query_tabular: query_tabular.xml annotate

annotate query_tabular.xml @ 14:3003fe70f297 draft

Uploaded

author	jjohnson
date	Fri, 09 Jun 2017 11:24:56 -0400
parents	fd16243931d6
children	5b4f6cf857cf

rev	line source
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	1 <tool id="query_tabular" name="Query Tabular" version="3.0.0">
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
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	4 <requirements>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	5 </requirements>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	6 <stdio>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	7 <exit_code range="1:" />
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	8 </stdio>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	9 <command><![CDATA[
8 ae27dab228b8 Uploaded jjohnson parents: 6 diff changeset	10 cat $query_file &&
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	11 #if $add_to_database.withdb:
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	12 #if $save_db:
8 ae27dab228b8 Uploaded jjohnson parents: 6 diff changeset	13 cp "$add_to_database.withdb" "$sqlitedb" &&
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	14 #else:
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	15 cp "$add_to_database.withdb" "$workdb" &&
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	16 #end if
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	17 #end if
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	18 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	19 #if $save_db
8 ae27dab228b8 Uploaded jjohnson parents: 6 diff changeset	20 -s "$sqlitedb"
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	21 #else
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	22 -s $workdb
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	23 #end if
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	24 -j $table_json
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	25 #if $sqlquery:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	26 -Q "$query_file"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	27 $no_header
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	28 -o $output
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	29 #end if
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	30 ]]></command>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	31 <configfiles>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	32 <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	33 $sqlquery
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	34 </configfile>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	35 <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	36 #import json
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	37 #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	38 #set $jtbls = []
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['tables'] = $jtbls
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	40 #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	41 #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	42 #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	43 #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	44 #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	45 #else
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	46 #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	47 #end if
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	48 #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	49 ## #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	50 ## #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	51 ## #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	52 #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	53 #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	54 #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	55 #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	56 #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	57 #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	58 #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	59 #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	60 #else
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	61 #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	62 #end if
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	63 #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	64 #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	65 #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	66 #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	67 #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	68 #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	69 #else:
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 $idx_non.append(str($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	71 #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	72 #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	73 #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	74 #set $jtbl['unique'] = $idx_unique
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	75 #end if
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	76 #if len($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	77 #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	78 #end if
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	79 #set $input_filters = []
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	80 #for $fi in $tbl.input_opts.linefilters:
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	81 #if $fi.filter.filter_type == 'skip':
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	82 #set $skip_lines = None
8 ae27dab228b8 Uploaded jjohnson parents: 6 diff changeset	83 #if str($fi.filter.skip_lines) != '':
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	84 #set $skip_lines = int($fi.filter.skip_lines)
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	85 #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0:
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	86 #set $skip_lines = int($tbl.table.metadata.comment_lines)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	87 #end if
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	88 #if $skip_lines is not None:
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	89 #set $filter_dict = dict()
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	90 #set $filter_dict['filter'] = str($fi.filter.filter_type)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	91 #set $filter_dict['count'] = $skip_lines
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	92 #silent $input_filters.append($filter_dict)
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	93 #end if
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	94 #elif $fi.filter.filter_type == 'comment':
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	95 #set $filter_dict = dict()
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	96 #set $filter_dict['filter'] = 'regex'
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	97 #set $filter_dict['pattern'] = '^' + str($fi.filter.comment_char)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	98 #set $filter_dict['action'] = 'exclude'
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	99 #silent $input_filters.append($filter_dict)
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	100 #elif $fi.filter.filter_type == 'regex':
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	101 #set $filter_dict = dict()
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	102 #set $filter_dict['filter'] = str($fi.filter.filter_type)
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	103 #set $filter_dict['pattern'] = str($fi.filter.regex_pattern)
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	104 #set $filter_dict['action'] = str($fi.filter.regex_action)
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	105 #silent $input_filters.append($filter_dict)
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	106 #elif $fi.filter.filter_type == 'replace':
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	107 #set $filter_dict = dict()
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	108 #set $filter_dict['filter'] = str($fi.filter.filter_type)
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	109 #set $filter_dict['column'] = int(str($fi.filter.column))
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	110 #set $filter_dict['pattern'] = str($fi.filter.regex_pattern)
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	111 #set $filter_dict['replace'] = str($fi.filter.regex_replace)
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	112 #silent $input_filters.append($filter_dict)
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	113 #elif str($fi.filter.filter_type).endswith('pend_line_num'):
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	114 #set $filter_dict = dict()
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	115 #set $filter_dict['filter'] = str($fi.filter.filter_type)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	116 #silent $input_filters.append($filter_dict)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	117 #elif $fi.filter.filter_type == 'normalize':
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	118 #set $filter_dict = dict()
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	119 #set $filter_dict['filter'] = str($fi.filter.filter_type)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	120 #set $filter_dict['columns'] = [int(str($ci)) for $ci in str($fi.filter.columns).split(',')]
