query_tabular: query_tabular.xml annotate

annotate query_tabular.xml @ 16:5b4f6cf857cf draft

Uploaded

author	jjohnson
date	Thu, 22 Jun 2017 09:14:56 -0400
parents	3003fe70f297
children	b9f797bf4f38

rev	line source
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	1 <tool id="query_tabular" name="Query Tabular" version="3.1.0">
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)
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	106 #elif $fi.filter.filter_type == 'select_columns':
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	107 #set $filter_dict = dict()
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	108 #set $filter_dict['filter'] = str($fi.filter.filter_type)
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	109 #set $filter_dict['columns'] = [int(str($ci)) for $ci in str($fi.filter.columns).split(',')]
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	110 #silent $input_filters.append($filter_dict)
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	111 #elif $fi.filter.filter_type == 'replace':
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	112 #set $filter_dict = dict()
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	113 #set $filter_dict['filter'] = str($fi.filter.filter_type)
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	114 #set $filter_dict['column'] = int(str($fi.filter.column))
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	115 #set $filter_dict['pattern'] = str($fi.filter.regex_pattern)
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	116 #set $filter_dict['replace'] = str($fi.filter.regex_replace)
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	117 #silent $input_filters.append($filter_dict)
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	118 #elif str($fi.filter.filter_type).endswith('pend_line_num'):
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	119 #set $filter_dict = dict()
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	120 #set $filter_dict['filter'] = str($fi.filter.filter_type)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	121 #silent $input_filters.append($filter_dict)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	122 #elif $fi.filter.filter_type == 'normalize':
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	123 #set $filter_dict = dict()
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	124 #set $filter_dict['filter'] = str($fi.filter.filter_type)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	125 #set $filter_dict['columns'] = [int(str($ci)) for $ci in str($fi.filter.columns).split(',')]
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	126 #set $filter_dict['separator'] = str($fi.filter.separator)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	127 #silent $input_filters.append($filter_dict)
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	128 #end if
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	129 #end for
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	130 #if $input_filters:
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	131 #set $jtbl['filters'] = $input_filters
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	132 #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	133 #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	134 #end for
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	135 #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	136 </configfile>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	137 </configfiles>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	138 <inputs>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	139 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	140 <section name="add_to_database" expanded="false" title="Add tables to an existing database">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	141 <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database"
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	142 help="Make sure your added table names are not already in this database"/>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	143 </section>
8 ae27dab228b8 Uploaded jjohnson parents: 6 diff changeset	144 <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	145 <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	146 <section name="input_opts" expanded="false" title="Filter Dataset Input">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	147 <repeat name="linefilters" title="Filter Tabular Input Lines">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	148 <conditional name="filter">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	149 <param name="filter_type" type="select" label="Filter By">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	150 <option value="skip">skip leading lines</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	151 <option value="comment">comment char</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	152 <option value="regex">by regex expression matching</option>
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	153 <option value="select_columns">select columns</option>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	154 <option value="replace">regex replace value in column</option>
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	155 <option value="prepend_line_num">prepend a line number column</option>
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	156 <option value="append_line_num">append a line number column</option>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	157 <option value="normalize">normalize list columns, replicates row for each item in list</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	158 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	159 <when value="skip">
8 ae27dab228b8 Uploaded jjohnson parents: 6 diff changeset	160 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines"
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	161 help="Leave blank to use the comment lines metadata for this dataset" />
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	162 </when>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	163 <when value="comment">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	164 <param name="comment_char" type="text" value="#" label="Comment line starting text">
8 ae27dab228b8 Uploaded jjohnson parents: 6 diff changeset	165 <sanitizer sanitize="False"/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	166 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	167 </when>
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	168 <when value="prepend_line_num"/>
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	169 <when value="append_line_num"/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	170 <when value="regex">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	171 <param name="regex_pattern" type="text" value="" label="regex pattern">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	172 <sanitizer sanitize="False"/>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	173 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	174 <param name="regex_action" type="select" label="action for regex match">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	175 <option value="exclude_match">exclude line on pattern match</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	176 <option value="include_match">include line on pattern match</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	177 <option value="exclude_find">exclude line if pattern found</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	178 <option value="include_find">include line if pattern found</option>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	179 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	180 </when>
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	181 <when value="select_columns">
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	182 <param name="columns" type="text" value="" label="enter column numbers to keep"
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	183 help="example: 1,4,2 (selects the first,fourth, and second columns)">
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	184 <validator type="regex" message="Column ordinal positions separated by commas">^([1-9]\d)(,[1-9]\d)*$</validator>
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	185 </param>
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	186 </when>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	187 <when value="replace">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	188 <param name="column" type="data_column" data_ref="table" label="Column to replace text"
