query_tabular: query_tabular.xml annotate

annotate query_tabular.xml @ 22:bed5018e7ae3 draft

Uploaded

author	jjohnson
date	Mon, 17 Jul 2017 15:22:04 -0400
parents	357fe86f245d
children

rev	line source
22 bed5018e7ae3 Uploaded jjohnson parents: 21 diff changeset	1 <tool id="query_tabular" name="Query Tabular" version="5.0.0">
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	2 <description>using sqlite sql</description>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	3
20 ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	4 <macros>
ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	5 <import>macros.xml</import>
ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	6 </macros>
ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	7
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	8 <requirements>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	9 </requirements>
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	10
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	11 <command detect_errors="exit_code"><![CDATA[
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	12 cat '$query_file' &&
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	13 #if $add_to_database.withdb:
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	14 #if $save_db:
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	15 cp '$add_to_database.withdb' '$sqlitedb' &&
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	16 #else:
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	17 cp '$add_to_database.withdb' '$workdb' &&
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	18 #end if
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	19 #end if
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	20 python '$__tool_directory__/query_tabular.py'
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	21 #if $save_db
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	22 -s '$sqlitedb'
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	23 #else
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	24 -s '$workdb'
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	25 #end if
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	26 -j '$table_json'
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	27 #if $sqlquery:
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	28 -Q '$query_file'
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	29 $no_header
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	30 -o '$output'
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	31 #end if
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	32 ]]></command>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	33 <configfiles>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	34 <configfile name="query_file">
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	35 $sqlquery
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	36 </configfile>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	37 <configfile name="table_json">
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	38 #import json
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	39 #set $jtbldef = dict()
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	40 #set $jtbls = []
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	41 #set $jtbldef['tables'] = $jtbls
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	42 #for $i,$tbl in enumerate($tables):
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	43 #set $jtbl = dict()
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	44 #set $jtbl['file_path'] = str($tbl.table)
4 9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	45 #if $tbl.tbl_opts.table_name:
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	46 #set $tname = str($tbl.tbl_opts.table_name)
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	47 #else
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	48 #set $tname = 't' + str($i + 1)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	49 #end if
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	50 #set $jtbl['table_name'] = $tname
4 9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	51 ## #if $tbl.tbl_opts.sel_cols:
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	52 ## #set $jtbl['sel_cols'] = $tbl.tbl_opts.sel_cols el_cols
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	53 ## #end if
5 19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	54 #if $tbl.tbl_opts.pkey_autoincr:
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	55 #set $jtbl['pkey_autoincr'] = str($tbl.tbl_opts.pkey_autoincr)
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	56 #end if
4 9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	57 #if $tbl.tbl_opts.col_names:
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	58 #set $col_names = str($tbl.tbl_opts.col_names)
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	59 #if $tbl.tbl_opts.load_named_columns:
3 3e3b3c883bec planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 2 diff changeset	60 #set $jtbl['load_named_columns'] = True
3e3b3c883bec planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty jjohnson parents: 2 diff changeset	61 #end if
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	62 #else
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	63 #set $col_names = ''
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	64 #end if
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	65 #set $jtbl['column_names'] = $col_names
4 9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	66 #set $idx_unique = []
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	67 #set $idx_non = []
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	68 #for $idx in $tbl.tbl_opts.indexes:
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	69 #if $idx.unique:
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	70 #silent $idx_unique.append(str($idx.index_columns))
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	71 #else:
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	72 #silent $idx_non.append(str($idx.index_columns))
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	73 #end if
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	74 #end for
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	75 #if len($idx_unique) > 0:
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	76 #set $jtbl['unique'] = $idx_unique
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	77 #end if
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	78 #if len($idx_non) > 0:
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	79 #set $jtbl['index'] = $idx_non
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	80 #end if
20 ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	81 #set $linefilters = $tbl.input_opts.linefilters
ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	82 @LINEFILTERS@
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	83 #if $input_filters:
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	84 #set $jtbl['filters'] = $input_filters
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	85 #end if
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	86 #set $jtbls += [$jtbl]
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	87 #end for
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	88 #echo $json.dumps($jtbldef)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	89 </configfile>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	90 </configfiles>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	91 <inputs>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	92 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	93 <section name="add_to_database" expanded="false" title="Add tables to an existing database">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	94 <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database"
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	95 help="Make sure your added table names are not already in this database"/>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	96 </section>
8 ae27dab228b8 Uploaded jjohnson parents: 6 diff changeset	97 <repeat name="tables" title="Database Table" min="0">
5 19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	98 <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	99 <section name="input_opts" expanded="false" title="Filter Dataset Input">
20 ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	100 <expand macro="macro_line_filters" />
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	101 </section>
