query_tabular: query_tabular.xml annotate

annotate query_tabular.xml @ 10:98bd1e29d669 draft default tip

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty

author	jjohnson
date	Wed, 20 Apr 2016 15:44:33 -0400
parents	b7f149b4792f
children

rev	line source
10 98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	1 <tool id="query_tabular" name="Query Tabular" version="0.1.3">
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
10 98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	44 #if $tbl.tbl_opts.pkey_autoincr:
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	45 #set $jtbl['pkey_autoincr'] = str($tbl.tbl_opts.pkey_autoincr)
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	46 #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	47 #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	48 #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	49 #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	50 #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	51 #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	52 #else
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	53 #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	54 #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	55 #set $jtbl['column_names'] = $col_names
8 6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	56 #if str($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	57 #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	58 #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	59 #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	60 #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	61 #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	62 #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	63 #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	64 #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	65 #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	66 #else:
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	67 #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	68 #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	69 #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	70 #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	71 #set $jtbl['unique'] = $idx_unique
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	72 #end if
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	73 #if len($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	74 #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	75 #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	76 #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	77 #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	78 #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	79 </configfile>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	80 </configfiles>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	81 <inputs>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	82 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
10 98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	83 <repeat name="tables" title="Database Table" min="1">
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	84 <param name="table" type="data" format="tabular" label="Tabular Dataset for 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	85 <section name="tbl_opts" expanded="false" title="Table Options">
10 98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	86 <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table">
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	87 <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help>
8 6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	88 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	89 </param>
10 98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	90 <param name="col_names" type="text" value="" optional="true" label="Specify Column Names">
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	91 <help>By default, table columns will be named: c1,c2,c3,...,cn (column names for a table must be unique)</help>
8 6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	92 <sanitizer sanitize="False"/>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	93 <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w\|"\S+[^,"]"\|`\S+[^,`]`\|[[]\S+[^,"][]])?(,([A-Za-z]\w\|"\S+."\|`\S+[^,`]`\|[[]\S+[^,"][]])?)*$</validator>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	94 </param>
10 98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	95 <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load the columns you have named into database"/>
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	96 <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name"
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	97 help="Only creates this additional column when a name is entered. (This can not be the same name as any of the other columns in this table.)">
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	98 <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator>
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	99 </param>
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	100 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" help="Leave blank to use the comment lines metadata for this dataset" />
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	101 <repeat name="indexes" title="Table Index">
8 6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	102 <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	103 <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	104 <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	105 <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	106 </param>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	107 </repeat>
6d9c91071884 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 7 diff changeset	108 </section>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	109 </repeat>
10 98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	110 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history"/>
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	111 <param name="sqlquery" type="text" area="true" size="10x80" value="" optional="true" label="SQL Query to generate tabular output">
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	112 <help>By default: tables are named: t1,t2,...,tn and columns in each table: c1,c2,...,cn</help>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	113 <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	114 <validator type="regex" message="">^(?ims)\sselect\s+.\s+from\s+.*$</validator>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	115 </param>