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	189 help=""/>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	190 <param name="regex_pattern" type="text" value="" label="regex pattern">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	191 <sanitizer sanitize="False"/>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	192 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	193 <param name="regex_replace" type="text" value="" label="replacement expression">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	194 <sanitizer sanitize="False"/>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	195 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	196 </when>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	197 <when value="normalize">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	198 <param name="columns" type="data_column" data_ref="table" multiple="True" label="Columns to split"
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	199 help="If multiple columns are selected, they should have the same length and separator on each line"/>
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	200 <param name="separator" type="text" value="," label="List item delimiter in column">
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	201 <sanitizer sanitize="False"/>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	202 <validator type="regex" message="Anything but TAB or Newline">^[^\t\n\r\f\v]+$</validator>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	203 </param>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	204 </when>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	205 </conditional>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	206 </repeat>
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	207 </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	208 <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	209 <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	210 <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	211 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	212 </param>
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	213 <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)">
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	214 <help>By default, table columns will be named: c1,c2,c3,...,cn (column names for a table must be unique)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	215 You can override the default names by entering a comma -separated list of names, e.g. ',name1,,,name2' would rename the second and fifth columns.
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	216 </help>
4 9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	217 <sanitizer sanitize="False"/>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	218 <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w\|"\S+[^,"]"\|`\S+[^,`]`\|[[]\S+[^,"][]])?(,([A-Za-z]\w\|"\S+."\|`\S+[^,`]`\|[[]\S+[^,"][]])?)*$</validator>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	219 </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	220 <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	221 <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	222 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	223 <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator>
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	224 </param>
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	225 <repeat name="indexes" title="Table Index">
4 9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	226 <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	227 <param name="index_columns" type="text" value="" label="Index on Columns">
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	228 <help>Create an index on the column names: e,g, c1 or c2,c4</help>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	229 <validator type="regex" message="Column name, separated by commes if more than one">^([A-Za-z]\w\|"\S+[^,"]"\|`\S+[^,`]`\|[[]\S+[^,"][]])(,([A-Za-z]\w\|"\S+."\|`\S+[^,`]`\|[[]\S+[^,"][]])?)*$</validator>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	230 </param>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	231 </repeat>
9d73dca48178 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty jjohnson parents: 3 diff changeset	232 </section>
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	233 </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	234 <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	235 <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	236 <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	237 <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	238 <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	239 </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	240 <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	241 </inputs>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	242 <outputs>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	243 <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	244 <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	245 </data>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	246 <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	247 <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	248 </data>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	249 </outputs>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	250 <tests>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	251
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	252 <test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	253 <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	254 <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	255 <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	256 <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	257 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	258 <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	259 <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	260 <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	261 <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	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(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	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,,DOB,"/>
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 <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	273 <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	274 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	275 <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	276 <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	277 </test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	278
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	279 <test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	280 <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	281 <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	282 <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	283 </repeat>
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="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	285 <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	286 </test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	287
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	288 <test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	289 <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	290 <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	291 <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	292 <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	293 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	294 <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	295 <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	296 <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	297 <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	298 </repeat>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	299 <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	300 <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	301 </test>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	302
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	303 </tests>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	304 <help><![CDATA[
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	305 =============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	306 Query Tabular
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	307 =============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	308
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	309 Inputs
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	310
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	311 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	312
6 03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	313 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	314
03842a4f71c6 Uploaded jjohnson parents: 5 diff changeset	315
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	316 Input Line Filters
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	317
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	318 As a tabular file is being read, line filters may be applied.
