $jtbl['index'] = $idx_non
8 6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	72 #end if
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	73 #set $jtbls += [$jtbl]
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	74 #end for
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	75 #echo $json.dumps($jtbldef)
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	76 </configfile>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	77 </configfiles>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	78 <inputs>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	79 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	80 <repeat name="tables" title="Add tables" min="1">
763c4f968dc6 Uploaded jjohnson parents: diff changeset	81 <param name="table" type="data" format="tabular" label="Dataset"/>
8 6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	82 <section name="tbl_opts" expanded="false" title="Table Options">
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	83 <param name="table_name" type="text" value="" optional="true" label="Table name">
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	84 <help>By default, tables will be named: t1,t2,...,tn</help>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	85 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	86 </param>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	87 <param name="col_names" type="text" value="" optional="true" label="Column names">
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	88 <help>By default, table columns will be named: c1,c2,c3,...,cn</help>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	89 <sanitizer sanitize="False"/>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	90 <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w\|"\S+[^,"]"\|`\S+[^,`]`\|[[]\S+[^,"][]])?(,([A-Za-z]\w\|"\S+."\|`\S+[^,`]`\|[[]\S+[^,"][]])?)*$</validator>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	91 </param>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	92 <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load named columns into database"/>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	93 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" help="Leave blank to use the datatype comment lines metadata" />
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	94 <repeat name="indexes">
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	95 <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	96 <param name="index_columns" type="text" value="" label="Index on Columns">
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	97 <help>Create an index on the column names: e,g, c1 or c2,c4</help>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	98 <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+[^,"][]])?)*$</validator>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	99 </param>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	100 </repeat>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	101 </section>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	102 </repeat>
2 ffa5e34a55c1 Uploaded jjohnson parents: 1 diff changeset	103 <param name="sqlquery" type="text" area="true" size="10x80" value="" optional="true" label="SQL Query">
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	104 <help>By default, tables will be named: t1,t2,...,tn</help>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	105 <sanitizer sanitize="False"/>
8 6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	106 <validator type="regex" message="">^(?ims)\sselect\s+.\s+from\s+.*$</validator>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	107 </param>
1 24f0911f75ee Uploaded jjohnson parents: 0 diff changeset	108 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers"/>
24f0911f75ee Uploaded jjohnson parents: 0 diff changeset	109
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	110 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	111 </inputs>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	112 <outputs>
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	113 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}">
2 ffa5e34a55c1 Uploaded jjohnson parents: 1 diff changeset	114 <filter>save_db or not (sqlquery and len(sqlquery) > 0)</filter>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	115 </data>
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	116 <data format="tabular" name="output" label="query results on ${on_string}">
2 ffa5e34a55c1 Uploaded jjohnson parents: 1 diff changeset	117 <filter>sqlquery and len(sqlquery) > 0</filter>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	118 </data>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	119 </outputs>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	120 <tests>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	121
763c4f968dc6 Uploaded jjohnson parents: diff changeset	122 <test>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	123 <repeat name="tables">
763c4f968dc6 Uploaded jjohnson parents: diff changeset	124 <param name="table" ftype="tabular" value="customers.tsv"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	125 <param name="table_name" value="customers"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	126 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	127 </repeat>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	128 <repeat name="tables">