4 9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	102 <section name="tbl_opts" expanded="false" title="Table Options">
5 19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	103 <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table">
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	104 <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help>
4 9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	105 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	106 </param>
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	107 <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)">
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	108 <help>By default, table columns will be named: c1,c2,c3,...,cn (column names for a table must be unique)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	109 You can override the default names by entering a comma -separated list of names, e.g. ',name1,,,name2' would rename the second and fifth columns.
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	110 </help>
4 9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	111 <sanitizer sanitize="False"/>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	112 <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w\|"\S+[^,"]"\|`\S+[^,`]`\|[[]\S+[^,"][]])?(,([A-Za-z]\w\|"\S+."\|`\S+[^,`]`\|[[]\S+[^,"][]])?)*$</validator>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	113 </param>
5 19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	114 <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load the columns you have named into database"/>
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	115 <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name"
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	116 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.)">
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	117 <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator>
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	118 </param>
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	119 <repeat name="indexes" title="Table Index">
4 9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	120 <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	121 <param name="index_columns" type="text" value="" label="Index on Columns">
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	122 <help>Create an index on the column names: e,g, c1 or c2,c4</help>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	123 <validator type="regex" message="Column name, separated by commes if more than one">^([A-Za-z]\w\|"\S+[^,"]"\|`\S+[^,`]`\|[[]\S+[^,"][]])(,([A-Za-z]\w\|"\S+."\|`\S+[^,`]`\|[[]\S+[^,"][]])?)*$</validator>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	124 </param>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	125 </repeat>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	126 </section>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	127 </repeat>
20 ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	128 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history"
ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	129 help="SQLite to tabular tool can run additional queries on this database"/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	130 <param name="sqlquery" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to generate tabular output">
5 19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	131 <help>By default: tables are named: t1,t2,...,tn and columns in each table: c1,c2,...,cn</help>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	132 <sanitizer sanitize="False"/>
4 9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	133 <validator type="regex" message="">^(?ims)\sselect\s+.\s+from\s+.*$</validator>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	134 </param>
5 19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	135 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers from tabular output"/>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	136 </inputs>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	137 <outputs>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	138 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}">
20 ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	139 <filter>save_db</filter>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	140 </data>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	141 <data format="tabular" name="output" label="query results on ${on_string}">
20 ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	142 <filter>not save_db or (sqlquery and len(sqlquery.strip()) > 0)</filter>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	143 </data>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	144 </outputs>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	145 <tests>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	146 <test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	147 <repeat name="tables">
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	148 <param name="table" ftype="tabular" value="customers.tsv"/>
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	149 <section name="input_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	150 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	151 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	152 <param name="filter_type" value="comment"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	153 <param name="comment_char" value="35"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	154 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	155 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	156 </section>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	157 <section name="tbl_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	158 <param name="table_name" value="customers"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	159 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	160 </section>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	161 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	162 <repeat name="tables">
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	163 <param name="table" ftype="tabular" value="sales.tsv"/>
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	164 <section name="input_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	165 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	166 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	167 <param name="filter_type" value="comment"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	168 <param name="comment_char" value="35"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	169 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	170 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	171 </section>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	172 <section name="tbl_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	173 <param name="table_name" value="sales"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	174 <param name="col_names" value="CustomerID,Date,SaleAmount"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	175 </section>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	176 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	177 <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"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	178 <output name="output" file="sales_results.tsv"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	179 </test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	180
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	181 <test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	182 <repeat name="tables">
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	183 <param name="table" ftype="tabular" value="customers.tsv"/>
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	184 <section name="input_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	185 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	186 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	187 <param name="filter_type" value="comment"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	188 <param name="comment_char" value="35"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	189 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	190 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	191 </section>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	192 <section name="tbl_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	193 <param name="col_names" value=",FirstName,LastName,,DOB,"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	194 </section>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	195 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	196 <repeat name="tables">