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	319
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	320 ::
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	321
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	322 - skip leading lines skip the first number of lines
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	323 - comment char omit any lines that start with the specified comment character
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	324 - by regex expression matching include/exclude lines the match the regex expression
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	325 - select columns choose to include only selected columns in the order specified
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	326 - 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	327 - 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	328 - 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	329 - normalize list columns replicates the line for each item in the specified list columns
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	330
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	331
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	332 Outputs
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 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	335
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	336 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	337
5 19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	338 (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	339
19ae309ec53c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty jjohnson parents: 4 diff changeset	340
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	341 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	342
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	343 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	344
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	345 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	346
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	347 Example
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	348
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	349 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	350
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	351 Dataset customers
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 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	354
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	355 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	356
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	357 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	358 #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	359 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	360 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	361 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	362 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	363 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	364 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	365
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	366 Dataset sales
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 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	369
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	370 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	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 #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	374 ============= ============ ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	375 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	376 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	377 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	378 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	379 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	380 ============= ============ ============
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 The query
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	383
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	384 ::
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	385
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	386 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	387 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	388 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	389
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	390 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	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 #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	394 ========== ======== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	395 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	396 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	397 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	398 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	399 ========== ======== ==========
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
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	402 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	403
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	404 ::
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 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	407 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	408 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	409
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	410 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	411
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	412 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	413
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	414 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	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 #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	418 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	419 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	420 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	421 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	422 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	423 =========== ========== ========== ===================== ========== ============
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	424
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	425
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	426 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	427
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	428 ::
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	429
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	430 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	431
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	432 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	433 FROM t1
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	434 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	435
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	436 Results:
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 =========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	439 #FirstName LastName
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	440 =========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	441 Steven Goldfish
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	442 Paula Brown
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	443 =========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	444
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 ::
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 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	449 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	450
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	451 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	452 FROM t1
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	453 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	454
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	455 Results:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	456
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	457
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	458 =========== ========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	459 #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	460 =========== ========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	461 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	462 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	463 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	464 =========== ========== ==========
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	465
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	466
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	467 Line Filtering Example
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	468 (Six filters are applied as the following file is read)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	469
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	470 ::
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	471
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	472 Input Tabular File:
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	473
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	474 #People with pets
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	475 Pets FirstName LastName DOB PetNames PetType
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	476 2 Paula Brown 24/05/78 Rex,Fluff dog,cat
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	477 1 Steven Jones 04/04/74 Allie cat
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	478 0 Jane Doe 24/05/78
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	479 1 James Smith 20/10/80 Spot
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	480
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	481
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	482 Filter 1 - append a line number column:
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	483
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	484 #People with pets 1
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	485 Pets FirstName LastName DOB PetNames PetType 2