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	121 #set $filter_dict['separator'] = str($fi.filter.separator)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	122 #silent $input_filters.append($filter_dict)
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	123 #end if
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	124 #end for
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	125 #if $input_filters:
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	126 #set $jtbl['filters'] = $input_filters
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	127 #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	128 #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	129 #end for
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	130 #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	131 </configfile>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	132 </configfiles>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	133 <inputs>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	134 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	135 <section name="add_to_database" expanded="false" title="Add tables to an existing database">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	136 <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database"
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	137 help="Make sure your added table names are not already in this database"/>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	138 </section>
8 ae27dab228b8 Uploaded jjohnson parents: 6 diff changeset	139 <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	140 <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	141 <section name="input_opts" expanded="false" title="Filter Dataset Input">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	142 <repeat name="linefilters" title="Filter Tabular Input Lines">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	143 <conditional name="filter">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	144 <param name="filter_type" type="select" label="Filter By">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	145 <option value="skip">skip leading lines</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	146 <option value="comment">comment char</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	147 <option value="regex">by regex expression matching</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	148 <option value="replace">regex replace value in column</option>
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	149 <option value="prepend_line_num">prepend a line number column</option>
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	150 <option value="append_line_num">append a line number column</option>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	151 <option value="normalize">normalize list columns, replicates row for each item in list</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	152 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	153 <when value="skip">
8 ae27dab228b8 Uploaded jjohnson parents: 6 diff changeset	154 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines"
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	155 help="Leave blank to use the comment lines metadata for this dataset" />
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	156 </when>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	157 <when value="comment">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	158 <param name="comment_char" type="text" value="#" label="Comment line starting text">
8 ae27dab228b8 Uploaded jjohnson parents: 6 diff changeset	159 <sanitizer sanitize="False"/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	160 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	161 </when>
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	162 <when value="prepend_line_num"/>
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	163 <when value="append_line_num"/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	164 <when value="regex">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	165 <param name="regex_pattern" type="text" value="" label="regex pattern">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	166 <sanitizer sanitize="False"/>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	167 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	168 <param name="regex_action" type="select" label="action for regex match">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	169 <option value="exclude_match">exclude line on pattern match</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	170 <option value="include_match">include line on pattern match</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	171 <option value="exclude_find">exclude line if pattern found</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	172 <option value="include_find">include line if pattern found</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	173 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	174 </when>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	175 <when value="replace">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	176 <param name="column" type="data_column" data_ref="table" label="Column to replace text"
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	177 help=""/>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	178 <param name="regex_pattern" type="text" value="" label="regex pattern">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	179 <sanitizer sanitize="False"/>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	180 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	181 <param name="regex_replace" type="text" value="" label="replacement expression">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	182 <sanitizer sanitize="False"/>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	183 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	184 </when>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	185 <when value="normalize">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	186 <param name="columns" type="data_column" data_ref="table" multiple="True" label="Columns to split"
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	187 help="If multiple columns are selected, they should have the same length and separator on each line"/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	188 <param name="separator" type="text" value="," label="List item delimiter in column">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	189 <sanitizer sanitize="False"/>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	190 <validator type="regex" message="Anything but TAB or Newline">^[^\t\n\r\f\v]+$</validator>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	191 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	192 </when>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	193 </conditional>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	194 </repeat>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	195 </section>
4 9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	196 <section name="tbl_opts" expanded="false" title="Table Options">
5 19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	197 <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table">
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	198 <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help>
4 9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	199 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	200 </param>
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	201 <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)">
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	202 <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	203 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	204 </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	205 <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	206 <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+[^,"][]])?)*$</validator>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	207 </param>
5 19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	208 <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load the columns you have named into database"/>
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	209 <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name"
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	210 help="Only creates this additional column when a name is entered. (This can not be the same name as any of the other columns in this table.)">
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	211 <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator>
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	212 </param>
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	213 <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	214 <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	215 <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	216 <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	217 <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	218 </param>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	219 </repeat>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	220 </section>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	221 </repeat>