763c4f968dc6 Uploaded jjohnson parents: diff changeset	129 <param name="table" ftype="tabular" value="sales.tsv"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	130 <param name="table_name" value="sales"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	131 <param name="col_names" value="CustomerID,Date,SaleAmount"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	132 </repeat>
2 ffa5e34a55c1 Uploaded jjohnson parents: 1 diff changeset	133 <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"/>
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	134 <output name="output" file="sales_results.tsv"/>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	135 </test>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	136
763c4f968dc6 Uploaded jjohnson parents: diff changeset	137 <test>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	138 <repeat name="tables">
763c4f968dc6 Uploaded jjohnson parents: diff changeset	139 <param name="table" ftype="tabular" value="customers.tsv"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	140 <param name="col_names" value=",FirstName,LastName,,DOB,"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	141 </repeat>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	142 <repeat name="tables">
763c4f968dc6 Uploaded jjohnson parents: diff changeset	143 <param name="table" ftype="tabular" value="sales.tsv"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	144 </repeat>
2 ffa5e34a55c1 Uploaded jjohnson parents: 1 diff changeset	145 <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;"/>
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	146 <output name="output" file="sales_results.tsv"/>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	147 </test>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	148
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	149 <test>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	150 <repeat name="tables">
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	151 <param name="table" ftype="tabular" value="customers.tsv"/>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	152 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	153 </repeat>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	154 <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)"/>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	155 <output name="output" file="regex_results.tsv"/>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	156 </test>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	157
763c4f968dc6 Uploaded jjohnson parents: diff changeset	158 <test>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	159 <repeat name="tables">
763c4f968dc6 Uploaded jjohnson parents: diff changeset	160 <param name="table" ftype="tabular" value="IEDB.tsv"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	161 <param name="table_name" value="iedb"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	162 <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"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	163 </repeat>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	164 <repeat name="tables">
763c4f968dc6 Uploaded jjohnson parents: diff changeset	165 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	166 <param name="table_name" value="mhc_summary"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	167 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	168 </repeat>
2 ffa5e34a55c1 Uploaded jjohnson parents: 1 diff changeset	169 <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"/>
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	170 <output name="output" file="query_results.tsv"/>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	171 </test>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	172
763c4f968dc6 Uploaded jjohnson parents: diff changeset	173 </tests>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	174 <help><![CDATA[
763c4f968dc6 Uploaded jjohnson parents: diff changeset	175 =============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	176 Query Tabular
763c4f968dc6 Uploaded jjohnson parents: diff changeset	177 =============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	178
763c4f968dc6 Uploaded jjohnson parents: diff changeset	179 Inputs
763c4f968dc6 Uploaded jjohnson parents: diff changeset	180
763c4f968dc6 Uploaded jjohnson parents: diff changeset	181 Loads tabular datasets into a SQLite_ data base.
763c4f968dc6 Uploaded jjohnson parents: diff changeset	182
763c4f968dc6 Uploaded jjohnson parents: diff changeset	183 Outputs
763c4f968dc6 Uploaded jjohnson parents: diff changeset	184
763c4f968dc6 Uploaded jjohnson parents: diff changeset	185 The results of a SQL query are output to the history as a tabular file.
763c4f968dc6 Uploaded jjohnson parents: diff changeset	186
763c4f968dc6 Uploaded jjohnson parents: diff changeset	187 The SQLite_ data base can also be saved and output as a dataset in the history.
763c4f968dc6 Uploaded jjohnson parents: diff changeset	188
763c4f968dc6 Uploaded jjohnson parents: diff changeset	189
763c4f968dc6 Uploaded jjohnson parents: diff changeset	190 For help in using SQLite_ see: http://www.sqlite.org/docs.html
763c4f968dc6 Uploaded jjohnson parents: diff changeset	191