10 98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	116 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers from tabular output"/>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	117 </inputs>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	118 <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	119 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}">
2 ffa5e34a55c1 Uploaded jjohnson parents: 1 diff changeset	120 <filter>save_db or not (sqlquery and len(sqlquery) > 0)</filter>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	121 </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	122 <data format="tabular" name="output" label="query results on ${on_string}">
2 ffa5e34a55c1 Uploaded jjohnson parents: 1 diff changeset	123 <filter>sqlquery and len(sqlquery) > 0</filter>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	124 </data>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	125 </outputs>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	126 <tests>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	127
763c4f968dc6 Uploaded jjohnson parents: diff changeset	128 <test>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	129 <repeat name="tables">
763c4f968dc6 Uploaded jjohnson parents: diff changeset	130 <param name="table" ftype="tabular" value="customers.tsv"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	131 <param name="table_name" value="customers"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	132 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	133 </repeat>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	134 <repeat name="tables">
763c4f968dc6 Uploaded jjohnson parents: diff changeset	135 <param name="table" ftype="tabular" value="sales.tsv"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	136 <param name="table_name" value="sales"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	137 <param name="col_names" value="CustomerID,Date,SaleAmount"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	138 </repeat>
2 ffa5e34a55c1 Uploaded jjohnson parents: 1 diff changeset	139 <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	140 <output name="output" file="sales_results.tsv"/>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	141 </test>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	142
763c4f968dc6 Uploaded jjohnson parents: diff changeset	143 <test>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	144 <repeat name="tables">
763c4f968dc6 Uploaded jjohnson parents: diff changeset	145 <param name="table" ftype="tabular" value="customers.tsv"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	146 <param name="col_names" value=",FirstName,LastName,,DOB,"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	147 </repeat>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	148 <repeat name="tables">
763c4f968dc6 Uploaded jjohnson parents: diff changeset	149 <param name="table" ftype="tabular" value="sales.tsv"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	150 </repeat>
2 ffa5e34a55c1 Uploaded jjohnson parents: 1 diff changeset	151 <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	152 <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	153 </test>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	154
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	155 <test>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	156 <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	157 <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	158 <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	159 </repeat>
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	160 <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	161 <output name="output" file="regex_results.tsv"/>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	162 </test>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	163
763c4f968dc6 Uploaded jjohnson parents: diff changeset	164 <test>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	165 <repeat name="tables">
763c4f968dc6 Uploaded jjohnson parents: diff changeset	166 <param name="table" ftype="tabular" value="IEDB.tsv"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	167 <param name="table_name" value="iedb"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	168 <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	169 </repeat>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	170 <repeat name="tables">
763c4f968dc6 Uploaded jjohnson parents: diff changeset	171 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	172 <param name="table_name" value="mhc_summary"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	173 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	174 </repeat>
2 ffa5e34a55c1 Uploaded jjohnson parents: 1 diff changeset	175 <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	176 <output name="output" file="query_results.tsv"/>
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	177 </test>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	178
763c4f968dc6 Uploaded jjohnson parents: diff changeset	179 </tests>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	180 <help><![CDATA[
763c4f968dc6 Uploaded jjohnson parents: diff changeset	181 =============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	182 Query Tabular
763c4f968dc6 Uploaded jjohnson parents: diff changeset	183 =============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	184
763c4f968dc6 Uploaded jjohnson parents: diff changeset	185 Inputs
763c4f968dc6 Uploaded jjohnson parents: diff changeset	186
763c4f968dc6 Uploaded jjohnson parents: diff changeset	187 Loads tabular datasets into a SQLite_ data base.
763c4f968dc6 Uploaded jjohnson parents: diff changeset	188
763c4f968dc6 Uploaded jjohnson parents: diff changeset	189 Outputs
763c4f968dc6 Uploaded jjohnson parents: diff changeset	190
763c4f968dc6 Uploaded jjohnson parents: diff changeset	191 The results of a SQL query are output to the history as a tabular file.
763c4f968dc6 Uploaded jjohnson parents: diff changeset	192
763c4f968dc6 Uploaded jjohnson parents: diff changeset	193 The SQLite_ data base can also be saved and output as a dataset in the history.
763c4f968dc6 Uploaded jjohnson parents: diff changeset	194
10 98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	195 (The SQLite to tabular tool can run additional queries on this database.)