5 19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	222 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history"/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	223 <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	224 <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	225 <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	226 <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	227 </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	228 <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	229 </inputs>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	230 <outputs>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	231 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}">
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	232 <filter>save_db or not (sqlquery and len(sqlquery) > 0)</filter>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	233 </data>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	234 <data format="tabular" name="output" label="query results on ${on_string}">
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	235 <filter>sqlquery and len(sqlquery) > 0</filter>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	236 </data>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	237 </outputs>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	238 <tests>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	239
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	240 <test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	241 <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	242 <param name="table" ftype="tabular" value="customers.tsv"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	243 <param name="table_name" value="customers"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	244 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/>
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="sales.tsv"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	248 <param name="table_name" value="sales"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	249 <param name="col_names" value="CustomerID,Date,SaleAmount"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	250 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	251 <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	252 <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	253 </test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	254
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	255 <test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	256 <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	257 <param name="table" ftype="tabular" value="customers.tsv"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	258 <param name="col_names" value=",FirstName,LastName,,DOB,"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	259 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	260 <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	261 <param name="table" ftype="tabular" value="sales.tsv"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	262 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	263 <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	264 <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	265 </test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	266
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	267 <test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	268 <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	269 <param name="table" ftype="tabular" value="customers.tsv"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	270 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	271 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	272 <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	273 <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	274 </test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	275
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	276 <test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	277 <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	278 <param name="table" ftype="tabular" value="IEDB.tsv"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	279 <param name="table_name" value="iedb"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	280 <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"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	281 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	282 <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	283 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	284 <param name="table_name" value="mhc_summary"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	285 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	286 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	287 <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"/>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	288 <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	289 </test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	290
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	291 </tests>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	292 <help><![CDATA[
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	293 =============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	294 Query Tabular
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	295 =============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	296
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	297 Inputs
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	298
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	299 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	300
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	301 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	302
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	303
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	304 Input Line Filters
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	305
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	306 As a tabular file is being read, line filters may be applied.
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	307
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	308 ::
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	309
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	310 - skip leading lines skip the first number of lines
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	311 - comment char omit any lines that start with the specified comment character
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	312 - by regex expression matching include/exclude lines the match the regex expression
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	313 - regex replace value in column replace a field in a column using a regex substitution (good for date reformatting)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	314 - prepend a line number column each line has the ordinal value of the line read by this filter as the first column
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	315 - append a line number column each line has the ordinal value of the line read by this filter as the last column
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	316 - normalize list columns replicates the line for each item in the specified list columns
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	317
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	318
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	319 Outputs
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	320
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	321 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	322
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	323 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	324
5 19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	325 (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	326
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	327
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	328 For help in using SQLite_ see: http://www.sqlite.org/docs.html
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	329
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	330 NOTE: input for SQLite dates input field must be in the format: YYYY-MM-DD for example: 2015-09-30
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	331
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	332 See: http://www.sqlite.org/lang_datefunc.html
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	333
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	334 Example
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	335
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	336 Given 2 tabular datasets: customers and sales
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	337
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	338 Dataset customers
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	339
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	340 Table name: "customers"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	341
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	342 Column names: "CustomerID,FirstName,LastName,Email,DOB,Phone"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	343
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	344 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	345 #CustomerID FirstName LastName Email DOB Phone
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	346 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	347 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	348 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	349 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	350 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	351 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	352