763c4f968dc6 Uploaded jjohnson parents: diff changeset	192 NOTE: input for SQLite dates input field must be in the format: YYYY-MM-DD for example: 2015-09-30
763c4f968dc6 Uploaded jjohnson parents: diff changeset	193
763c4f968dc6 Uploaded jjohnson parents: diff changeset	194 See: http://www.sqlite.org/lang_datefunc.html
763c4f968dc6 Uploaded jjohnson parents: diff changeset	195
763c4f968dc6 Uploaded jjohnson parents: diff changeset	196 Example
763c4f968dc6 Uploaded jjohnson parents: diff changeset	197
763c4f968dc6 Uploaded jjohnson parents: diff changeset	198 Given 2 tabular datasets: customers and sales
763c4f968dc6 Uploaded jjohnson parents: diff changeset	199
763c4f968dc6 Uploaded jjohnson parents: diff changeset	200 Dataset customers
763c4f968dc6 Uploaded jjohnson parents: diff changeset	201
763c4f968dc6 Uploaded jjohnson parents: diff changeset	202 Table name: "customers"
763c4f968dc6 Uploaded jjohnson parents: diff changeset	203
763c4f968dc6 Uploaded jjohnson parents: diff changeset	204 Column names: "CustomerID,FirstName,LastName,Email,DOB,Phone"
763c4f968dc6 Uploaded jjohnson parents: diff changeset	205
763c4f968dc6 Uploaded jjohnson parents: diff changeset	206 =========== ========== ========== ===================== ========== ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	207 #CustomerID FirstName LastName Email DOB Phone
763c4f968dc6 Uploaded jjohnson parents: diff changeset	208 =========== ========== ========== ===================== ========== ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	209 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
763c4f968dc6 Uploaded jjohnson parents: diff changeset	210 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
763c4f968dc6 Uploaded jjohnson parents: diff changeset	211 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
763c4f968dc6 Uploaded jjohnson parents: diff changeset	212 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
763c4f968dc6 Uploaded jjohnson parents: diff changeset	213 =========== ========== ========== ===================== ========== ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	214
763c4f968dc6 Uploaded jjohnson parents: diff changeset	215 Dataset sales
763c4f968dc6 Uploaded jjohnson parents: diff changeset	216
763c4f968dc6 Uploaded jjohnson parents: diff changeset	217 Table name: "sales"
763c4f968dc6 Uploaded jjohnson parents: diff changeset	218
763c4f968dc6 Uploaded jjohnson parents: diff changeset	219 Column names: "CustomerID,Date,SaleAmount"
763c4f968dc6 Uploaded jjohnson parents: diff changeset	220
763c4f968dc6 Uploaded jjohnson parents: diff changeset	221 ============= ============ ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	222 #CustomerID Date SaleAmount
763c4f968dc6 Uploaded jjohnson parents: diff changeset	223 ============= ============ ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	224 2 2004-05-06 100.22
763c4f968dc6 Uploaded jjohnson parents: diff changeset	225 1 2004-05-07 99.95
763c4f968dc6 Uploaded jjohnson parents: diff changeset	226 3 2004-05-07 122.95
763c4f968dc6 Uploaded jjohnson parents: diff changeset	227 3 2004-05-13 100.00
763c4f968dc6 Uploaded jjohnson parents: diff changeset	228 4 2004-05-22 555.55
763c4f968dc6 Uploaded jjohnson parents: diff changeset	229 ============= ============ ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	230
763c4f968dc6 Uploaded jjohnson parents: diff changeset	231 The query
763c4f968dc6 Uploaded jjohnson parents: diff changeset	232
763c4f968dc6 Uploaded jjohnson parents: diff changeset	233 ::
763c4f968dc6 Uploaded jjohnson parents: diff changeset	234
763c4f968dc6 Uploaded jjohnson parents: diff changeset	235 SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales"
763c4f968dc6 Uploaded jjohnson parents: diff changeset	236 FROM customers join sales on customers.CustomerID = sales.CustomerID
763c4f968dc6 Uploaded jjohnson parents: diff changeset	237 GROUP BY customers.CustomerID ORDER BY TotalSales DESC;
763c4f968dc6 Uploaded jjohnson parents: diff changeset	238
763c4f968dc6 Uploaded jjohnson parents: diff changeset	239 Produces this tabular output:
763c4f968dc6 Uploaded jjohnson parents: diff changeset	240
763c4f968dc6 Uploaded jjohnson parents: diff changeset	241 ========== ======== ==========
763c4f968dc6 Uploaded jjohnson parents: diff changeset	242 #FirstName LastName TotalSales
763c4f968dc6 Uploaded jjohnson parents: diff changeset	243 ========== ======== ==========
763c4f968dc6 Uploaded jjohnson parents: diff changeset	244 James Smith 555.55
763c4f968dc6 Uploaded jjohnson parents: diff changeset	245 Paula Brown 222.95
763c4f968dc6 Uploaded jjohnson parents: diff changeset	246 Steven Goldfish 100.22
763c4f968dc6 Uploaded jjohnson parents: diff changeset	247 John Smith 99.95
763c4f968dc6 Uploaded jjohnson parents: diff changeset	248 ========== ======== ==========
763c4f968dc6 Uploaded jjohnson parents: diff changeset	249
763c4f968dc6 Uploaded jjohnson parents: diff changeset	250
763c4f968dc6 Uploaded jjohnson parents: diff changeset	251 If the optional Table name and Column names inputs are not used, the query would be:
763c4f968dc6 Uploaded jjohnson parents: diff changeset	252
763c4f968dc6 Uploaded jjohnson parents: diff changeset	253 ::
763c4f968dc6 Uploaded jjohnson parents: diff changeset	254
763c4f968dc6 Uploaded jjohnson parents: diff changeset	255 SELECT t1.c2 as "FirstName", t1.c3 as "LastName", sum(t2.c3) as "TotalSales"