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	197 <param name="table" ftype="tabular" value="sales.tsv"/>
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	198 <section name="input_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	199 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	200 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	201 <param name="filter_type" value="skip"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	202 <param name="skip_lines" value="1"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	203 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	204 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	205 </section>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	206 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	207 <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;"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	208 <output name="output" file="sales_results.tsv"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	209 </test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	210
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	211 <test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	212 <repeat name="tables">
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	213 <param name="table" ftype="tabular" value="customers.tsv"/>
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	214 <section name="input_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	215 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	216 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	217 <param name="filter_type" value="skip"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	218 <param name="skip_lines" value="1"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	219 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	220 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	221 </section>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	222 <section name="tbl_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	223 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	224 </section>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	225 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	226 <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)"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	227 <output name="output" file="regex_results.tsv"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	228 </test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	229
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	230 <test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	231 <repeat name="tables">
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	232 <param name="table" ftype="tabular" value="IEDB.tsv"/>
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	233 <section name="input_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	234 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	235 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	236 <param name="filter_type" value="comment"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	237 <param name="comment_char" value="35"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	238 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	239 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	240 </section>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	241 <section name="tbl_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	242 <param name="table_name" value="iedb"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	243 <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"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	244 </section>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	245 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	246 <repeat name="tables">
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	247 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	248 <section name="input_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	249 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	250 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	251 <param name="filter_type" value="skip"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	252 <param name="skip_lines" value="1"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	253 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	254 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	255 </section>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	256 <section name="tbl_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	257 <param name="table_name" value="mhc_summary"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	258 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	259 </section>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	260 </repeat>
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	261 <param name="sqlquery" value="select iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank"/>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	262 <output name="output" file="query_results.tsv"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	263 </test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	264
18 b9f797bf4f38 Uploaded jjohnson parents: 16 diff changeset	265 <test>
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	266 <section name="add_to_database">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	267 <param name="withdb" ftype="sqlite" value="testdb.sqlite"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	268 </section>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	269 <repeat name="tables">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	270 <param name="table" ftype="tabular" value="pets.tsv"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	271 <section name="input_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	272 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	273 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	274 <param name="filter_type" value="regex"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	275 <param name="regex_pattern" value="^\d+"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	276 <param name="regex_action" value="include_find"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	277 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	278 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	279 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	280 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	281 <param name="filter_type" value="comment"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	282 <param name="comment_char" value="35"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	283 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	284 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	285 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	286 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	287 <param name="filter_type" value="append_line_num"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	288 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	289 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	290 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	291 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	292 <param name="filter_type" value="select_columns"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	293 <param name="columns" value="7,2,3,4,1"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	294 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	295 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	296 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	297 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	298 <param name="filter_type" value="replace"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	299 <param name="column" value="c4"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	300 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	301 <param name="regex_replace" value="19\3-\2-\1"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	302 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	303 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	304 </section>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	305 <section name="tbl_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	306 <param name="table_name" value="people"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	307 <param name="col_names" value="id,first,last,dob,pets"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	308 </section>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	309 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	310 <param name="sqlquery" value="SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	311 <output name="output" file="add_to_db_results.tsv"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	312 </test>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	313