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	353 Dataset sales
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	354
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	355 Table name: "sales"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	356
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	357 Column names: "CustomerID,Date,SaleAmount"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	358
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	359 ============= ============ ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	360 #CustomerID Date SaleAmount
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	361 ============= ============ ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	362 2 2004-05-06 100.22
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	363 1 2004-05-07 99.95
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	364 3 2004-05-07 122.95
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	365 3 2004-05-13 100.00
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	366 4 2004-05-22 555.55
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	367 ============= ============ ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	368
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	369 The query
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	370
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	371 ::
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	372
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	373 SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	374 FROM customers join sales on customers.CustomerID = sales.CustomerID
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	375 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	376
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	377 Produces this tabular output:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	378
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	379 ========== ======== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	380 #FirstName LastName TotalSales
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	381 ========== ======== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	382 James Smith 555.55
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	383 Paula Brown 222.95
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	384 Steven Goldfish 100.22
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	385 John Smith 99.95
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	386 ========== ======== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	387
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	388
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	389 If the optional Table name and Column names inputs are not used, the query would be:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	390
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	391 ::
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	392
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	393 SELECT t1.c2 as "FirstName", t1.c3 as "LastName", sum(t2.c3) as "TotalSales"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	394 FROM t1 join t2 on t1.c1 = t2.c1
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	395 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	396
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	397 You can selectively name columns, e.g. on the customers input you could just name columns 2,3, and 5:
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 Column names: ,FirstName,LastName,,BirthDate
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	400
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	401 Results in the following data base table
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	402
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	403 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	404 #c1 FirstName LastName c4 BirthDate c6
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	405 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	406 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	407 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	408 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	409 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	410 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	411
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	412
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	413 Regular_expression_ functions are included for:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	414
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	415 ::
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	416
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	417 matching: re_match('pattern',column)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	418
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	419 SELECT t1.FirstName, t1.LastName
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	420 FROM t1
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	421 WHERE re_match('^.*\.(net\|org)$',c4)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	422
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	423 Results:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	424
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	425 =========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	426 #FirstName LastName
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	427 =========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	428 Steven Goldfish
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	429 Paula Brown
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	430 =========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	431
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	432
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	433 ::
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	434
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	435 searching: re_search('pattern',column)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	436 substituting: re_sub('pattern','replacement,column)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	437
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	438 SELECT t1.FirstName, t1.LastName, re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	439 FROM t1
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	440 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	441
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	442 Results:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	443
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	444
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	445 =========== ========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	446 #FirstName LastName DOB
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	447 =========== ========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	448 Steven Goldfish 04/04/74
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	449 Paula Brown 24/05/78
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	450 James Smith 20/10/80
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	451 =========== ========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	452
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	453
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	454 Line Filtering Example
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	455 (Six filters are applied as the following file is read)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	456
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	457 ::
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	458
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	459 Input Tabular File:
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	460
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	461 #People with pets
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	462 Pets FirstName LastName DOB PetNames PetType
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	463 2 Paula Brown 24/05/78 Rex,Fluff dog,cat
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	464 1 Steven Jones 04/04/74 Allie cat
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	465 0 Jane Doe 24/05/78
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	466 1 James Smith 20/10/80 Spot
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	467
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	468
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	469 Filter 1 - append a line number column:
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	470
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	471 #People with pets 1
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	472 Pets FirstName LastName DOB PetNames PetType 2
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	473 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	474 1 Steven Jones 04/04/74 Allie cat 4
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	475 0 Jane Doe 24/05/78 5
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	476 1 James Smith 20/10/80 Spot 6
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	477
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	478 Filter 2 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	479