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	486 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	487 1 Steven Jones 04/04/74 Allie cat 4
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	488 0 Jane Doe 24/05/78 5
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	489 1 James Smith 20/10/80 Spot 6
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	490
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	491 Filter 2 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	492
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	493 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	494 1 Steven Jones 04/04/74 Allie cat 4
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	495 0 Jane Doe 24/05/78 5
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	496 1 James Smith 20/10/80 Spot 6
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	497
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	498 Filter 3 - append a line number column:
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	499
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	500 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3 1
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	501 1 Steven Jones 04/04/74 Allie cat 4 2
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	502 0 Jane Doe 24/05/78 5 3
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	503 1 James Smith 20/10/80 Spot 6 4
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	504
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	505 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	506
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	507 2 Paula Brown 1978-05-24 Rex,Fluff dog,cat 3 1
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	508 1 Steven Jones 1974-04-04 Allie cat 4 2
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	509 0 Jane Doe 1978-05-24 5 3
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	510 1 James Smith 1980-10-20 Spot 6 4
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	511
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	512 Filter 5 - normalize list columns[5,6]:
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	513
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	514 2 Paula Brown 1978-05-24 Rex dog 3 1
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	515 2 Paula Brown 1978-05-24 Fluff cat 3 1
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	516 1 Steven Jones 1974-04-04 Allie cat 4 2
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	517 0 Jane Doe 1978-05-24 5 3
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	518 1 James Smith 1980-10-20 Spot 6 4
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	519
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	520 Filter 6 - append a line number column:
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	521
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	522 2 Paula Brown 1978-05-24 Rex dog 3 1 1
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	523 2 Paula Brown 1978-05-24 Fluff cat 3 1 2
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	524 1 Steven Jones 1974-04-04 Allie cat 4 2 3
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	525 0 Jane Doe 1978-05-24 5 3 4
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	526 1 James Smith 1980-10-20 Spot 6 4 5
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	527
fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	528
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	529 Table name: pets
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	530
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	531 Table columns: Pets,FirstName,LastName,Birthdate,PetNames,PetType,line_num,entry_num,row_num
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	532
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	533 Query: SELECT * FROM pets
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	534
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	535 Result:
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	536
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	537 ====== ========== ======== ========== ========= ======== ========= ========== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	538 #Pets FirstName LastName BirthDate PetNames PetType line_num entry_num row_num
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	539 ====== ========== ======== ========== ========= ======== ========= ========== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	540 2 Paula Brown 1978-05-24 Rex dog 3 1 1
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	541 2 Paula Brown 1978-05-24 Fluff cat 3 1 2
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	542 1 Steven Jones 1974-04-04 Allie cat 4 2 3
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	543 0 Jane Doe 1978-05-24 5 3 4
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	544 1 James Smith 1980-10-20 Spot 6 4 5
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	545 ====== ========== ======== ========== ========= ======== ========= ========== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	546
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	547
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	548 Normalizing by Line Filtering into 2 Tables
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	549
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	550 People Table
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	551
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	552 ::
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	553
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	554 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	555 Filter 2 - append a line number column:
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	556 Filter 3 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format)
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	557 Filter 4 - select columns 7,2,3,4,1
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	558
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	559 Table: People
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	560 Columns: id,FirstName,LastName,DOB,Pets
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	561
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	562 == ========= ======== ========== ====
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	563 id FirstName LastName DOB Pets
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	564 == ========= ======== ========== ====
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	565 1 Paula Brown 1978-05-24 2
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	566 2 Steven Jones 1974-04-04 1
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	567 3 Jane Doe 1978-05-24 0
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	568 4 James Smith 1980-10-20 1
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	569 == ========= ======== ========== ====
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	570
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	571
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	572 Pet Table
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	573
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	574 ::
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	575
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	576 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	577 Filter 2 - append a line number column:
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	578 Filter 3 - by regex expression matching [exclude]: '^0\t' (exclude lines with no pets)
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	579 Filter 4 - normalize list columns[5,6]:
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	580 Filter 5 - select columns 7,5,6
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	581
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	582 Table: Pet
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	583 Columns: id,PetName,PetType
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	584
16 5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	585 == ======== ========
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	586 id PetName PetType
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	587 == ======== ========
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	588 1 Rex dog
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	589 1 Fluff cat
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	590 2 Allie cat
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	591 4 Spot
5b4f6cf857cf Uploaded jjohnson parents: 14 diff changeset	592 == ======== ========
14 3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	593
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	594
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	595 Query: SELECT FirstName,LastName,PetName FROM People join Pet on People.id = Pet.id WHERE PetType = 'cat';
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	596
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	597 Result:
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	598
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	599 ========= ======== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	600 FirstName LastName PetName
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	601 ========= ======== ========
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	602 Paula Brown Fluff
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	603 Steven Jones Allie
3003fe70f297 Uploaded jjohnson parents: 11 diff changeset	604 ========= ======== ========
11 fd16243931d6 Uploaded jjohnson parents: 8 diff changeset	605
0 926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	606 .. _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	607 .. _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	608
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	609 ]]></help>
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty jjohnson parents: diff changeset	610 </tool>

Mercurial > repos > jjohnson > query_tabular

annotate query_tabular.xml @ 16:5b4f6cf857cf draft