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	196
98bd1e29d669 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 9 diff changeset	197
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	198
763c4f968dc6 Uploaded jjohnson parents: diff changeset	199 For help in using SQLite_ see: http://www.sqlite.org/docs.html
763c4f968dc6 Uploaded jjohnson parents: diff changeset	200
763c4f968dc6 Uploaded jjohnson parents: diff changeset	201 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	202
763c4f968dc6 Uploaded jjohnson parents: diff changeset	203 See: http://www.sqlite.org/lang_datefunc.html
763c4f968dc6 Uploaded jjohnson parents: diff changeset	204
763c4f968dc6 Uploaded jjohnson parents: diff changeset	205 Example
763c4f968dc6 Uploaded jjohnson parents: diff changeset	206
763c4f968dc6 Uploaded jjohnson parents: diff changeset	207 Given 2 tabular datasets: customers and sales
763c4f968dc6 Uploaded jjohnson parents: diff changeset	208
763c4f968dc6 Uploaded jjohnson parents: diff changeset	209 Dataset customers
763c4f968dc6 Uploaded jjohnson parents: diff changeset	210
763c4f968dc6 Uploaded jjohnson parents: diff changeset	211 Table name: "customers"
763c4f968dc6 Uploaded jjohnson parents: diff changeset	212
763c4f968dc6 Uploaded jjohnson parents: diff changeset	213 Column names: "CustomerID,FirstName,LastName,Email,DOB,Phone"
763c4f968dc6 Uploaded jjohnson parents: diff changeset	214
763c4f968dc6 Uploaded jjohnson parents: diff changeset	215 =========== ========== ========== ===================== ========== ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	216 #CustomerID FirstName LastName Email DOB Phone
763c4f968dc6 Uploaded jjohnson parents: diff changeset	217 =========== ========== ========== ===================== ========== ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	218 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
763c4f968dc6 Uploaded jjohnson parents: diff changeset	219 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
763c4f968dc6 Uploaded jjohnson parents: diff changeset	220 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
763c4f968dc6 Uploaded jjohnson parents: diff changeset	221 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
763c4f968dc6 Uploaded jjohnson parents: diff changeset	222 =========== ========== ========== ===================== ========== ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	223
763c4f968dc6 Uploaded jjohnson parents: diff changeset	224 Dataset sales
763c4f968dc6 Uploaded jjohnson parents: diff changeset	225
763c4f968dc6 Uploaded jjohnson parents: diff changeset	226 Table name: "sales"
763c4f968dc6 Uploaded jjohnson parents: diff changeset	227
763c4f968dc6 Uploaded jjohnson parents: diff changeset	228 Column names: "CustomerID,Date,SaleAmount"
763c4f968dc6 Uploaded jjohnson parents: diff changeset	229
763c4f968dc6 Uploaded jjohnson parents: diff changeset	230 ============= ============ ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	231 #CustomerID Date SaleAmount
763c4f968dc6 Uploaded jjohnson parents: diff changeset	232 ============= ============ ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	233 2 2004-05-06 100.22
763c4f968dc6 Uploaded jjohnson parents: diff changeset	234 1 2004-05-07 99.95
763c4f968dc6 Uploaded jjohnson parents: diff changeset	235 3 2004-05-07 122.95
763c4f968dc6 Uploaded jjohnson parents: diff changeset	236 3 2004-05-13 100.00
763c4f968dc6 Uploaded jjohnson parents: diff changeset	237 4 2004-05-22 555.55
763c4f968dc6 Uploaded jjohnson parents: diff changeset	238 ============= ============ ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	239
763c4f968dc6 Uploaded jjohnson parents: diff changeset	240 The query
763c4f968dc6 Uploaded jjohnson parents: diff changeset	241
763c4f968dc6 Uploaded jjohnson parents: diff changeset	242 ::
763c4f968dc6 Uploaded jjohnson parents: diff changeset	243
763c4f968dc6 Uploaded jjohnson parents: diff changeset	244 SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales"
763c4f968dc6 Uploaded jjohnson parents: diff changeset	245 FROM customers join sales on customers.CustomerID = sales.CustomerID
763c4f968dc6 Uploaded jjohnson parents: diff changeset	246 GROUP BY customers.CustomerID ORDER BY TotalSales DESC;
763c4f968dc6 Uploaded jjohnson parents: diff changeset	247
763c4f968dc6 Uploaded jjohnson parents: diff changeset	248 Produces this tabular output:
763c4f968dc6 Uploaded jjohnson parents: diff changeset	249
763c4f968dc6 Uploaded jjohnson parents: diff changeset	250 ========== ======== ==========
763c4f968dc6 Uploaded jjohnson parents: diff changeset	251 #FirstName LastName TotalSales
763c4f968dc6 Uploaded jjohnson parents: diff changeset	252 ========== ======== ==========
763c4f968dc6 Uploaded jjohnson parents: diff changeset	253 James Smith 555.55
763c4f968dc6 Uploaded jjohnson parents: diff changeset	254 Paula Brown 222.95
763c4f968dc6 Uploaded jjohnson parents: diff changeset	255 Steven Goldfish 100.22
763c4f968dc6 Uploaded jjohnson parents: diff changeset	256 John Smith 99.95