763c4f968dc6 Uploaded jjohnson parents: diff changeset	256 FROM t1 join t2 on t1.c1 = t2.c1
763c4f968dc6 Uploaded jjohnson parents: diff changeset	257 GROUP BY t1.c1 ORDER BY TotalSales DESC;
763c4f968dc6 Uploaded jjohnson parents: diff changeset	258
763c4f968dc6 Uploaded jjohnson parents: diff changeset	259 You can selectively name columns, e.g. on the customers input you could just name columns 2,3, and 5:
763c4f968dc6 Uploaded jjohnson parents: diff changeset	260
763c4f968dc6 Uploaded jjohnson parents: diff changeset	261 Column names: ,FirstName,LastName,,BirthDate
763c4f968dc6 Uploaded jjohnson parents: diff changeset	262
763c4f968dc6 Uploaded jjohnson parents: diff changeset	263 Results in the following data base table
763c4f968dc6 Uploaded jjohnson parents: diff changeset	264
763c4f968dc6 Uploaded jjohnson parents: diff changeset	265 =========== ========== ========== ===================== ========== ============
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	266 #c1 FirstName LastName c4 BirthDate c6
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	267 =========== ========== ========== ===================== ========== ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	268 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
763c4f968dc6 Uploaded jjohnson parents: diff changeset	269 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
763c4f968dc6 Uploaded jjohnson parents: diff changeset	270 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
763c4f968dc6 Uploaded jjohnson parents: diff changeset	271 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
763c4f968dc6 Uploaded jjohnson parents: diff changeset	272 =========== ========== ========== ===================== ========== ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	273
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	274 Regular_expression_ functions are included for:
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	275
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	276 ::
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	277
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	278 matching: re_match('pattern',column)
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	279
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	280 SELECT t1.FirstName, t1.LastName
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	281 FROM t1
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	282 WHERE re_match('^.*\.(net\|org)$',c4)
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	283
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	284 Results:
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	285
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	286 =========== ==========
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	287 #FirstName LastName
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	288 =========== ==========
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	289 Steven Goldfish
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	290 Paula Brown
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	291 =========== ==========
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	292
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	293
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	294 ::
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	295
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	296 searching: re_search('pattern',column)
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	297 substituting: re_sub('pattern','replacement,column)
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	298
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	299 SELECT t1.FirstName, t1.LastName, re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB"
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	300 FROM t1
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	301 WHERE re_search('[hp]er',c4)
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	302
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	303 Results:
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	304
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	305 =========== ========== ==========
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	306 #FirstName LastName DOB
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	307 =========== ========== ==========
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	308 Steven Goldfish 04/04/74
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	309 Paula Brown 24/05/78
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	310 James Smith 20/10/80
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	311 =========== ========== ==========
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	312
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	313 .. _Regular_expression: https://docs.python.org/release/2.7/library/re.html
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	314 .. _SQLite: http://www.sqlite.org/index.html
763c4f968dc6 Uploaded jjohnson parents: diff changeset	315
763c4f968dc6 Uploaded jjohnson parents: diff changeset	316 ]]></help>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	317 </tool>

Mercurial > repos > jjohnson > query_tabular

annotate query_tabular.xml @ 9:b7f149b4792f draft