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	480 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	481 1 Steven Jones 04/04/74 Allie cat 4
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	482 0 Jane Doe 24/05/78 5
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	483 1 James Smith 20/10/80 Spot 6
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	484
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	485 Filter 3 - append a line number column:
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	486
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	487 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3 1
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	488 1 Steven Jones 04/04/74 Allie cat 4 2
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	489 0 Jane Doe 24/05/78 5 3
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	490 1 James Smith 20/10/80 Spot 6 4
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	491
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	492 Filter 4 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	493
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	494 2 Paula Brown 1978-05-24 Rex,Fluff dog,cat 3 1
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	495 1 Steven Jones 1974-04-04 Allie cat 4 2
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	496 0 Jane Doe 1978-05-24 5 3
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	497 1 James Smith 1980-10-20 Spot 6 4
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	498
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	499 Filter 5 - normalize list columns[5,6]:
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	500
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	501 2 Paula Brown 1978-05-24 Rex dog 3 1
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	502 2 Paula Brown 1978-05-24 Fluff cat 3 1
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	503 1 Steven Jones 1974-04-04 Allie cat 4 2
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	504 0 Jane Doe 1978-05-24 5 3
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	505 1 James Smith 1980-10-20 Spot 6 4
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	506
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	507 Filter 6 - append a line number column:
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	508
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	509 2 Paula Brown 1978-05-24 Rex dog 3 1 1
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	510 2 Paula Brown 1978-05-24 Fluff cat 3 1 2
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	511 1 Steven Jones 1974-04-04 Allie cat 4 2 3
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	512 0 Jane Doe 1978-05-24 5 3 4
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	513 1 James Smith 1980-10-20 Spot 6 4 5
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	514
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	515
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	516 Table name: pets
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	517
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	518 Table columns: Pets,FirstName,LastName,Birthdate,PetNames,PetType,line_num,entry_num,row_num
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	519
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	520 Query: SELECT * FROM pets
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	521
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	522 Result:
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	523
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	524 ====== ========== ======== ========== ========= ======== ========= ========== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	525 #Pets FirstName LastName BirthDate PetNames PetType line_num entry_num row_num
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	526 ====== ========== ======== ========== ========= ======== ========= ========== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	527 2 Paula Brown 1978-05-24 Rex dog 3 1 1
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	528 2 Paula Brown 1978-05-24 Fluff cat 3 1 2
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	529 1 Steven Jones 1974-04-04 Allie cat 4 2 3
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	530 0 Jane Doe 1978-05-24 5 3 4
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	531 1 James Smith 1980-10-20 Spot 6 4 5
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	532 ====== ========== ======== ========== ========= ======== ========= ========== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	533
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	534
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	535 Normalizing by Line Filtering into 2 Tables
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	536
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	537 People Table
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	538
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	539 ::
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	540
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	541 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	542 Filter 2 - append a line number column:
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	543 Filter 3 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format)
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	544
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	545 Table: People
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	546 Columns: Pets,FirstName,LastName,DOB,,,id
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	547
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	548 ==== ========= ======== ========== ==
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	549 Pets FirstName LastName DOB id
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	550 ==== ========= ======== ========== ==
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	551 2 Paula Brown 1978-05-24 1
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	552 1 Steven Jones 1974-04-04 2
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	553 0 Jane Doe 1978-05-24 3
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	554 1 James Smith 1980-10-20 4
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	555 ==== ========= ======== ========== ==
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	556
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	557
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	558 Pet Table
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	559
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	560 ::
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	561
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	562 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	563 Filter 2 - append a line number column:
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	564 Filter 3 - by regex expression matching [exclude]: '^0\t' (exclude lines with no pets)
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	565 Filter 4 - normalize list columns[5,6]:
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	566
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	567 Table: Pet
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	568 Columns: ,,,,PetName,PetType,id
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	569
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	570 ======== ======== ==
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	571 PetName PetType id
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	572 ======== ======== ==
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	573 Rex dog 1
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	574 Fluff cat 1
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	575 Allie cat 2
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	576 Spot 4
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	577 ======== ======== ==
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	578
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	579
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	580 Query: SELECT FirstName,LastName,PetName FROM People join Pet on People.id = Pet.id WHERE PetType = 'cat';
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	581
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	582 Result:
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	583
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	584 ========= ======== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	585 FirstName LastName PetName
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	586 ========= ======== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	587 Paula Brown Fluff
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	588 Steven Jones Allie
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	589 ========= ======== ========
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	590
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	591 .. _Regular_expression: https://docs.python.org/release/2.7/library/re.html
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	592 .. _SQLite: http://www.sqlite.org/index.html
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	593
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	594 ]]></help>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	595 </tool>

Mercurial > repos > jjohnson > query_tabular

annotate query_tabular.xml @ 14:3003fe70f297 draft