763c4f968dc6 Uploaded jjohnson parents: diff changeset	257 ========== ======== ==========
763c4f968dc6 Uploaded jjohnson parents: diff changeset	258
763c4f968dc6 Uploaded jjohnson parents: diff changeset	259
763c4f968dc6 Uploaded jjohnson parents: diff changeset	260 If the optional Table name and Column names inputs are not used, the query would be:
763c4f968dc6 Uploaded jjohnson parents: diff changeset	261
763c4f968dc6 Uploaded jjohnson parents: diff changeset	262 ::
763c4f968dc6 Uploaded jjohnson parents: diff changeset	263
763c4f968dc6 Uploaded jjohnson parents: diff changeset	264 SELECT t1.c2 as "FirstName", t1.c3 as "LastName", sum(t2.c3) as "TotalSales"
763c4f968dc6 Uploaded jjohnson parents: diff changeset	265 FROM t1 join t2 on t1.c1 = t2.c1
763c4f968dc6 Uploaded jjohnson parents: diff changeset	266 GROUP BY t1.c1 ORDER BY TotalSales DESC;
763c4f968dc6 Uploaded jjohnson parents: diff changeset	267
763c4f968dc6 Uploaded jjohnson parents: diff changeset	268 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	269
763c4f968dc6 Uploaded jjohnson parents: diff changeset	270 Column names: ,FirstName,LastName,,BirthDate
763c4f968dc6 Uploaded jjohnson parents: diff changeset	271
763c4f968dc6 Uploaded jjohnson parents: diff changeset	272 Results in the following data base table
763c4f968dc6 Uploaded jjohnson parents: diff changeset	273
763c4f968dc6 Uploaded jjohnson parents: diff changeset	274 =========== ========== ========== ===================== ========== ============
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	275 #c1 FirstName LastName c4 BirthDate c6
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	276 =========== ========== ========== ===================== ========== ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	277 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
763c4f968dc6 Uploaded jjohnson parents: diff changeset	278 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
763c4f968dc6 Uploaded jjohnson parents: diff changeset	279 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
763c4f968dc6 Uploaded jjohnson parents: diff changeset	280 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
763c4f968dc6 Uploaded jjohnson parents: diff changeset	281 =========== ========== ========== ===================== ========== ============
763c4f968dc6 Uploaded jjohnson parents: diff changeset	282
4 afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	283 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	284
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 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	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 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	290 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	291 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	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 Results:
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 #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	297 =========== ==========
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	298 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	299 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	300 =========== ==========
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	301
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 ::
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 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	306 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	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 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	309 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	310 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	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 Results:
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	313
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	314 =========== ========== ==========
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	315 #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	316 =========== ========== ==========
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	317 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	318 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	319 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	320 =========== ========== ==========
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	321
afdbc7198353 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: 2 diff changeset	322 .. _Regular_expression: https://docs.python.org/release/2.7/library/re.html
0 763c4f968dc6 Uploaded jjohnson parents: diff changeset	323 .. _SQLite: http://www.sqlite.org/index.html
763c4f968dc6 Uploaded jjohnson parents: diff changeset	324
763c4f968dc6 Uploaded jjohnson parents: diff changeset	325 ]]></help>
763c4f968dc6 Uploaded jjohnson parents: diff changeset	326 </tool>

Mercurial > repos > jjohnson > query_tabular

annotate query_tabular.xml @ 10:98bd1e29d669 draft default tip