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	314 <test>
18 b9f797bf4f38 Uploaded jjohnson parents: 16 diff changeset	315 <repeat name="tables">
b9f797bf4f38 Uploaded jjohnson parents: 16 diff changeset	316 <param name="table" ftype="tabular" value="pets.tsv"/>
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	317 <section name="input_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	318 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	319 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	320 <param name="filter_type" value="regex"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	321 <param name="regex_pattern" value="^\d+"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	322 <param name="regex_action" value="include_find"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	323 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	324 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	325 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	326 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	327 <param name="filter_type" value="comment"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	328 <param name="comment_char" value="35"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	329 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	330 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	331 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	332 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	333 <param name="filter_type" value="append_line_num"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	334 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	335 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	336 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	337 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	338 <param name="filter_type" value="select_columns"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	339 <param name="columns" value="7,2,3,4,1"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	340 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	341 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	342 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	343 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	344 <param name="filter_type" value="replace"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	345 <param name="column" value="c4"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	346 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	347 <param name="regex_replace" value="19\3-\2-\1"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	348 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	349 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	350 </section>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	351 <section name="tbl_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	352 <param name="table_name" value="people"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	353 <param name="col_names" value="id,first,last,dob,pets"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	354 </section>
18 b9f797bf4f38 Uploaded jjohnson parents: 16 diff changeset	355 </repeat>
b9f797bf4f38 Uploaded jjohnson parents: 16 diff changeset	356 <repeat name="tables">
b9f797bf4f38 Uploaded jjohnson parents: 16 diff changeset	357 <param name="table" ftype="tabular" value="pets.tsv"/>
21 357fe86f245d Uploaded jjohnson parents: 20 diff changeset	358 <section name="input_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	359 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	360 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	361 <param name="filter_type" value="regex"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	362 <param name="regex_pattern" value="^\d+"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	363 <param name="regex_action" value="include_find"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	364 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	365 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	366 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	367 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	368 <param name="filter_type" value="append_line_num"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	369 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	370 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	371 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	372 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	373 <param name="filter_type" value="select_columns"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	374 <param name="columns" value="c7,c5,c6"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	375 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	376 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	377 <repeat name="linefilters">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	378 <conditional name="filter">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	379 <param name="filter_type" value="normalize"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	380 <param name="columns" value="c2,c3"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	381 <param name="separator" value=","/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	382 </conditional>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	383 </repeat>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	384 </section>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	385 <section name="tbl_opts">
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	386 <param name="table_name" value="pet"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	387 <param name="col_names" value="id,name,animal"/>
357fe86f245d Uploaded jjohnson parents: 20 diff changeset	388 </section>
18 b9f797bf4f38 Uploaded jjohnson parents: 16 diff changeset	389 </repeat>
b9f797bf4f38 Uploaded jjohnson parents: 16 diff changeset	390 <param name="sqlquery" value="SELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'"/>
b9f797bf4f38 Uploaded jjohnson parents: 16 diff changeset	391 <output name="output" file="pet_normalized_query_results.tsv"/>
b9f797bf4f38 Uploaded jjohnson parents: 16 diff changeset	392 </test>
b9f797bf4f38 Uploaded jjohnson parents: 16 diff changeset	393
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	394 </tests>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	395 <help><![CDATA[
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	396 =============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	397 Query Tabular
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	398 =============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	399
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	400 Inputs
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	401
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	402 Loads tabular datasets into a SQLite_ data base.
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	403
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	404 An existing SQLite_ data base can be used as input, and any selected tabular datasets will be added as new tables in that data base.
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	405
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	406
20 ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	407 @LINEFILTERS_HELP@
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	408
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	409
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	410 Outputs
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	411
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	412 The results of a SQL query are output to the history as a tabular file.
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	413
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	414 The SQLite_ data base can also be saved and output as a dataset in the history.
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	415
5 19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	416 (The SQLite to tabular tool can run additional queries on this database.)
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	417
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	418
20 ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	419 @QUERY_HELP@
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	420
20 ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	421 @LINEFILTERS_HELP_EXAMPLE@
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	422
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	423
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	424 Table name: pets
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	425
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	426 Table columns: Pets,FirstName,LastName,Birthdate,PetNames,PetType,line_num,entry_num,row_num
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	427
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	428 Query: SELECT * FROM pets
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	429
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	430 Result:
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	431
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	432 ====== ========== ======== ========== ========= ======== ========= ========== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	433 #Pets FirstName LastName BirthDate PetNames PetType line_num entry_num row_num
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	434 ====== ========== ======== ========== ========= ======== ========= ========== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	435 2 Paula Brown 1978-05-24 Rex dog 3 1 1
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	436 2 Paula Brown 1978-05-24 Fluff cat 3 1 2
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	437 1 Steven Jones 1974-04-04 Allie cat 4 2 3
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	438 0 Jane Doe 1978-05-24 5 3 4
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	439 1 James Smith 1980-10-20 Spot 6 4 5
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	440 ====== ========== ======== ========== ========= ======== ========= ========== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	441
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	442
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	443 Normalizing by Line Filtering into 2 Tables
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	444
20 ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	445 *Relational database opertions work with single-valued column entries.
ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	446 To apply relational operations to tabular files that contain fields with lists of values,
ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	447 we need to "normalize" those fields, duplicating lines for each item in the list.
ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	448 In this example we create 2 tables, one for single-valued fields and a second with list-valued fields normalized.
ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	449 Becauce we add a line number first for each table, we can join the 2 tables on the line number column.*
ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	450 https://en.wikipedia.org/wiki/First_normal_form
ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	451
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	452 People Table
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	453
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	454 ::
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	455
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	456 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	457 Filter 2 - append a line number column:
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	458 Filter 3 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format)
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	459 Filter 4 - select columns 7,2,3,4,1
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	460
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	461 Table: People
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	462 Columns: id,FirstName,LastName,DOB,Pets
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	463
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	464 == ========= ======== ========== ====
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	465 id FirstName LastName DOB Pets
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	466 == ========= ======== ========== ====
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	467 1 Paula Brown 1978-05-24 2
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	468 2 Steven Jones 1974-04-04 1
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	469 3 Jane Doe 1978-05-24 0
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	470 4 James Smith 1980-10-20 1
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	471 == ========= ======== ========== ====
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	472
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	473
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	474 Pet Table
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	475
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	476 ::
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	477
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	478 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	479 Filter 2 - append a line number column:
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	480 Filter 3 - by regex expression matching [exclude]: '^0\t' (exclude lines with no pets)
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	481 Filter 4 - normalize list columns[5,6]:
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	482 Filter 5 - select columns 7,5,6
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	483
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	484 Table: Pet
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	485 Columns: id,PetName,PetType
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	486
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	487 == ======== ========
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	488 id PetName PetType
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	489 == ======== ========
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	490 1 Rex dog
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	491 1 Fluff cat
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	492 2 Allie cat
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	493 4 Spot
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	494 == ======== ========
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	495
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	496
20 ab27c4bd14b9 Uploaded jjohnson parents: 18 diff changeset	497 Query: SELECT FirstName,LastName,PetName FROM People JOIN Pet ON People.id = Pet.id WHERE PetType = 'cat';
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	498
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	499 Result:
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	500
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	501 ========= ======== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	502 FirstName LastName PetName
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	503 ========= ======== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	504 Paula Brown Fluff
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	505 Steven Jones Allie
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	506 ========= ======== ========
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	507
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	508
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	509 ]]></help>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	510 </tool>

Mercurial > repos > jjohnson > query_tabular

annotate query_tabular.xml @ 22:bed5018e7ae3 draft